DOCSLIB.ORG

Genetic Basis for Plasma Amino Acid Concentrations Based on Absolute Quantification: a Genome-Wide Association Study in the Japa

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genetic Basis for Plasma Amino Acid Concentrations Based on Absolute Quantification: a Genome-Wide Association Study in the Japa European Journal of Human Genetics https://doi.org/10.1038/s41431-018-0296-y ARTICLE Genetic basis for plasma amino acid concentrations based on absolute quantification: a genome-wide association study in the Japanese population 1 1 2 2,3 2 Akira Imaizumi ● Yusuke Adachi ● Takahisa Kawaguchi ● Koichiro Higasa ● Yasuharu Tabara ● 2,4 4 2 1 1 Kazuhiro Sonomura ● Taka-aki Sato ● Meiko Takahashi ● Toshimi Mizukoshi ● Hiro-o Yoshida ● 1 1 1 1 1 5 Naoko Kageyama ● Chisato Okamoto ● Mariko Takasu ● Maiko Mori ● Yasushi Noguchi ● Nobuhisa Shimba ● 1 2 2 Hiroshi Miyano ● Ryo Yamada ● Fumihiko Matsuda Received: 5 March 2018 / Revised: 15 October 2018 / Accepted: 25 October 2018 © The Author(s) 2019. This article is published with open access Abstract To assess the use of plasma free amino acids (PFAAs) as biomarkers for metabolic disorders, it is essential to identify genetic factors that influence PFAA concentrations. PFAA concentrations were absolutely quantified by liquid chromatography–mass spectrometry using plasma samples from 1338 Japanese individuals, and genome-wide quantitative 1234567890();,: 1234567890();,: trait locus (QTL) analysis was performed for the concentrations of 21 PFAAs. We next conducted a conditional QTL analysis using the concentration of each PFAA adjusted by the other 20 PFAAs as covariates to elucidate genetic determinants that influence PFAA concentrations. We identified eight genes that showed a significant association with PFAA concentrations, of which two, SLC7A2 and PKD1L2, were identified. SLC7A2 was associated with the plasma levels of arginine and ornithine, and PKD1L2 with the level of glycine. The significant associations of these two genes were revealed in the conditional QTL analysis, but a significant association between serine and the CPS1 gene disappeared when glycine was used as a covariate. We demonstrated that conditional QTL analysis is useful for determining the metabolic pathways predominantly used for PFAA metabolism. Our findings will help elucidate the physiological roles of genetic components that control the metabolism of amino acids. Introduction Circulating metabolite concentrations in the body can serve Supplementary information The online version of this article (https:// as useful biomarkers for the diagnosis, prognosis, and risk doi.org/10.1038/s41431-018-0296-y) contains supplementary assessment of diseases, particularly for metabolic disorders material, which is available to authorized users. such as diabetes, dyslipidemia, and hypertension [1–8]. * Akira Imaizumi Among these metabolites, the free amino acids in plasma [email protected] (PFAAs) are key regulators of metabolic pathways, and * Fumihiko Matsuda their concentrations are influenced by both genetic and [email protected] environmental factors, such as the diet [9–14]. Recently, several genome-wide association studies 1 Institute for Innovation, Ajinomoto Co., Inc., (GWAS) also identified genetic variations associated with Kawasaki, Kanagawa 210-8681, Japan PFAAs in European populations [9–11, 13, 15]. However, 2 Center for Genomic Medicine, Kyoto University Graduate School the influence of heritability and whether these loci are of Medicine, Kyoto 606-8507, Japan shared among other human populations are still unknown. 3 Department of Genome Analysis, Institute of Biomedical Science, In addition, metabolite concentrations are influenced by Kansai Medical University, Hirakata, Osaka 573-1010, Japan other metabolites within the same metabolic pathway. 