Codon Signature Extremes In Eukaryote genomes

2006 ◽  
Vol 52 (3-4) ◽  
pp. 281-297 ◽  
Author(s):  
Samuel Karlin ◽  
Dorit Carmelli
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Mammalian Species ◽  
Life Domains ◽  
Codon Site ◽  
Bacterial Genomes ◽  
Noncoding Regions ◽  
Genome Wide ◽  
Eukaryotic Genomes

Twenty-one complete eukaryotic genomes are compared for codon signature biases. The codon signature refers to the dinucleotide relative abundance values at codon sites {1, 2}, {2, 3}, and {3, 4} (4 = 1 of the next codon site). The genomes under study include human, mouse, chicken, three invertebrates, one plant species, eight fungi, and six protists. The dinucleotide CpG is significantly underrepresented at all contiguous codon sites and drastically suppressed in noncoding regions in mammalian species, in yeast-like genomes, in the dicot Arabidopsis thaliana, but not in the filamentous fungi Neurospora crassa and Asperigillus fumigatus, and in the protist Entamoeba histolytica. The dinucleotide TpA, probably due to DNA structural weaknesses, is underrepresented genome-wide and significantly underrepresented in the codon signature for all contiguous codon sites in mammals, inverterbrates, plants, and fungi, but somewhat restricted to codon sites {1, 2} among protists helping in avoidance of stop codons. The amino acid Ser, not of abundance in bacterial genomes, generally ranks among the two most used amino acids among eukaryotes ostensibly resulting from greater activity in the nucleus. The observed differences are linked to specifics of methylation, context-dependent mutation, DNA repair, and replication. For example, the amino acid Leu is broadly abundant in all life domains generally resulting from extra occurrences of the codon TTR, R purine. The malarial protist Plasmodium falciparum shows many codon signature extremes.

scholarly journals The assembly of CD1e is controlled by an N-terminal propeptide which is processed in endosomal compartments

2009 ◽  
Vol 419 (3) ◽  
pp. 661-668 ◽  
Author(s):  
Blandine Maître ◽  
Catherine Angénieux ◽  
Virginie Wurtz ◽  
Emilie Layre ◽  
Martine Gilleron ◽  
...  
Keyword(s):  
Amino Acids ◽  
Dendritic Cells ◽  
Amino Acid ◽  
Mammalian Species ◽  
Soluble Form ◽  
Β2 Microglobulin ◽  
Immature Dendritic Cells ◽  
Soluble Molecule ◽  
Α Chain ◽  
Acidic Compartments

CD1e displays unique features in comparison with other CD1 proteins. CD1e accumulates in Golgi compartments of immature dendritic cells and is transported directly to lysosomes, where it is cleaved into a soluble form. In these latter compartments, CD1e participates in the processing of glycolipid antigens. In the present study, we show that the N-terminal end of the membrane-associated molecule begins at amino acid 20, whereas the soluble molecule consists of amino acids 32–333. Thus immature CD1e includes an N-terminal propeptide which is cleaved in acidic compartments and so is absent from its mature endosomal form. Mutagenesis experiments demonstrated that the propeptide controls the assembly of the CD1e α-chain with β2-microglobulin, whereas propeptide-deleted CD1e molecules are immunologically active. Comparison of CD1e cDNAs from different mammalian species indicates that the CD1e propeptide is conserved during evolution, suggesting that it may also optimize the generation of CD1e molecules in other species.

scholarly journals RESISTÊNCIA DE PLANTAS DANINHAS: SELEÇÃO OU INDUÇÃO À MUTAÇÃO PELOS HERBICIDAS INIBIDORES DE ACETOLACTATO

2002 ◽  
Vol 12 ◽  
Author(s):  
RIBAS ANTONIO VIDAL ◽  
LARISSA MACEDO WINKLER
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Dna Replication ◽  
Branched Chain Amino Acids ◽  
Amino Acid Synthesis ◽  
Replication Errors ◽  
Resistance To Herbicides ◽  
Branched Chain ◽  
Weed Resistance

