scholarly journals Comparative genomic analysis reveals a monophyletic cold adapted Arthrobacter cluster from polar and alpine regions

2019 ◽  
Author(s):  
Liang Shen ◽  
Yongqin Liu ◽  
Baiqing Xu ◽  
Ninglian Wang ◽  
Sten Anslan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Low Temperature ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Cold Adapted ◽  
Monophyletic Cluster ◽  
Alpine Regions ◽  
Wide Range

AbstractDecrease in the frequency of arginine and increase in lysine are the trends that have been identified in the genomes of cold adapted bacteria. However, some cold adapted taxa show only limited or no detectable changes in the frequencies of amino acid composition. Here, we examined Arthrobacter spp. genomes from a wide range of environments on whether the genomic adaptations can be conclusively identified across genomes of taxa from polar and alpine regions. Phylogenetic analysis with a concatenated alignment of 119 orthologous proteins revealed a monophyletic clustering of seven polar and alpine isolated strains. Significant changes in amino acid composition related to cold adaptation were exclusive to seven of the twenty-nine strains from polar and alpine regions. Analysis of significant indicator genes and cold shock genes also revealed that clear differences could only be detected in the same seven strains. These unique characteristics may result from a vast exchange of genome content at the node leading to the monophyletic cold adapted Arthrobacter cluster predicted by the birth-and-death model. We then experimentally validated that strains with significant changes in amino acid composition have a better capacity to grow at low temperature than the mesophilic strains.ImportanceAcquisition of novel traits through horizontal gene transfer at the early divergence of the monophyletic cluster may accelerate their adaptation to low temperature. Our study reached a clear relationship between adaptation to cold and genomic features and would advanced in understanding the ambiguous results produced by the previous studies on genomic adaption to cold temperature.

scholarly journals Pseudo amino acid composition improves antifreeze protein prediction

2014 ◽  
Author(s):  
Sukanta Mondal ◽  
Priyadarshini P. Pai
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Support Vector ◽  
Order Information ◽  
Biotechnological Applications ◽  
Pseudo Amino Acid Composition ◽  
Cold Temperatures ◽  
Wide Range ◽  
Prediction Approach

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area did not cover introduction of sequence order information, known to represent important properties of various proteins and protein systems for prediction of their attributes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden’s Index (Sensitivity + Specificity -1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications.

scholarly journals Determination of qualitative composition and quantitative content of amino acids in garlic bulbs and leaves

2017 ◽  
Author(s):  
A. I. Fedosov ◽  
V. S. Kyslychenko ◽  
O. M. Novosel
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Glutamic Acid ◽  
Amino Acid Composition ◽  
Aspartic Acid ◽  
Acid Composition ◽  
Bound State ◽  
Quantitative Content ◽  
Wide Range ◽  
Plant Amino Acids

Introduction. Plant amino acids have an important impact on functioning of various systems and organs of human body. In addition, they possess a wide range of pharmacotherapeutic properties, improve the digestion and potentiate the activity of biologically active compounds present in plants. Thus, the search of plant species that contain a large complex of plant amino acids and are used as food is of current interest. Garlic (Allium sativum L.) from Alliaceae family is one of such plants, and has been used since ancient times for the treatment of various disorders.The aim of the study – to determine the composition and quantitative content of free and bound amino acids of garlic bulbs and leaves.Research methods. The amino acid composition was determined using the high-performance liquid chromatography (HPLC) method.Results and Discussion. 16 amino acids were detected in garlic bulbs as a result of the experiment. Arginine (3.04 %) and proline (1.56 %) were found to be accumulated infree state, while glutamic acid (10.59 %), aspartic acid (6.06 %) and arginine (5.94 %) prevailed in bound state. 15 free and 16 bound amino acids were identified and quantified in garlic leaves. Glutamic acid (2.11 %), leucine (1.79 %), valine (1.77 %), isoleucine (1.52 %), treonine and phenylalanine (1.44 %) dominated infree state, and glutamic acid (28.49 %), aspartic acid (12.90 %) and leucine (7.61 %) prevailed in bound state. Methionine was found only in bound state in garlic leaves.Conclusions. The amino acid composition of garlic bulbs and leaves was studied using the HPLC method. 16 amino acids in both free and bound state were detected and their content was determined in garlic bulbs, while in garlic leaves – 15 free and 16 bound amino acids. The results of the experiment showed that methionine is present only in bound state in garlic leaves.

