scholarly journals Highly expressed proteins prefer less informative amino acids

2016 ◽  
Author(s):  
Guang-Zhong Wang
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Information Processing ◽  
Amino Acid ◽  
Copy Number ◽  
Selective Pressure ◽  
Interacting Proteins ◽  
Simple Method ◽  
Amount Of Information ◽  
Information Processing Perspective

AbstractThe transcriptional and translational systems are essentially information processing systems. However, how to quantify the amount of information decoded during expression remains a mystery. Here, we have proposed a simple method to evaluate the amount of information transcribed and translated during gene expression. We found that although proteins with a high copy number have more information translated, the average number of bits per amino acid is not high. The negative correlation between protein copy number and bits per amino acid indicates the selective pressure to reduce translational errors. Moreover, interacting proteins have similar bits per residue translated. All of these findings highlight the importance of understanding transcription and translation from an information processing perspective.

scholarly journals Regulation of rat magnocellular neurosecretory system by D-aspartate: evidence for biological role(s) of a naturally occurring free D-amino acid in mammals

2000 ◽  
Vol 167 (2) ◽  
pp. 247-252 ◽  
Author(s):  
H Wang ◽  
H Wolosker ◽  
J Pevsner ◽  
SH Snyder ◽  
DJ Selkoe
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Physiological Function ◽  
Neurosecretory System ◽  
Milk Ejection ◽  
Magnocellular Neurons ◽  
Rat Hypothalamus ◽  
Naturally Occurring

Little evidence is available for the physiological function of D-amino acids in species other than bacteria. Here we demonstrate that naturally occurring freed -aspartate (D-Asp) is present in all magnocellular neurons of rat hypothalamus. The levels of this naturally occurring D-amino acid were elevated during lactation and returned to normal thereafter in the magnocellular neurosecretory system, which produces oxytocin, a hormone responsible for milk ejection during lactation. Intraperitoneal injections of D-Asp reproducibly increased oxytocin gene expression and decreased the concentration of circulating oxytocin in vivo. Similar changes were observed in the vasopressin system. These results provide evidence for the role(s) of naturally occurring free D-Asp in mammalian physiology. The findings argue against the conventional concept that only L-stereoisomers of amino acids are functional in higher species.

Characterization and regulation of the gene expression of amino acid transport system A (SNAT2) in rat mammary gland

2006 ◽  
Vol 291 (5) ◽  
pp. E1059-E1066 ◽  
Author(s):  
Adriana López ◽  
Nimbe Torres ◽  
Victor Ortiz ◽  
Gabriela Alemán ◽  
Rogelio Hernández-Pando ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Mammary Gland ◽  
Amino Acid ◽  
Transport System ◽  
Amino Acid Transport ◽  
Acid Transport ◽  
Amino Acid Transport System ◽  
System A ◽  
Rat Mammary Gland

Amino acid transport via system A plays an important role during lactation, promoting the uptake of small neutral amino acids, mainly alanine and glutamine. However, the regulation of gene expression of system A [sodium-coupled neutral amino acid transporter (SNAT)2] in mammary gland has not been studied. The aim of the present work was to understand the possible mechanisms of regulation of SNAT2 in the rat mammary gland. Incubation of gland explants in amino acid-free medium induced the expression of SNAT2, and this response was repressed by the presence of small neutral amino acids or by actinomycin D but not by large neutral or cationic amino acids. The half-life of SNAT2 mRNA was 67 min, indicating a rapid turnover. In addition, SNAT2 expression in the mammary gland was induced by forskolin and PMA, inducers of PKA and PKC signaling pathways, respectively. Inhibitors of PKA and PKC pathways partially prevented the upregulation of SNAT2 mRNA during adaptive regulation. Interestingly, SNAT2 mRNA was induced during pregnancy and to a lesser extent at peak lactation. β-Estradiol stimulated the expression of SNAT2 in mammary gland explants; this stimulation was prevented by the estrogen receptor inhibitor ICI-182780. Our findings clearly demonstrated that the SNAT2 gene is regulated by multiple pathways, indicating that the expression of this amino acid transport system is tightly controlled due to its importance for the mammary gland during pregnancy and lactation to prepare the gland for the transport of amino acids during lactation.

scholarly journals The Use of GC-, Codon-, and Amino Acid-frequencies to Understand the Evolutionary Forces at a Genomic Scale

2019 ◽  
Author(s):  
Arne Elofsson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Selective Pressure ◽  
Amino Acid Level ◽  
Gc Content ◽  
Frequency Variation ◽  
Evolutionary Forces ◽  
Charged Amino Acids ◽  
Plausible Model ◽  
Selective Forces