A resistência de plantas daninhas aos herbicidas, principalmente os inibidores da síntese de aminoácidos ramificados (isoleucina, leucina e valina), está se propagando no Brasil. A literatura propõem que a resistência aos herbicidas ocorre devido à seleção de indivíduos mutantes já presentes na comunidade vegetal aspergida pelo herbicida. Contudo, durante a replicação do DNA ocorrem erros que são corrigidos por diversas proteínas. Já foi identificada a composição de aminoácidos das proteínas do grupo MutS, responsáveis pela correção de erros replicativos em Arabidopsis thaliana. Com base na elevada composição dos aminoácidos ramificados nas proteínas do grupo MutS, este trabalho questiona se a ausência desses aminoácidos em momentos críticos da replicação do DNA pode estar prejudicando a correção dos erros do DNA das plantas daninhas. Comparações são feitas entre possíveis efeitos de inibidores de acetolactato sintase (ALS) e de enol-piruvil-shiquimatofosfato- sintase (EPSPS). Com base nessas informações sugere-se que herbicidas inibidores da síntese de aminoácidos ramificados podem propiciar o aparecimento de mais indivíduos mutantes resistentes aos mesmos. WEED RESISTANCE: SELECTION OR INDUCTION TO MUTATION BY INHIBITORS OF ACETO LACTATE SYNTASE HERBICIDES Abstract The weed resistance to herbicides is widely spread in Brazil, mainly for the compounds inhibitors of the synthesis of branched-chain amino acids, isoleucine, leucine and valine. The literature proposes that the resistance to herbicides appears as result of selection of mutant individual plants existent in the weed flora prior to herbicide application. However, during DNA replication occur replication errors, that are corrected by several proteins. It is already known the amino acid composition of the proteins from the group MutS, responsible for the correction of replication errors in Arabidopsis thaliana. Based on the high composition of branched-chain amino acids on the group MutS proteins, in this work it is hypothesized that the absence of these amino acids on critical moments of the DNA replication can be interfering on the correction of the DNA replication errors in weeds. Possible effect of aceto lactate syntase (ALS) and enolpyruvil- shiquimato-phosphate syntase (EPSPS) inhibithing herbicides are compared. This review suggests that herbicides inhibitor of branched chain amino acid synthesis can trigger the appearance of more mutant weeds resistant to the herbicides when sprayed by these compounds.

scholarly journals Preparation and characterization of armadillo submandibular glycoproteins

1977 ◽  
Vol 161 (1) ◽  
pp. 37-47 ◽  
Author(s):  
A M Wu ◽  
W Pigman
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Mammalian Species ◽  
Chemical Properties ◽  
Glycoprotein B ◽  
Molar Ratio ◽  
Cellulose Acetate Electrophoresis ◽  
Acetylneuraminic Acid ◽  
Neutral Sugars ◽  
Mucus Glycoproteins

The nine-banded armadillo (Dasypus novemcinctus mexicanus Peters) was chosen for this study so that a comparison could be made of the salivary mucus glycoproteins of an ancient mammalian species with those derived from previously studied, more highly evolved species. Two mucus glycoproteins, armadillo submandibular glycoprotein A and armadillo submandibular glycoprotein B, were prepared from the armadillo submandibular gland by a modification of the method of Tettamanti & Pigman (1968) (Arch. Biochem. Biophys. 124, 41-50). The composition of glycoprotein A is the simplest one among the known mucus glycoproteins. Six amino acids constitute 98.5 mol/100mol of the protein of glycoprotein A and 82 mol/100 mol of that of glycoprotein B. These are serine and threonine (which make up 40-50% of the molar amino acid composition), glutamic acid, glycine alanine and valine. Proline is absent from glycoprotein A and comprises only 2.3% of glycoprotein B. For both glycoproteins, the protein content, as determined by the method of Lowry, Rosebrough, Farr & Randall (1951) (J. Biol. Chem 193, 265-275), with bovine serum albumin as standard, was nearly 60% higher than when determined by the sum of the amino acids. The ratios of total mol of amino acid/total mol of carbohydrate are 1:0.63 for glycoprotein A and 1:0.68 for glycoprotein B, N-Acetylneuraminic acid and N-acetylgalactosamine, in a molar ratio of about 0.35:1.00, are the principal carbohydrates present in both glycoproteins. Neutral sugars seem to be absent from glycoprotein A, but galactose and fucose are present in glycoprotein B. The carbohydrate side chains in glycoprotein A are composed of about two-thirds monosaccharide and one-third disaccharide residues, whereas those of glycoprotein B are more complex. For both glycoproteins, essentially all of the N-acetylgalactosamine was attached O-glycosidically to the hydroxyamino acid residues of the protein core. The linkage of N-acetylneuraminic acid glycoprotein A was extremely sensitive to dilute acid and neuraminidase. Glycoprotein B has chemical properties similar to those of glycoprotein A. However, whereas glycoprotein A was susceptible to both Clostridium perfringens and Vibrio cholerae neuraminidases, only the latter enzyme had an effect on glycoprotein B at pH 4.75. Both glycoproteins were homogeneous by cellulose acetate electrophoresis and ultracentrifugal analyses. The apparent mol.wts. of glycoprotein A and glycoprotein B were 7.8 X 10(4) and 3.1 X 10(4) respectively.