scholarly journals Pseudo amino acid composition improves antifreeze protein prediction

2014 ◽  
Author(s):  
Sukanta Mondal ◽  
Priyadarshini P. Pai
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Support Vector ◽  
Order Information ◽  
Biotechnological Applications ◽  
Pseudo Amino Acid Composition ◽  
Cold Temperatures ◽  
Wide Range ◽  
Prediction Approach

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area did not cover introduction of sequence order information, known to represent important properties of various proteins and protein systems for prediction of their attributes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden’s Index (Sensitivity + Specificity -1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications.

scholarly journals AMINO ACID COMPOSITION OF STEVIA RAW MATERIALS OF DIFFERENT ORIGIN

2021 ◽  
pp. 113-119
Author(s):  
Evgeny Evgenievich Kurdyukov ◽  
Elena Fedorovna Semenova ◽  
Ol'ga Aleksandrovna Vodopyanova ◽  
Yakov Petrovich Moiseev ◽  
Olesya Petrovna Rodina ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Raw Materials ◽  
Stevia Rebaudiana ◽  
Essential Amino Acids ◽  
Stevia Rebaudiana Bertoni ◽  
Wide Range ◽  
The Republic

Dried stevia leaves (Stevia rebaudiana Bertoni) were used as objects of research. We studied the leaves of stevia varieties Ramon sweetener grown in the Penza region, the leaves of stevia varieties Ramon sweetener grown in the Tver region, Krasnodar region, the Republic of Crimea, as well as imported raw stevia from India and Paraguay. The purpose of this work is a comparative study of the amino acid composition of raw stevia grown in different conditions. The amino acid composition of stevia leaves (Stevia rebaudiana Bertoni) was revealed by capillary electrophoresis.13 amino acids were identified, of which eight are "essential" (lysine, phenylalanine, histidine, leucine, isoleucine, methionine, valine, threonine). The proportion of essential amino acids in stevia raw materials ranged from 2.99 to 4.64%. The content of interchangeable acids was: tyrosine from 0.24% to 0.36%, Proline from 0.44 to 0.68%, serine from 0.77 to 1.03%, alanine from 0.48 to 0.83%, glycine from 0.40 to 0.68%. The total amount of amino acids detected is higher in the Ramon sweetener variety grown in the Penza region (9.52%) compared to other samples, the lowest amount is found in stevia grown in Paraguay (6.46%). The results obtained indicate the prospects for further studies of the amino acid composition of Stevia rebaudiana and can characterize this species as a source of valuable medicinal substances with a wide range of pharmacological activity.

scholarly journals Pseudo amino acid composition improves antifreeze protein prediction

2014 ◽  
Author(s):  
Sukanta Mondal ◽  
Priyadarshini P. Pai
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Support Vector ◽  
Order Information ◽  
Biotechnological Applications ◽  
Pseudo Amino Acid Composition ◽  
Cold Temperatures ◽  
Wide Range ◽  
Prediction Approach

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area did not cover introduction of sequence order information, known to represent important properties of various proteins and protein systems for prediction of their attributes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden’s Index (Sensitivity + Specificity -1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications.

scholarly journals Amino-acid composition and balance of collagen containing raw materials

2018 ◽  
Vol 56 (4) ◽  
pp. 492-503
Author(s):  
A. V. Meleshchenya ◽  
T. A. Savelyeva ◽  
S. А. Gordynets ◽  
I. V. Kaltovich
Keyword(s):  
Amino Acid ◽  
Connective Tissue ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Raw Materials ◽  
Raw Material ◽  
Meat Industry ◽  
Food Protein ◽  
Isoleucine Leucine ◽  
Wide Range

