scholarly journals A discriminator code-based DTD surveillance ensures faithful glycine delivery for protein biosynthesis in bacteria

2018 ◽  
Author(s):  
Santosh Kumar Kuncha ◽  
Katta Suma ◽  
Komal Ishwar Pawar ◽  
Jotin Gogoi ◽  
Satya Brata Routh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Selection Pressure ◽  
Protein Biosynthesis ◽  
Strong Selection ◽  
Base Specificity ◽  
Activity Difference ◽  
Discriminator Base

AbstractD-aminoacyl-tRNA deacylase (DTD) acts on achiral glycine, in addition to D-amino acids, attached to tRNA. We have recently shown that this activity enables DTD to clear non-cognate Gly-tRNAAla with 1000-fold higher efficiency than its activity on Gly-tRNAGly, indicating tRNA-based modulation of DTD (Pawar et al., 2017). Here, we show that tRNA’s discriminator base predominantly accounts for this activity difference and is the key to selection by DTD. Accordingly, the uracil discriminator base, serving as a negative determinant, prevents Gly-tRNAGly misediting by DTD and this protection is augmented by EF-Tu. Intriguingly, eukaryotic DTD has inverted discriminator base specificity and uses only G3•U70 for tRNAGly/Ala discrimination. Moreover, DTD prevents alanine-to-glycine misincorporation in proteins rather than only recycling mischarged tRNAAla. Overall, the study reveals the unique co-evolution of DTD and discriminator base, “reciprocally” in Bacteria and Eukarya, and suggests DTD’s strong selection pressure on bacterial tRNAGlys to retain a pyrimidine discriminator code.

scholarly journals A discriminator code–based DTD surveillance ensures faithful glycine delivery for protein biosynthesis in bacteria

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Santosh Kumar Kuncha ◽  
Katta Suma ◽  
Komal Ishwar Pawar ◽  
Jotin Gogoi ◽  
Satya Brata Routh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Selection Pressure ◽  
Protein Biosynthesis ◽  
Strong Selection ◽  
Base Specificity ◽  
Activity Difference ◽  
Discriminator Base

D-aminoacyl-tRNA deacylase (DTD) acts on achiral glycine, in addition to D-amino acids, attached to tRNA. We have recently shown that this activity enables DTD to clear non-cognate Gly-tRNAAla with 1000-fold higher efficiency than its activity on Gly-tRNAGly, indicating tRNA-based modulation of DTD (Pawar et al., 2017). Here, we show that tRNA’s discriminator base predominantly accounts for this activity difference and is the key to selection by DTD. Accordingly, the uracil discriminator base, serving as a negative determinant, prevents Gly-tRNAGly misediting by DTD and this protection is augmented by EF-Tu. Intriguingly, eukaryotic DTD has inverted discriminator base specificity and uses only G3•U70 for tRNAGly/Ala discrimination. Moreover, DTD prevents alanine-to-glycine misincorporation in proteins rather than only recycling mischarged tRNAAla. Overall, the study reveals the unique co-evolution of DTD and discriminator base, and suggests DTD’s strong selection pressure on bacterial tRNAGlys to retain a pyrimidine discriminator code.

The Role of Copy Number Variation in Psychiatric Disorders

2018 ◽  
pp. 84-95
Author(s):  
Elliott Rees ◽  
George Kirov
Keyword(s):  
Autism Spectrum Disorders ◽  
Copy Number ◽  
Selection Pressure ◽  
Copy Number Variants ◽  
Autism Spectrum ◽  
High Odds ◽  
Strong Selection ◽  
Increase Risk ◽  
Number Variation

Copy number variants (CNVs) are deletions, duplications, inversions, or translocations of large DNA segments. They can play a significant role in human disease. Thirteen CNVs have received strong statistical support for involvement in schizophrenia. They are all rare in cases (<1%), much rarer among controls, and have high odds ratios (ORs) for causing disease. The same CNVs also increase risk for autism spectrum disorders, developmental delay, and medical/physical comorbidities. The penetrance of these CNVs for any disorder is relatively high, ranging from 10% for 15q11.2 deletions to nearly 100% for deletions at 22q11.2. Strong selection pressure operates against carriers of these CNVs. Most of these are formed by non-allelic homologous recombination (NAHR), which leads to high mutation rates, thus maintaining the rates of these CNVs in the general population, despite the strong selection forces.