scholarly journals Amino acid composition of the milk of some mammalian species changes with stage of lactation

1994 ◽  
Vol 72 (6) ◽  
pp. 845-853 ◽  
Author(s):  
Teresa A. Davis ◽  
Hanh V. Nguyen ◽  
Roselina Garcia-Bravo ◽  
Marta L. Fiorotto ◽  
Evelyn M. Jackson ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Concentration ◽  
Mammalian Species ◽  
Amino Acid Pattern ◽  
Amino Acid Concentration ◽  
Total Amino Acid ◽  
Papio Cynocephalus ◽  
Mature Milk

To determine whether the amino acid composition of milk changes during lactation, we compared the amino acid pattern (concentration of each individual amino acid relative to the total amino acid concentration) of colostrum with that of mature milk in six mammalian species. In the human, horse, pig and cow, the pattern of amino acids changed between colostrum and mature milk: glutamate, proline, methionine, isoleucine and lysine increased; cystine, glycine, serine, threonine and alanine decreased. In these four species, the total amino acid concentration also decreased 75% between colostrum and mature milk. In the baboon (Papio cynocephalus anubis and Papio cynocephalus anubis/Papio cynocephalus cynocephalus) and rhesus monkey (Macaca mulatta), however, there was little change in the pattern of amino acids between colostrum and mature milk, and total amino acid concentration decreased only about 25% between colostrum and mature milk. Mature milk rather than colostrum was the most similar among the three primates in both amino acid pattern and total amino acid concentration. We conclude, in those species in which total amino acid concentrations decline substantially between colostrum and mature milk, amino acid patterns also change. The presence of a change in amino acid pattern and total amino acid concentration during lactation appears to be unrelated to phylogenetic order.

Tryptophan-Requiring Mutants of the Plant Arabidopsis thaliana

Science ◽  
1988 ◽  
Vol 240 (4850) ◽  
pp. 305-310 ◽  
Author(s):  
ROBERT L. LAST ◽  
GERALD R. FINK
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Second Step ◽  
Recessive Trait ◽  
Whole Plant ◽  
Tryptophan Pathway ◽  
Morphological Defects ◽  
Plant Level ◽  
Plant Arabidopsis Thaliana

Although amino acid auxotrophs are among the most frequently isolated mutations in microorganisms, no mutants that require amino acids have been isolated at the whole plant level. Tryptophan-requiring mutants of the cruciferous plant Arabidopsis thaliana have now been isolated by selecting for resistance to 5-methylanthranilic acid. The tryptophan requirement of one mutant, trpl-1, results from a defect in the second step of the tryptophan pathway catalyzed by anthranilate phosphoribosyl transferase. Mutant trpl-1 plants are highly fluorescent and aromatic because they accumulate anthranilic acid and anthranilate β-glucoside. Plants homozygous for the trpl-1 mutation exhibit a syndrome of morphological defects suggestive of a defect in the biosynthesis, metabolism, or localization of a tryptophan derivative such as auxin. All of these morphological phenotypes cosegregate with the tryptophan requirement as a simple Mendelian recessive trait.