1AbstractIt is well known that the GC content varies enormously between organisms; this is believed to be caused by a combination of mutational preferences and selective pressure. Within coding regions, the variation of GC is more substantial in position three and smaller in position one and two. Less well known is that this variation also has an enormous impact on the frequency of amino acids as their codons vary in GC content. For instance, the fraction of alanines in different proteomes varies from 1.1% to 16.5%. In general, the frequency of different amino acids correlates strongly with the number of codons, the GC content of these codons and the genomic GC contents. However, there are clear and systematic deviations from the expected frequencies. Some amino acids are more frequent than expected by chance, while others are less frequent. A plausible model to explain this is that there exist two different selective forces acting on the genes; First, there exists a force acting to maintain the overall GC level and secondly there exists a selective force acting on the amino acid level. Here, we use the divergence in amino acid frequency from what is expected by the GC content to analyze the selective pressure acting on codon frequencies in the three kingdoms of life. We find four major selective forces; First, the frequency of serine is lower than expected in all genomes, but most in prokaryotes. Secondly, there exist a selective pressure acting to balance positively and negatively charged amino acids, which results in a reduction of arginine and negatively charged amino acids. This results in a reduction of arginine and all the negatively charged amino acids. Thirdly, the frequency of the hydrophobic residues encoded by a T in the second codon position does not change with GC. Their frequency is lower in eukaryotes than in prokaryotes. Finally, some amino acids with unique properties, such as proline glycine and proline, are limited in their frequency variation.

scholarly journals Effects of nitrogen levels on gene expression and amino acid metabolism in Welsh onion

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chen Zhao ◽  
Guanchu Ma ◽  
Lin Zhou ◽  
Song Zhang ◽  
Le Su ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Protein Biosynthesis ◽  
Amino Acid Content ◽  
Growth And Yield ◽  
Welsh Onion ◽  
Amino Acid Synthesis

Abstract Background Welsh onion constitutes an important crop due to its benefits in traditional medicine. Nitrogen is an important nutrient for plant growth and yield; however, little is known about its influence on the mechanisms of Welsh onion regulation genes. In this study, we introduced a gene expression and amino acid analysis of Welsh onion treated with different concentrations of nitrogen (N0, N1, and N2 at 0 kg/ha, 130 kg/ha, and 260 kg/ha, respectively). Results Approximately 1,665 genes were differentially regulated with different concentrations of nitrogen. Gene ontology enrichment analysis revealed that the genes involved in metabolic processes, protein biosynthesis, and transportation of amino acids were highly represented. KEGG analysis indicated that the pathways were related to amino acid metabolism, cysteine, beta-alanine, arginine, proline, and glutathione. Differential gene expression in response to varying nitrogen concentrations resulted in different amino acid content. A close relationship between gene expression and the content of amino acids was observed. Conclusions This work examined the effects of nitrogen on gene expression and amino acid synthesis and provides important evidence on the efficient use of nitrogen in Welsh onion.

scholarly journals The Effects of Dietary Glycine on the Acetic Acid-Induced Mouse Model of Colitis

2020 ◽  
Vol 2020 ◽  
pp. 1-8 ◽  
Author(s):  
Xin Wu ◽  
Yongmin Zheng ◽  
Jie Ma ◽  
Jie Yin ◽  
Shuai Chen
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Acetic Acid ◽  
Amino Acid ◽  
Mouse Model ◽  
Intestinal Microbiota ◽  
Intestinal Inflammation ◽  
Serum Concentrations ◽  
Intestinal Immunity ◽  
Chronic Intestinal Inflammation

Inflammatory bowel disease, a gut disease that is prevalent worldwide, is characterized by chronic intestinal inflammation, such as colitis, and disorder of the gut microbiome. Glycine (Gly) is the simplest amino acid and functions as an anti-inflammatory immune-nutrient and intestinal microbiota regulator. This study aimed at investigating the effect of Gly on colitis induced in mice by intrarectal administration of 5% acetic acid (AA). Bodyweight and survival rates were monitored, and colonic length and weight, serum amino acid concentrations, intestinal inflammation-related gene expression, and colonic microbiota abundances were analyzed. The results showed that Gly dietary supplementation had no effect on the survival rate or the ratio of colonic length to weight. However, Gly supplementation reversed the AA-induced increase in serum concentrations of amino acids such as glutamate, leucine, isoleucine, and valine. Furthermore, Gly inhibited colonic gene expression of interleukin- (IL-) 1β and promoted IL-10 expression in colitis mice. Gly supplementation also reversed the AA-induced reduction in the abundance of bacteria such as Clostridia, Ruminococcaceae, and Clostridiales. This change in the intestinal microbiota was possibly attributable to the changes in colonic IL-10 expression and serum concentrations of valine and leucine. In sum, Gly supplementation regulated the serum concentrations of amino acids, the levels of colonic immune-associated gene expression, and the intestinal microbiota in a mouse model of colitis. These findings enhance our understanding of the role of Gly in regulating metabolism, intestinal immunity, and the gut microbiota in animals afflicted with colitis.

scholarly journals Quantitative Analysis of Amino Acids Using Papre Chromatography

1956 ◽  
Vol 9 (2) ◽  
pp. 281 ◽  
Author(s):  
RH Hackman ◽  
Mahian Lazarus
Keyword(s):  
Amino Acids ◽  
Quantitative Analysis ◽  
Amino Acid ◽  
Protein Hydrolysate ◽  
Simple Method ◽  
One Dimensional ◽  
Straight Line ◽  
Line Relationship

