Amino Acid Catabolism
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Characterization of L-Serine Deaminases, Sdaa (PA2448) and Sdab 2 (PA5379), and Their Potential Role in Pseudomonas Aeruginosa 3 Pathogenesis 4 5 Sixto M
bioRxiv preprint doi: https://doi.org/10.1101/394957; this version posted August 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Characterization of L-serine deaminases, SdaA (PA2448) and SdaB 2 (PA5379), and their potential role in Pseudomonas aeruginosa 3 pathogenesis 4 5 Sixto M. Leal1,6, Elaine Newman2 and Kalai Mathee1,3,4,5 * 6 7 Author affiliations: 8 9 1Department of Biological Sciences, College of Arts Sciences and 10 Education, Florida International University, Miami, United States of 11 America 12 2Department of Biological Sciences, Concordia University, Montreal, 13 Canada 14 3Department of Molecular Microbiology and Infectious Diseases, Herbert 15 Wertheim College of Medicine, Florida International University, Miami, 16 United States of America 17 4Biomolecular Sciences Institute, Florida International University, Miami, 18 United States of America 19 20 Present address: 21 22 5Department of Human and Molecular Genetics, Herbert Wertheim 23 College of Medicine, Florida International University, Miami, United States 24 of America 25 6Case Western Reserve University, United States of America 26 27 28 *Correspondance: Kalai Mathee, MS, PhD, 29 [email protected] 30 31 Telephone : 1-305-348-0628 32 33 Keywords: Serine Catabolism, Central Metabolism, TCA Cycle, Pyruvate, 34 Leucine Responsive Regulatory Protein (LRP), One Carbon Metabolism 35 Running title: P. aeruginosa L-serine deaminases 36 Subject category: Pathogenicity and Virulence/Host Response 37 1 bioRxiv preprint doi: https://doi.org/10.1101/394957; this version posted August 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Effects of Dietary L-Glutamine Or L-Glutamine Plus L-Glutamic Acid
Brazilian Journal of Poultry Science Revista Brasileira de Ciência Avícola Effects of Dietary L-Glutamine or L-Glutamine Plus ISSN 1516-635X Oct - Dec 2015 / Special Issue L-Glutamic Acid Supplementation Programs on the Nutrition - Poultry feeding additives / 093-098 Performance and Breast Meat Yield Uniformity of http://dx.doi.org/10.1590/1516-635xSpecialIssue 42-d-Old Broilers Nutrition-PoultryFeedingAdditives093-098 Author(s) ABSTRACT Ribeiro Jr VIII This study aimed at evaluating four dietary L-Glutamine (L-Gln) Albino LFTI or L-Gln plus L-Glutamate (L-Glu) supplementation programs on the Rostagno HSI Hannas MII performance, breast yield, and uniformity of broilers. A total of 2,112 Ribeiro CLNIII one-d-old male Cobb 500® broilers were distributed according to a Vieira RAIII randomized block design in a 2 × 4 factorial arrangement (L-Gln or L-Gln Araújo WAG deIV Pessoa GBSII plus L-Glu × 4 supplementation programs), totaling eight treatments Messias RKGIII with 12 replicates of 22 broilers each. The supplementation programs Silva DL daIII consisted of the dietary inclusion or not of 0.4% of L-Gln or L-Gln plus L-Glu for four different periods: 0 days (negative control), 9d, 21d, and 42d. Feed intake (FI, g), body weight gain (BWG, g), feed conversion I Federal University of Viçosa, Department ratio (FCR, kg/kg), coefficient of variation of body weight (CV, %), body of Animal Science, Av PH Rolfs S/N, Viçosa 36570-000, MG, Brazil weight uniformity (UNIF, %), breast weight (BW, g), breast yield (BY, II Ajinomoto do Brasil Ind. e Com. de %), coefficient of variation of breast weight (CVB), breast uniformity Alimentos Ltda. -
Amphibolic Nature of Krebs Cycle
Amphibolic nature of Krebs Cycle How what we are is what we eat • In aerobic organisms, the citric acid cycle is an amphibolic pathway, one that serves in both catabolic and anabolic processes. • Since the citric acid does both synthesis (anabolic) and breakdown (catabolic) activities, it is called an amphibolic pathway • The citric acid cycle is amphibolic (i.e it is both anabolic and catabolic in its function). • It is said to be an AMPHIBOLIC pathway, because it functions in both degradative or catabolic and biosynthetic or anabolic reactions (amphi = both) A central metabolic pathway or amphibolic pathway is a set of reactions which permit