scholarly journals The Impact of Photorespiratory Glycolate Oxidase Activity on Arabidopsis thaliana Leaf Soluble Amino Acid Pool Sizes during Acclimation to Low Atmospheric CO2 Concentrations

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 501
Author(s):  
Younès Dellero ◽  
Caroline Mauve ◽  
Mathieu Jossier ◽  
Michael Hodges
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Atmospheric Co2 ◽  
Glycolate Oxidase ◽  
Wild Type ◽  
Low Co2 ◽  
Co2 Concentrations ◽  
Atmospheric Co2 Concentrations ◽  
The Impact

Photorespiration is a metabolic process that removes toxic 2-phosphoglycolate produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase. It is essential for plant growth under ambient air, and it can play an important role under stress conditions that reduce CO2 entry into the leaf thus enhancing photorespiration. The aim of the study was to determine the impact of photorespiration on Arabidopsis thaliana leaf amino acid metabolism under low atmospheric CO2 concentrations. To achieve this, wild-type plants and photorespiratory glycolate oxidase (gox) mutants were given either short-term (4 h) or long-term (1 to 8 d) low atmospheric CO2 concentration treatments and leaf amino acid levels were measured and analyzed. Low CO2 treatments rapidly decreased net CO2 assimilation rate and triggered a broad reconfiguration of soluble amino acids. The most significant changes involved photorespiratory Gly and Ser, aromatic and branched-chain amino acids as well as Ala, Asp, Asn, Arg, GABA and homoSer. While the Gly/Ser ratio increased in all Arabidopsis lines between air and low CO2 conditions, low CO2 conditions led to a higher increase in both Gly and Ser contents in gox1 and gox2.2 mutants when compared to wild-type and gox2.1 plants. Results are discussed with respect to potential limiting enzymatic steps with a special emphasis on photorespiratory aminotransferase activities and the complexity of photorespiration.

scholarly journals Complementary α-arrestin-ubiquitin ligase complexes control nutrient transporter endocytosis in response to amino acids

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Vasyl Ivashov ◽  
Johannes Zimmer ◽  
Sinead Schwabl ◽  
Jennifer Kahlhofer ◽  
Sabine Weys ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Ubiquitin Ligase ◽  
Amino Acid Transporters ◽  
General Amino Acid Control ◽  
Amino Acid Availability ◽  
Genome Wide ◽  
A Genome ◽  
Lysine Residues ◽  
Nutrient Transporter

How cells adjust nutrient transport across their membranes is incompletely understood. Previously, we have shown that S. cerevisiae broadly re-configures the nutrient transporters at the plasma membrane in response to amino acid availability, through endocytosis of sugar- and amino acid transporters (AATs) (Müller et al., 2015). A genome-wide screen now revealed that the selective endocytosis of four AATs during starvation required the α-arrestin family protein Art2/Ecm21, an adaptor for the ubiquitin ligase Rsp5, and its induction through the general amino acid control pathway. Art2 uses a basic patch to recognize C-terminal acidic sorting motifs in AATs and thereby instructs Rsp5 to ubiquitinate proximal lysine residues. When amino acids are in excess, Rsp5 instead uses TORC1-activated Art1 to detect N-terminal acidic sorting motifs within the same AATs, which initiates exclusive substrate-induced endocytosis. Thus, amino acid excess or starvation activate complementary α-arrestin-Rsp5-complexes to control selective endocytosis and adapt nutrient acquisition.

scholarly journals Expression of AtAAP Gene Family and Endosperm-Specific Expression of AtAAP1 Gene Promotes Amino Acid Absorption in Arabidopsis thaliana and Maize

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1668
Author(s):  
Zhanyu Chen ◽  
Yingying Zhang ◽  
Jiating Zhang ◽  
Bei Fan ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Transmembrane Protein ◽  
Expression Patterns ◽  
Reproductive Organs ◽  
Amino Acid Permease ◽  
Specific Expression ◽  
Vegetative Organs ◽  
Amino Acid Contents