A simple method for the quantitative analysis of amino [teids [n'eHent ill a protein hydrolysate, or in other mixtures of amino aeids, is deserihocl. The amino aeids are separated on one�dimensional paper chromatogmllls, fOUl" solvent syst;mns being used to resolvo 17 amino acids. The chromatogrums are treatm! with a suitable reagent; to detect the spots corresponding to each amino acid . .!Daeh chromatogram, {,ftcr being made somi�t,mllsparent with dimeth:vlphthalato, is scanned nutomnticnlly, with a densitometer, and the intensity of the light transmitted by the coloured spots is recorded on light-sensitive paper. A straight line relationship was found to hold, [or all amino acids, boi;wcell conccnh'ntioll and log per cent. transmission, Tho most useful range of amino aoid OOllcolltmtion was 2 5 mlYI although tho mothod is usable in tho rango 1-"10 mlVl. 'l'he method includes a nnmber of nOW tOclllli(juOS and tho HYOeage cooflicient of variation for a sillglo readillg for an an1ino n.eid is 5-7 pOl' COllt.

Amino Acid Handbook

PEDIATRICS ◽  
1957 ◽  
Vol 19 (6) ◽  
pp. 1163-1163
Author(s):  
SAMUEL J. FOMON
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amount Of Information ◽  
Chromatographic Methods ◽  
Methods Of Analysis ◽  
General Field

As indicated by the title, the book is strictly a reference work and will be primarily useful to individuals working in the general field of chemistry and metabolism of amino acids. The emphasis on technology and factual material, rather than on reiteration of controversial interpretations of available data, has allowed the authors to encompass a surprising amount of information in a book of modest size. The first portion of this handbook deals primarily with chemical, microbiologic and, especially, chromatographic methods of analysis of amino acids.

scholarly journals Amino acid limitation regulates gene expression

1999 ◽  
Vol 58 (3) ◽  
pp. 625-632 ◽  
Author(s):  
Alain Bruhat ◽  
Céline Jousse ◽  
Pierre Fafournoux
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Essential Amino Acids ◽  
Mrna Levels ◽  
Dependent Manner ◽  
Control Of Gene Expression

In mammals, the plasma concentration of amino acids is affected by nutritional or pathological conditions. For example, an alteration in the amino acid profile has been reported when there is a deficiency of any one or more of the essential amino acids, a dietary imbalance of amino acids, or an insufficient intake of protein. We examined the role of amino acid limitation in regulating mammalian gene expression. Depletion of arginine, cystine and all essential amino acids leads to induction of insulin-like growth factor-binding protein-1 (IGFBP-1) mRNA and protein expression in a dose-dependent manner. Moreover, exposure of HepG2 cells to amino acids at a concentration reproducing the amino acid concentration found in portal blood of rats fed on a low-protein diet leads to a significantly higher (P < 0·0002) expression of IGFBP-1. Using CCAAT/enhancer-binding protein homologous protein (CHOP) induction by leucine deprivation as a model, we have characterized the molecular mechanisms involved in the regulation of gene expression by amino acids. We have shown that leucine limitation leads to induction of CHOP mRNA and protein. Elevated mRNA levels result from both an increase in the rate of CHOP transcription and an increase in mRNA stability. We have characterized two elements of the CHOP gene that are essential to the transcriptional activation produced by an amino acid limitation. These findings demonstrate that an amino acid limitation, as occurs during dietary protein deficiency, can induce gene expression. Thus, amino acids by themselves can play, in concert with hormones, an important role in the control of gene expression.

On the Relationships between the Genetic Code Coevolution Hypothesis and the Physicochemical Hypothesis

1991 ◽  
Vol 46 (3-4) ◽  
pp. 305-312 ◽  
Author(s):  
Massimo Di Giulio
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Comparative Study ◽  
Genetic Code ◽  
Selective Pressure ◽  
Active Role ◽  
Selective Pressures ◽  
Evolutionary Hypothesis

This paper analyzes the relationships between the genetic code coevolution hypothesis and the physicochemical hypothesis by means of a comparative study of the precursor-product amino acid pairs on which the former hypothesis is based. Even if the coevolution between the biosynthetic relationships of amino acids and the organization of the genetic code is not questioned in this paper, the results and the arguments used lead us to believe that the selective pressures considered essential by the physicochemical postulates, played a more active role than that of the precursor-product relationships in defining the allocation of these amino acids in the genetic code. It is furthermore pointed out that the two evolutionary hypothesis might be aspects of the same selective pressure, and thus difficult to differentiate.

Increases in circulating amino acids with in-feed antibiotics correlated with gene expression of intestinal amino acid transporters in piglets

Amino Acids ◽  
2017 ◽  
Vol 49 (9) ◽  
pp. 1587-1599 ◽  
Author(s):  
Miao Yu ◽  
Chunlong Mu ◽  
Yuxiang Yang ◽  
Chuanjian Zhang ◽  
Yong Su ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Transporters
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