the interconversion of several metabolites, and represents the end of the catabolism and the beginning of anabolism • The KREBS CYCLE or citric acid cycle is a series of reactions that degrades acetyl CoA to yield carbon dioxide, and energy, which is used to produce NADH, H+ and FADH. • The KREBS CYCLE connects the catabolic pathways that begin with the digestion and degradation of foods in stages 1 and 2 with the oxidation of substrates in stage 3 that generates most of the energy for ATP synthesis. • The citric acid cycle is the final common pathway in the oxidation of fuel molecules. In stage 3 of metabolism, citric acid is a final common catabolic intermediate in the form of acetylCoA. • This is why the citric acid cycle is called a central metabolic pathway. Anaplerosis and Cataplerosis Anaplerosis is a series of enzymatic reactions in which metabolic intermediates enter the citric acid cycle from the cytosol. Cataplerosis is the opposite, a process where intermediates leave the citric acid cycle and enter the cytosol. -
Novel Neuroprotective Compunds for Use in Parkinson's Disease
Novel neuroprotective compounds for use in Parkinson’s disease A thesis submitted to Kent State University in partial Fulfillment of the requirements for the Degree of Master of Science By Ahmed Shubbar December, 2013 Thesis written by Ahmed Shubbar B.S., University of Kufa, 2009 M.S., Kent State University, 2013 Approved by ______________________Werner Geldenhuys ____, Chair, Master’s Thesis Committee __________________________,Altaf Darvesh Member, Master’s Thesis Committee __________________________,Richard Carroll Member, Master’s Thesis Committee ___Eric_______________________ Mintz , Director, School of Biomedical Sciences ___Janis_______________________ Crowther , Dean, College of Arts and Sciences ii Table of Contents List of figures…………………………………………………………………………………..v List of tables……………………………………………………………………………………vi Acknowledgments.…………………………………………………………………………….vii Chapter 1: Introduction ..................................................................................... 1 1.1 Parkinson’s disease .............................................................................................. 1 1.2 Monoamine Oxidases ........................................................................................... 3 1.3 Monoamine Oxidase-B structure ........................................................................... 8 1.4 Structural differences between MAO-B and MAO-A .............................................13 1.5 Mechanism of oxidative deamination catalyzed by Monoamine Oxidases ............15 1 .6 Neuroprotective effects -
Amino Acids, Glutamine, and Protein Metabolism in Very Low Birth Weight Infants
0031-3998/05/5806-1259 PEDIATRIC RESEARCH Vol. 58, No. 6, 2005 Copyright © 2005 International Pediatric Research Foundation, Inc. Printed in U.S.A. Amino Acids, Glutamine, and Protein Metabolism in Very Low Birth Weight Infants PRABHU S. PARIMI, MARK M. KADROFSKE, LOURDES L. GRUCA, RICHARD W. HANSON, AND SATISH C. KALHAN Department of Pediatrics, Schwartz Center for Metabolism and Nutrition, Case Western Reserve University School of Medicine, MetroHealth Medical Center, Cleveland, Ohio, 44109 ABSTRACT Glutamine has been proposed to be conditionally essential for 5 h (AA1.5) resulted in decrease in rate of appearance (Ra) of premature infants, and the currently used parenteral nutrient phenylalanine and urea, but had no effect on glutamine Ra. mixtures do not contain glutamine. De novo glutamine synthesis Infusion of amino acids at 3.0 g/kg/d for 20 h resulted in increase (DGln) is linked to inflow of carbon into and out of the tricar- in DGln, leucine transamination, and urea synthesis, but had no boxylic acid (TCA) cycle. We hypothesized that a higher supply effect on Ra phenylalanine (AA-Ext). These data show an acute of parenteral amino acids by increasing the influx of amino acid increase in parenteral amino acid–suppressed proteolysis, how- carbon into the TCA cycle will enhance the rate of DGln. Very ever, such an effect was not seen when amino acids were infused low birth weight infants were randomized to receive parenteral for 20 h and resulted in an increase in glutamine synthesis. amino acids either 1.5 g/kg/d for 20 h followed by 3.0 g/kg/d for (Pediatr Res 58: 1259–1264, 2005) 5 h (AA1.5) or 3.0 g/kg/d for 20 h followed by 1.5 g/kg/d for 5 h (AA3.0). -