The amino acid permease (AAP) is an important transmembrane protein that is involved in the absorption and transport of amino acids in plants. We investigated the expression patterns of AtAAP genes in Arabidopsis thaliana, based on quantitative real-time PCR. The results revealed differential expression patterns of eight AtAAP genes in different tissues, with five genes (AtAAP1, AtAAP2, AtAAP6, AtAAP7, and AtAAP8) expressed at relatively high levels in both flowers and siliques, suggesting their shared functions in the accumulation of amino acids. In transgenic plants, with endosperm-specific overexpression of AtAAP1, both AtAAP1 and AtAAP6 were up-regulated in both the roots and siliques, while AtAAP2, AtAAP3, AtAAP4, and AtAAP5 showed similar expression levels in the stems and siliques, whereas AtAAP7 and AtAAP8 were expressed at their highest levels in the stems and roots. The results of the amino acid affinity experiments revealed varied absorption capacities for different amino acids, by AtAAP1, and increased acid amino contents in the reproductive organs. These results were verified in transgenic maize plants, with the overexpression of AtAAP1, revealing higher amino acid contents in the reproductive organs than those of the vegetative organs. Our study clearly demonstrated that the endosperm-specific promoter increased the amino acid contents in the reproductive organs and improved the effective utilization of organic nitrogen in plants.

scholarly journals Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Julie L Aspden ◽  
Ying Chen Eyre-Walker ◽  
Rose J Phillips ◽  
Unum Amin ◽  
Muhammad Ali S Mumtaz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Open Reading Frames ◽  
Small Peptides ◽  
Functional Roles ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Reading Frames ◽  
Small Open Reading Frames

Thousands of small Open Reading Frames (smORFs) with the potential to encode small peptides of fewer than 100 amino acids exist in our genomes. However, the number of smORFs actually translated, and their molecular and functional roles are still unclear. In this study, we present a genome-wide assessment of smORF translation by ribosomal profiling of polysomal fractions in Drosophila. We detect two types of smORFs bound by multiple ribosomes and thus undergoing productive translation. The ‘longer’ smORFs of around 80 amino acids resemble canonical proteins in translational metrics and conservation, and display a propensity to contain transmembrane motifs. The ‘dwarf’ smORFs are in general shorter (around 20 amino-acid long), are mostly found in 5′-UTRs and non-coding RNAs, are less well conserved, and have no bioinformatic indicators of peptide function. Our findings indicate that thousands of smORFs are translated in metazoan genomes, reinforcing the idea that smORFs are an abundant and fundamental genome component.

scholarly journals Mendelian Randomization Study on Amino Acid Metabolism Suggests Tyrosine as Causal Trait for Type 2 Diabetes

Nutrients ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3890
Author(s):  
Susanne Jäger ◽  
Rafael Cuadrat ◽  
Clemens Wittenbecher ◽  
Anna Floegel ◽  
Per Hoffmann ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Amino Acids ◽  
Amino Acid ◽  
Mendelian Randomization ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Inverse Association ◽  
Genome Wide

Circulating levels of branched-chain amino acids, glycine, or aromatic amino acids have been associated with risk of type 2 diabetes. However, whether those associations reflect causal relationships or are rather driven by early processes of disease development is unclear. We selected diabetes-related amino acid ratios based on metabolic network structures and investigated causal effects of these ratios and single amino acids on the risk of type 2 diabetes in two-sample Mendelian randomization studies. Selection of genetic instruments for amino acid traits relied on genome-wide association studies in a representative sub-cohort (up to 2265 participants) of the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam Study and public data from genome-wide association studies on single amino acids. For the selected instruments, outcome associations were drawn from the DIAGRAM (DIAbetes Genetics Replication And Meta-analysis, 74,124 cases and 824,006 controls) consortium. Mendelian randomization results indicate an inverse association for a per standard deviation increase in ln-transformed tyrosine/methionine ratio with type 2 diabetes (OR = 0.87 (0.81–0.93)). Multivariable Mendelian randomization revealed inverse association for higher log10-transformed tyrosine levels with type 2 diabetes (OR = 0.19 (0.04–0.88)), independent of other amino acids. Tyrosine might be a causal trait for type 2 diabetes independent of other diabetes-associated amino acids.

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