4 Life Science Laboratories, Shimadzu Corporation, Seika, Kyoto Therefore, genome-wide quantitative trait locus (QTL) 619-0237, Japan analyses conditioned on the other amino acids sharing the 5 R&D Planning Dept., Ajinomoto Co., Inc, Tokyo 104-8315, Japan same pathway are necessary. A. Imaizumi et al. Fig. 1 Flow diagram of the QC processes and QTL analyses using the PFAA concentrations of Japanese subjects from the Nagahama Study In this study, we sought to elucidate genetic determinants (HPLC–ESI–MS). The methods were previously developed that influence PFAA concentrations. We conducted a QTL and verified by the authors [16–19]. analysis of PFAAs measured by an absolute quantification Quantification was considered successful when the method using plasma samples from 1338 Japanese obtained value was within the determination range of the individuals. calibration curve. PFAA concentrations for QTL analysis Materials and methods For the QTL analysis, we prepared three adjusted PFAA Subjects and ethics concentrations from the measured absolute concentrations of PFAAs. The first adjusted concentration was adjusted for Participants were recruited from the Nagahama sex and age by linear regression after Box-Cox transfor- Prospective Genome Cohort for Comprehensive Human mation. The second was adjusted by the other 20 PFAAs Bioscience (the Nagahama Study). All of the subjects by multiple linear regression after the first adjustment. were approved by the Institutional Review Board and the For this regression analysis, explanatory variables were ethics committees of each institute, to which donors selected by the step-wise function (stepwiseglm) in gave written informed consent, in accordance with the MATLAB, with P = 0.001 and P = 0.01 as inclusion and national guidelines. exclusion criteria, respectively. The third was adjusted by one of the other PFAAs by linear regression after the Absolute quantification of PFAA concentrations first adjustment. The concentrations of 21 PFAAs from 2,084 individuals SNP genotyping and quality control (QC) process who participated in the Nagahama study in 2008 (n = 1124) and 2009 (n = 960) were quantified. Blood samples (5 ml) A total of 1594 samples were genotyped using three com- were collected from forearm veins after overnight mercially available Illumina genotyping arrays (Illumina, fasting into tubes containing ethylenediaminetetraacetic Inc., San Diego, CA): Human610-Quad BeadChip (610 K), acid (EDTA; Termo, Tokyo, Japan). The plasma was HumanOmni-2.5-Quad BeadChip (2.5M-4), and extracted by centrifugation at 2010×g at 4 °C for 15 min and HumanOmni-2.5-8 BeadChip (2.5M-8). The 1,124 subjects then stored at –80 °C. After deproteinizing the thawed recruited in 2008 were genotyped using 610 K (n = 1,113) plasma samples using 80% acetonitrile, the samples were or both 610 K and 2.5M-4 (n = 11). The 470 subjects subjected to pre-column derivatization, then the absolute recruited in 2009 were genotyped using 610 K (n = 101), concentrations, the absolute concentrations of the 2.5M-4 (n = 293), 2.5M-8 (n = 62), or both 610 K and PFAAs were measured by high performance liquid chro- 2.5M-4 (n = 14). In total, 2,638,338 SNPs were genotyped matography - electrospray ionization mass spectrometry in the arrays. As shown in Fig. 1, through a sample QC Genetic basis for plasma amino acid concentrations based on absolute quantification: a genome-wide. process, 256 samples were excluded from the analysis: In silico analysis of genetic variants 3 genetic outliers identified by principal component analysis (PCA), 138 relatives, and 115 samples with a The exome sequencing data of 300 Japanese individuals call rate of SNPs < 0.95. Through a marker QC process, from the Human Genetic Variation Database (HGVD) were 1,200,574 SNPs were excluded: 138,990 SNPs with a used to identify candidates for genetic variants with a call rate < 0.99, 1,187 SNPs with deviation from Hardy– functional impact on PFAA concentrations [22, 23]. Pair- Weinberg equilibrium (P < 1.0 × 10–6), and 1,060,397 wise linkage disequilibrium (LD) coefficients (r2) were SNPs with a variant allele frequency < 1%. After the calculated using PLINK [20]. The impacts of the non- QC processes, 1,437,764 SNPs in 1338 samples remained synonymous variants were predicted using the Ensembl for the GWA studies. Of these, 266,274 SNPs shared Variant Effect Predictor [24], which is based on the