The Citric Acid Cycle the Catabolism of Acetyl-Coa
Al-Sham Private University Faculty Of Pharmacy The Citric Acid Cycle The Catabolism of Acetyl-CoA Lecturer Prof. Abboud Al-Saleh 1 Prof.Abboud AL-Saleh 10/1/2018 BIOMEDICAL IMPORTANCE • The citric acid cycle (Krebs cycle, tricarboxylic acid cycle) is a series of reactions in mitochondria that oxidize acetyl residues (as acetyl-CoA) and reduce coenzymes that upon reoxidation are linked to the formation of ATP. • TCA is the final common pathway for the aerobic oxidation of carbohydrate, lipid, and protein because glucose, fatty acids, and most amino acids are metabolized to acetyl-CoA or intermediates of the cycle. 2 Prof.Abboud AL-Saleh 10/1/2018 • TCA also has a central role in gluconeogenesis, lipogenesis, and interconversion of amino acids. Many of these processes occur in most tissues, but the liver is the only tissue in which all occur to a significant extent. • The repercussions are therefore profound when, for example, large numbers of hepatic cells are damaged as in acute hepatitis or as in cirrhosis. • Very few, if any, genetic abnormalities of TCA enzymes have been reported; such abnormalities would be incompatible with life or normal development 3 Prof.Abboud AL-Saleh 10/1/2018 Summary • The cycle starts with reaction between the acetyl moiety of acetyl-CoA and the four-carbon dicarboxylic acid oxaloacetate, forming a six-carbon tricarboxylic acid, citrate. • In the subsequent reactions, two molecules of CO2 are released and oxaloacetate is regenerated (Figure). • Only a small quantity of oxaloacetate is needed for the oxidation of a large quantity of acetyl-CoA. • oxaloacetate may be considered to play a catalytic role. -
Catabolism Iii
Nitrogen Catabolism Glycogenolysis Protein Fat catabolism Catabolism Fatty Acid Amino-acid GlycolysisDegradation catabolism Pyruvate Oxidation Krebs' Cycle Phosphorylation Oxidative CATABOLISM III: Digestion and Utilization of Proteins • Protein degradation • Protein turnover – The ubiquitin pathway – Protein turnover is tightly regulated • Elimination of nitrogen – By fish, flesh and fowl – How is the N of amino acids liberated and eliminated? • How are amino acids oxidized for energy 1 Protein Catabolism Sources of AMINO ACIDS: •Dietary amino acids that exceed body’s protein synthesis needs •Excess amino acids from protein turnover (e.g., proteolysis and regeneration of proteins) •Proteins in the body can be broken down (muscle wasting) to supply amino acids for energy when carbohydrates are scarce (starvation, diabetes mellitus). •Carnivores use amino acids for energy more than herbivores, plants, and most microorganisms Protein Catabolism The Digestion Pathway • Pro-enzymes are secreted (zymogens) and the environment activates them by specific proteolysis. • Pepsin hydrolyzes protein into peptides in the stomach. • Trypsin and chymotrypsin hydrolyze proteins and larger peptides into smaller peptides in the small intestine. • Aminopeptidase and carboxypeptidases A and B degrade peptides into amino acids in the small intestine. 2 Protein Catabolism The Lysosomal Pathway • Endocytosis, either receptor-mediated, phagocytosis, or pinocytosis engulfs extra- cellular proteins into vesicles. • These internal vesicles fuse as an early endosome. • This early endosome is acidified by the KFERQ Substrates vATPase (“v” for vesicular). • Components that are recycled, like receptors, HSPA8 are sequestered in smaller vesicles to create Co-chaperones the multivesicular body (MVB), sometimes called a late endosome. • If set for degradation, it will fuse with a KFERQ primary lysosome (red) which contains many cathepsin-type proteases. -
Production of L-Asparaginase II by Escherichia Coli HOWARD CEDAR and JAMES H