A prospective source of additional food protein in the meat industry is collagen-containing raw materials: pork skin, connective tissue obtained at meat trimming, collagen-containing by-products, etc., which can be used as part of proteinand-fat emulsions. Collagen emulsions have a wide range of functional properties: moisture and fat retention, foam and gelling abilities, emulsifying activity, active foam, emulsions and dispersions stabilizers, so they can be used as a technological additive in the meat industry. Therefore, the most important task in the process is the complete use of collagen-containing raw materials with the maximum implementation of its properties. The paper presents the results of studies on determining the amino acid composition and balance of collagen-containing raw materials: pork skin, beef tendons, lungs, rumen, beef lips and ears, pork ears, udder, spleen, omasum, skin, head, feet, caruncle, stomach and intestines of poultry. It was determined that collagen-containing raw material contains all the essential amino acids: isoleucine, leucine, lysine, methionine and cysteine, phenylalanine and tyrosine, threonine, valine with the amino acid count in the range of 17.1–185.0 %. At the same time, a more balanced amino acid composition in comparison with other types of collagen-containing raw materials is shown by: pork skin, udder, beef lips and trachea, chitterlings, omasum, rumen, lungs and spleen as evidenced by high values of amino acid score (up to 185 %), essential amino acid index (up to 1.1), utility factor of the amino acid composition (up to 0.84), as well as the approximate values of the comparable redundancy index (0.0007–0.0043). The research results confirm the prospectiveness of combining muscle and connective tissue proteins in recipes of meat products of high nutritional and biological value.

scholarly journals DETERMINATION OF AMINO ACID COMPOSITION OF BROСCOLI CABBAGE PROTEIN

2018 ◽  
Vol 3 ◽  
pp. 25-32
Author(s):  
Svitlana Belinska ◽  
Nataliia Kamienieva ◽  
Stanislava Levytska ◽  
Sergiy Rogalskiy
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Fruits And Vegetables ◽  
Scientific Database ◽  
Biological Value ◽  
Geographical Regions ◽  
Wide Range ◽  
Dispensable Amino Acids

A wide range of fresh fruits and vegetables grown in different geographical areas and represented in international trade networks has changed the consumers' approaches to their choice. The determining criterion of choice is the biological value of plant raw materials, is determined by the content of amino acids, vitamins, mineral elements, β-carotene, which play a significant role in ensuring the functioning of the human body. The chemical composition of fruits and vegetables is highly variable and depends on the type, variety of vegetables, agro climatic conditions of their cultivation, storage characteristics and requires study. The study of the amino acid composition and biological value of the protein of the broccoli varieties of French and Dutch selections, which are regionalized in Ukraine, will determine the most promising varieties in order to provide the population with full-fledged proteins of plant origin. The amino acid composition of the protein of the broccoli Parthenon, Belstar F1, Quinta F1, Monaco F1 is regionalized and suitable for cultivation in different geographical regions of Ukraine. Calculation of the amino acidic score and biological value of the broccoli cabbage protein on which the varieties were ranked. 8 indispensable and 8 dispensable amino acids are identified and quantified. It is found that the greatest content of indispensable amino acids is characteristic for cabbage varieties Parthenon (41.95 mg/100 mg protein) and Belstar F1 (42.26 mg/100 mg protein). All the investigated varieties of broccoli cabbage don’t differ significantly in this indicator. A high content of glutamic acid (from 16.27 to 18.43 mg/100 mg protein), aspartic acid (from 9.54 to 10.56 mg/100 mg protein), arginine (from 6.02 to 6.90 mg) is found in the dispensable amino acids in broccoli cabbage varieties/100 mg). The calculated amino acid scores show that the broccoli cabbage protein is a valuable source of isoleucine, methionine, phenylalanine and tryptophan. The score of methionine, tryptophan and isoleucine ranges from 165.1 % to 183.1 %; from 121.0 to 156.0 % and from 115.3 to 127.8 % respectively. Species of broccoli cabbage are identified, the protein of which has the highest biological value. The performed calculations confirm that the highest biological value is possessed by the broccoli cabbage protein of Quinta F1 variety (64.2 %). This variety is the most balanced in its amino acid composition compared to other varieties. The biological value of the protein of the varieties of Monaco F1, the Parthenon is different and amounted to 63.2 % and 63.1 %, respectively. The lowest biological value is found for the protein Belstar F1 – 60.5 %. The research results of the amino acid composition and biological value of the broccoli cabbage protein of varieties bred and grown in different countries will contribute to the expansion of the scientific database on the effect of climatic growing conditions on the biological value of the broccoli cabbage protein. The obtained results can also be useful for specialists in the agrarian sector and the fruit and vegetable industry.