Effects of milk proteins supplementation on muscle protein synthesis

2019 ◽  
Vol 49 (6) ◽  
pp. 1275-1286
Author(s):  
Milena Casagranda ◽  
Priscila Berti Zanella ◽  
Alexandra Ferreira Vieira ◽  
Rodrigo Cauduro Oliveira Macedo
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Muscle Protein ◽  
Muscle Protein Synthesis ◽  
Protein Biosynthesis ◽  
Nitrogen Compound ◽  
Milk Proteins ◽  
Control Group ◽  
Content Type ◽  
Protein Sources

Purpose The purpose of the study was to evaluate the acute effect of milk proteins supplementation, compared to another nitrogen compound on muscle protein synthesis. Design/methodology/approach The search was conducted on MEDLINE® (via PUBMED®), Cochrane and Embase databases, using the terms “whey proteins,” “caseins,” “milk proteins,” “protein biosynthesis,” “human” and its related entry terms. The selected outcome was fractional synthetic rate (FSR) before (0) and 3 h after consumption of milk proteins, compared to supplementation with other protein sources or isolated amino acids. Findings The results were expressed as mean difference (MD) of absolute values between treatments with confidence interval (CI) of 95 per cent. Of the 1,913 identified studies, 4 were included, with a total of 74 participants. Milk proteins generated a greater FSR (MD 0.03 per cent/h, CI 95 per cent 0.02-0.04; p < 0.00001), compared to control group. Acute consumption of milk proteins promotes higher increase in FSR than other protein sources or isolated amino acids. Originality/value This paper is a systematic review of the effects of milk proteins supplementation, which is considered an important subject because of its large consumption among athletes and physical exercise practitioners.

HORMONES AND PROTEIN BIOSYNTHESIS IN ISOLATED RAT DIAPHRAGM

1959 ◽  
Vol 18 (4) ◽  
pp. 381-394 ◽  
Author(s):  
K. L. MANCHESTER ◽  
F. G. YOUNG
Keyword(s):  
Amino Acids ◽  
Glucose Uptake ◽  
Protein Biosynthesis ◽  
Metabolic Inhibitors ◽  
Minimal Amount ◽  
Rat Diaphragm ◽  
Rat Serum ◽  
Significant Stimulation ◽  
Normal Rat

SUMMARY 1. With rat diaphragm in vitro, addition of insulin to the medium so as to give a concentration as low as 0·05 mu./ml. of the hormone, stimulated the incorporation of [14C]glycine into protein of tissue. Simultaneous addition of glucose to the medium did not affect either the minimal amount of insulin required to produce a significant stimulation of incorporation of glycine, or the magnitude of the effect of the small concentration of insulin used. 2. Addition of a mixture of oxidized A and B chains of the insulin molecule did not affect incorporation of a mixture of labelled amino acids into the protein of isolated diaphragm, but a degraded insulin (DHA-insulin), which has about 15% of the activity of insulin in stimulating glucose uptake by diaphragm, was found to stimulate incorporation of [14C]glycine to an extent comparable with its effect in stimulating glucose-uptake. 3. Addition of rat serum, or the dipping of diaphragm in a medium containing insulin, stimulated incorporation of [14C]glycine into protein of diaphragm. Both these effects and the stimulation produced by insulin in vitro were abolished when the medium contained an antiserum to insulin. 4. Addition in vitro of growth hormone (GH) stimulated incorporation of [14C]glycine into protein of diaphragm from the hypophysectomized rat but had no effect on diaphragm from the normal rat, whether or not a small dose of insulin was also added in vitro. The action of GH in promoting incorporation of [14C]glycine into protein of diaphragm from the hypophysectomized rat was not neutralized by insulin antiserum. 5. Corticotrophin, cortisol, thyroxine, vitamin B12, vitamin D2 and linoleic acid all had no observable effect on incorporation of labelled amino acids into diaphragm. Glucagon stimulated incorporation, but the stimulation was abolished by the in vitro addition of antiserum to insulin and was probably attributable to the presence of a trace of insulin in the glucagon. 6. Anaerobiosis, and the addition of various metabolic inhibitors, were found to suppress incorporation of [14C]glycine into diaphragm protein almost entirely.

scholarly journals Протеїновий і амінокислотний обмін у м’язах курчат-бройлерів кросу КОББ 500 на тлі застосування кормової добавки «Гумілід»

2017 ◽  
Vol 19 (77) ◽  
pp. 110-116
Author(s):  
E.O. Myhaylenko ◽  
O.O. Dyomshyna ◽  
L.M. Stepchenko
Keyword(s):  
Amino Acids ◽  
Broiler Chickens ◽  
Protein Biosynthesis ◽  
Mitochondrial Fraction ◽  
Feed Additives ◽  
Protective Mechanism ◽  
Mitochondrial Fractions ◽  
Adaptive Processes ◽  
Simultaneous Decrease ◽  
The Impact

The article presents data on the study of the impact of feed additives «Humilid» indicators on protein and amino acid metabolism of muscles of broiler chickens cross the COBB 500.The study tested that birds which additived Humilid the water increase in the muscles of total protein, which represented the largest share of the cytosolic and mitochondrial fractions. In homogenate of muscle, the total amount of protein increased by 10% in cytosolic and 20% in mitochondrial, which makes it possible to assert that stimulate the synthesis of cytosolic proteins is influenced Humilid and stimulated the formation chondriome of myocytes. Also, the data indicate an intensification of the use of amino acids for protein biosynthesis and adaptive processes, confirmed by increased in muscle mitochondrial fraction 2 times activity of gamma-glutamyltranspeptidase, which is involved in the transport of amino acids and glutathione in mitochondria that seen as a protective mechanism. The research has shown increased 3 times in cytosolic fraction activity of alanine aminotransferase and the simultaneous decrease in lactate dehydrogenase. Calculate the ratio activity of LDH/ALT showed bias towards anaerobic conversion of glucose to glucose-alanine cycle, more efficient way of recovery and using of glucose.