JOURNAL OF BACTERIOLOGY, Dec. 1968, p. 2043-2048 Vol. 96, No. 6 Copyright @ 1968 American Society for Microbiology Printed in U.S.A. Production of L-Asparaginase II by Escherichia coli HOWARD CEDAR AND JAMES H. SCHWARTZ Department of Microbiology, New York University School ofMedicine, New York, New York 10016 Received for publication 30 July 1968 L-Asparaginase II was synthesized at constant rates by Escherichia coli under anaerobic conditions. The enzyme was produced optimally by bacteria grown between pH 7 and 8 at 37 C. Although some enzyme was formed aerobically, be- tween 100 and 1,000 times more asparaginase II was produced during anaerobic growth in media enriched with high concentrations of a variety of amino acids. Bacteria grown under these conditions should provide a rich starting material for the large-scale production of the enzyme. No single amino acid specifically induced the synthesis of the asparaginase, nor did L-asparagine, even when it was used as the only source of nitrogen. The enzyme was produced at lower rates in the presence of sugars; glucose was the most inhibitory. Deamidation of L-asparagine by extracts of the conditions which control the production of Escherichia coli was first reported in 1957 by asparaginase II. Tsuji (28). E. coli was later shown to produce two distinct asparaginases (L-asparagine amido- MATERIALS AND METHODS hydrolase, EC 3.5.1 .1) which differ in a number For most of the experiments, we used E. coli K-12 of properties, perhaps most significantly in wild type. We also used strain 22-64, which lacks their markedly different affinities for asparagine citrate synthase (10), and strain 309-1, which lacks (5, 24, 27). -
Detection and Formation Scenario of Citric Acid, Pyruvic Acid, and Other Possible Metabolism Precursors in Carbonaceous Meteorites
Detection and formation scenario of citric acid, pyruvic acid, and other possible metabolism precursors in carbonaceous meteorites George Coopera,1, Chris Reeda, Dang Nguyena, Malika Cartera, and Yi Wangb aExobiology Branch, Space Science Division, National Aeronautics and Space Administration-Ames Research Center, Moffett Field, CA 94035; and bDevelopment, Planning, Research, and Analysis/ZymaX Forensics Isotope, 600 South Andreasen Drive, Suite B, Escondido, CA 92029 Edited by David Deamer, University of California, Santa Cruz, CA, and accepted by the Editorial Board July 1, 2011 (received for review April 12, 2011) Carbonaceous meteorites deliver a variety of organic compounds chained three-carbon (3C) pyruvic acid through the eight-carbon to Earth that may have played a role in the origin and/or evolution (8C) 7-oxooctanoic acid and the branched 6C acid, 3-methyl- of biochemical pathways. Some apparently ancient and critical 4-oxopentanoic acid (β-methyl levulinic acid), Fig. 1, Table S1. metabolic processes require several compounds, some of which 2-methyl-4-oxopenanoic acid (α-methyl levulinic acid) is tenta- are relatively labile such as keto acids. Therefore, a prebiotic setting tively identified (i.e., identified by mass spectral interpretation for any such individual process would have required either a only). As a group, these keto acids are relatively unusual in that continuous distant source for the entire suite of intact precursor the ketone carbon is located in a terminal-acetyl group rather molecules and/or an energetic and compact local synthesis, parti- than at the second carbon as in most of the more biologically cularly of the more fragile members. -
Introduction to Proteins and Amino Acids Introduction
Introduction to Proteins and Amino Acids Introduction • Twenty percent of the human body is made up of proteins. Proteins are the large, complex molecules that are critical for normal functioning of cells. • They are essential for the structure, function, and regulation of the body’s tissues and organs. • Proteins are made up of smaller units called amino acids, which are building blocks of proteins. They are attached to one another by peptide bonds forming a long chain of proteins. Amino acid structure and its classification • An amino acid contains both a carboxylic group and an amino group. Amino acids that have an amino group bonded directly to the alpha-carbon are referred to as alpha amino acids. • Every alpha amino acid has a carbon atom, called an alpha carbon, Cα ; bonded to a carboxylic acid, –COOH group; an amino, –NH2 group; a hydrogen atom; and an R group that is unique for every amino acid. Classification of amino acids • There are 20 amino acids. Based on the nature of their ‘R’ group, they are classified based on their polarity as: Classification based on essentiality: Essential amino acids are the amino acids which you need through your diet because your body cannot make them. Whereas non essential amino acids are the amino acids which are not an essential part of your diet because they can be synthesized by your body. Essential Non essential Histidine Alanine Isoleucine Arginine Leucine Aspargine Methionine Aspartate Phenyl alanine Cystine Threonine Glutamic acid Tryptophan Glycine Valine Ornithine Proline Serine Tyrosine Peptide bonds • Amino acids are linked together by ‘amide groups’ called peptide bonds. -
Lecture: 28 TRANSAMINATION, DEAMINATION and DECARBOXYLATION
Lecture: 28 TRANSAMINATION, DEAMINATION AND DECARBOXYLATION Protein metabolism is a key physiological process in all forms of life. Proteins are converted to amino acids and then catabolised. The complete hydrolysis of a polypeptide requires mixture of peptidases because individual peptidases do not cleave all peptide bonds. Both exopeptidases and endopeptidases are required for complete conversion of protein to amino acids. Amino acid metabolism The amino acids not only function as energy metabolites but also used as precursors of many physiologically important compounds such as heme, bioactive amines, small peptides, nucleotides and nucleotide coenzymes. In normal human beings about 90% of the energy requirement is met by oxidation of carbohydrates and fats. The remaining 10% comes from oxidation of the carbon skeleton of amino acids. Since the 20 common protein amino acids are distinctive in terms of their carbon skeletons, amino acids require unique degradative pathway. The degradation of the carbon skeletons of 20 amino acids converges to just seven metabolic intermediates namely. i. Pyruvate ii. Acetyl CoA iii. Acetoacetyl CoA iv. -Ketoglutarate v. Succinyl CoA vi. Fumarate vii. Oxaloacetate Pyruvate, -ketoglutarate, succinyl CoA, fumarate and oxaloacetate can serve as precursors for glucose synthesis through gluconeogenesis.Amino acids giving rise to these intermediates are termed as glucogenic. Those amino acids degraded to yield acetyl CoA or acetoacetate are termed ketogenic since these compounds are used to synthesize ketone bodies. Some amino acids are both glucogenic and ketogenic (For example, phenylalanine, tyrosine, tryptophan and threonine. Catabolism of amino acids The important reaction commonly employed in the breakdown of an amino acid is always the removal of its -amino group. -
Amino Acid Chemistry
Handout 4 Amino Acid and Protein Chemistry ANSC 619 PHYSIOLOGICAL CHEMISTRY OF LIVESTOCK SPECIES Amino Acid Chemistry I. Chemistry of amino acids A. General amino acid structure + HN3- 1. All amino acids are carboxylic acids, i.e., they have a –COOH group at the #1 carbon. 2. All amino acids contain an amino group at the #2 carbon (may amino acids have a second amino group). 3. All amino acids are zwitterions – they contain both positive and negative charges at physiological pH. II. Essential and nonessential amino acids A. Nonessential amino acids: can make the carbon skeleton 1. From glycolysis. 2. From the TCA cycle. B. Nonessential if it can be made from an essential amino acid. 1. Amino acid "sparing". 2. May still be essential under some conditions. C. Essential amino acids 1. Branched chain amino acids (isoleucine, leucine and valine) 2. Lysine 3. Methionine 4. Phenyalanine 5. Threonine 6. Tryptophan 1 Handout 4 Amino Acid and Protein Chemistry D. Essential during rapid growth or for optimal health 1. Arginine 2. Histidine E. Nonessential amino acids 1. Alanine (from pyruvate) 2. Aspartate, asparagine (from oxaloacetate) 3. Cysteine (from serine and methionine) 4. Glutamate, glutamine (from α-ketoglutarate) 5. Glycine (from serine) 6. Proline (from glutamate) 7. Serine (from 3-phosphoglycerate) 8. Tyrosine (from phenylalanine) E. Nonessential and not required for protein synthesis 1. Hydroxyproline (made postranslationally from proline) 2. Hydroxylysine (made postranslationally from lysine) III. Acidic, basic, polar, and hydrophobic amino acids A. Acidic amino acids: amino acids that can donate a hydrogen ion (proton) and thereby decrease pH in an aqueous solution 1.