scholarly journals Pseudo amino acid composition improves antifreeze protein prediction

2014 ◽  
Author(s):  
Sukanta Mondal ◽  
Priyadarshini P. Pai
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Support Vector ◽  
Order Information ◽  
Biotechnological Applications ◽  
Pseudo Amino Acid Composition ◽  
Cold Temperatures ◽  
Wide Range ◽  
Prediction Approach

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area did not cover introduction of sequence order information, known to represent important properties of various proteins and protein systems for prediction of their attributes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden’s Index (Sensitivity + Specificity -1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications.

scholarly journals Economical Evolution: Microbes Reduce the Synthetic Cost of Extracellular Proteins

mBio ◽  
2010 ◽  
Vol 1 (3) ◽  
Author(s):  
Daniel R. Smith ◽  
Matthew R. Chapman
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Pseudomonas Syringae ◽  
Extracellular Proteins ◽  
Compositional Bias ◽  
Type I ◽  
Content Type ◽  
Wide Range

ABSTRACT Protein evolution is not simply a race toward improved function. Because organisms compete for limited resources, fitness is also affected by the relative economy of an organism’s proteome. Indeed, many abundant proteins contain relatively high percentages of amino acids that are metabolically less taxing for the cell to make, thus reducing cellular cost. However, not all abundant proteins are economical, and many economical proteins are not particularly abundant. Here we examined protein composition and found that the relative synthetic cost of amino acids constrains the composition of microbial extracellular proteins. In Escherichia coli, extracellular proteins contain, on average, fewer energetically expensive amino acids independent of their abundance, length, function, or structure. Economic pressures have strategically shaped the amino acid composition of multicomponent surface appendages, such as flagella, curli, and type I pili, and extracellular enzymes, including type III effector proteins and secreted serine proteases. Furthermore, in silico analysis of Pseudomonas syringae, Mycobacterium tuberculosis, Saccharomyces cerevisiae, and over 25 other microbes spanning a wide range of GC content revealed a broad bias toward more economical amino acids in extracellular proteins. The synthesis of any protein, especially those rich in expensive aromatic amino acids, represents a significant investment. Because extracellular proteins are lost to the environment and not recycled like other cellular proteins, they present a greater burden on the cell, as their amino acids cannot be reutilized during translation. We hypothesize that evolution has optimized extracellular proteins to reduce their synthetic burden on the cell. IMPORTANCE Microbes secrete proteins to perform essential interactions with their environment, such as motility, pathogenesis, biofilm formation, and resource acquisition. However, because microbes generally lack protein import systems, secretion is often a one-way street. Consequently, secreted proteins are less likely to be recycled by the cell due to environmental loss. We demonstrate that evolution has in turn selected these extracellular proteins for increased economy at the level of their amino acid composition. Compared to their cellular counterparts, extracellular proteins have fewer synthetically expensive amino acids and more inexpensive amino acids. The resulting bias lessens the loss of cellular resources due to secretion. Furthermore, this economical bias was observed regardless of the abundance, length, structure, or function of extracellular proteins. Thus, it appears that economy may address the compositional bias seen in many extracellular proteins and deliver further insight into the forces driving their evolution.

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