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 Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides

2020 ◽  
Author(s):  
Matthew H Zimmer ◽  
Michiel JM Niesen ◽  
Thomas F Miller
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Conformational Changes ◽  
Protein Biosynthesis ◽  
Essential Amino Acids ◽  
Structural Features ◽  
Applied Force ◽  
Catalytic Center ◽  
Force Propagation ◽  
Force Transduction

AbstractForce-sensitive arrest peptides regulate protein biosynthesis by stalling the ribosome as they are translated. Synthesis can be resumed when the nascent arrest peptide experiences a pulling force of sufficient magnitude to break the stall. Efficient stalling is dependent on the specific identity of a large number of amino acids, including amino acids which are tens of angstroms away from the peptidyl transferase center (PTC). The mechanism of force-induced restart and the role of these essential amino acids far from the PTC is currently unknown. We use hundreds of independent molecular dynamics trajectories spanning over 120 μs in combination with kinetic analysis to characterize the barriers along the force-induced restarting pathway for the arrest peptide SecM. We find that the essential amino acids far from the PTC play a major role in controlling the transduction of applied force. In successive states along the stall-breaking pathway, the applied force propagates up the nascent chain until it reaches the C-terminus of SecM and the PTC, inducing conformational changes that allow for restart of translation. A similar mechanism of force propagation through multiple states is observed in the VemP stall-breaking pathway, but secondary structure in VemP allows for heterogeneity in the order of transitions through intermediate states. Results from both arrest peptides explain how residues that are tens of angstroms away from the catalytic center of the ribosome impact stalling efficiency by mediating the response to an applied force and shielding the amino acids responsible for maintaining the stalled state of the PTC.Significance StatementAs nascent proteins are synthesized by the ribosome, their interactions with the environment can create pulling forces on the nascent protein that can be transmitted to the ribosome’s catalytic center. These forces can affect the rate and even the outcome of translation. We use simulations to characterize the pathway of force transduction along arrest peptides and discover how secondary structure in the nascent protein and its interactions with the ribosome exit tunnel impede force propagation. This explains how amino acids in arrest peptides that are tens of angstroms away from the ribosome’s catalytic center contribute to stalling, and, more broadly, suggests how structural features in the nascent protein dictate the ribosome’s ability to functionally respond to its environment.

Essential amino acids and their need by lactating cows

2020 ◽  
pp. 30-46
Author(s):  
V. Ryadchikov ◽  
A. Tantawi
Keyword(s):  
Amino Acids ◽  
Crude Protein ◽  
Milk Protein ◽  
Protein Biosynthesis ◽  
Essential Amino Acids ◽  
Absolute Number ◽  
Factorial Method ◽  
Lactating Cows ◽  
Metabolic Protein ◽  
Daily Milk Yield

Metabolic protein is the main source of truly absorbed amino acids. The determination of metabolic protein and metabolic acids is an important, but very difficult task. To do this, you need to know the exact number of incoming protein fractions in the small intestine as part of the duodenal fl ow of chymus, their digestibility, the fl ow of metabolism of essential amino acids from the intestine to the bloodstream and the coefficients of their use for milk protein biosynthesis and maintenance of life. The purpose of the research was to determine the need of lactating cows for metabolic essential amino acids by factorial method. During the researches, developed standards needs to metabolic essential amino acids for lactating cows (g/kg) milk with a content of 3,3 % (33 g/kg) crude protein and 3,15 % (31,5 g/kg) of pure protein and to maintain 1 kg/body weight 0,75, which allows to calculate the daily requirement in the absolute number of amino acids (g). The assessment of security of rations of lactating cows metabolic lysine and methionine has been shown coincidence with the norms of needs in the amount of 93 %; daily milk yield of natural milk under this provision of lysine and methionine were 38,7 % and 39,4. The availability of metabolic methionine was at the level of 77-85 %, which is explained by the unprocessed coefficients of transformation of metabolic methionine into pure methionine of milk protein. In the total duodenal fl ow of amino acids approximately 60-70 % is microbial protein and 30-40 % is non-degradable protein in the rumen. It has been found that the digestibility of dry and organic matter in the rumen and the general digestive tract in relation to UDP:DP 35: 65 % crude protein is 2-3 % (absolute) higher than for UDP:DP = 50:50 % crude protein.

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