SIFT among all of the arrays were defined as intersectional [25] and PolyPhen [26] algorithms. Expression QTL SNPs. All of the QC procedures were processed using (eQTL) analysis data (release version 8.0) were also PLINK ver. 1.07 [20]. Both genotype and PFAA con- downloaded from the HGVD [22]. centrations data of Nagahama study is deposited on the Japanese Genotype-phenotype Archive affiliated to the DDBJ (DNA Data Bank of Japan), via National Bioscience Results DataBase (NBDC), Japan. The data is accessible on hum0012 at https://ddbj.nig.ac.jp/jga/viewer/permit/dataset/ PFAA profiling JGAD00000000012. We measured the PFAA concentrations by an absolute Imputation quantification method using HPLC–ESI–MS [16–19]. The concentrations of 21 PFAAs were quantified successively in The 1,437,764 SNPs from 1,338 samples used for the GWA all of the samples (N = 2,094). The PFAA concentrations in studies were imputed using MACH ver. 1.0 [21]. An the 1,338 samples used for GWAS are summarized with imputation panel was generated using the genotyping data biochemical parameters in Table 1. The means, standard of 665 Nagahama Study samples that were not used for the deviations, and ranges of the absolute concentrations were present GWA analyses and contained the results of comparable to those obtained in an independent study in a 1,560,699 SNPs with Illumina HumanCoreExome Bead- Japanese population, except for arginine, glutamate, and Chip (Exome), HumanOmni2.5 S BeadChip (2.5 S), 2.5M- ornithine [27]. The averaged levels of glutamate and orni- 4, and 2.5M-8 arrays. Of these 665 samples, 478 were thine higher, and that of arginine was lower, than in the genotyped using all of the arrays, and 187 were genotyped previous study. using the Exome, 2.5 S, and 2.5M-4. Imputed SNPs with a variant allele frequency > 1% or an r2 < 0.5 were excluded QTL analysis of PFAAs (GWAS-1) from the subsequent association analysis. Finally, 1,288,202 SNPs from the 1338 samples were fixed with 1,021,918 A flow diagram of the QC processes and QTL analyses is additional SNPs. shown in Fig. 1. The first QTL analysis was conducted for each PFAA concentration, which was adjusted for sex and QTL analysis age after Box-Cox transformation, with 266,274 intersec- tional SNPs of 1338 samples (GWAS-1).
Load more

Recommended publications
  • Part One Amino Acids As Building Blocks
    Part One Amino Acids as Building Blocks Amino Acids, Peptides and Proteins in Organic Chemistry. Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. Hughes Copyright Ó 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32102-5 j3 1 Amino Acid Biosynthesis Emily J. Parker and Andrew J. Pratt 1.1 Introduction The ribosomal synthesis of proteins utilizes a family of 20 a-amino acids that are universally coded by the translation machinery; in addition, two further a-amino acids, selenocysteine and pyrrolysine, are now believed to be incorporated into proteins via ribosomal synthesis in some organisms. More than 300 other amino acid residues have been identified in proteins, but most are of restricted distribution and produced via post-translational modification of the ubiquitous protein amino acids [1]. The ribosomally encoded a-amino acids described here ultimately derive from a-keto acids by a process corresponding to reductive amination. The most important biosynthetic distinction relates to whether appropriate carbon skeletons are pre-existing in basic metabolism or whether they have to be synthesized de novo and this division underpins the structure of this chapter. There are a small number of a-keto acids ubiquitously found in core metabolism, notably pyruvate (and a related 3-phosphoglycerate derivative from glycolysis), together with two components of the tricarboxylic acid cycle (TCA), oxaloacetate and a-ketoglutarate (a-KG). These building blocks ultimately provide the carbon skeletons for unbranched a-amino acids of three, four, and five carbons, respectively. a-Amino acids with shorter (glycine) or longer (lysine and pyrrolysine) straight chains are made by alternative pathways depending on the available raw materials.
    [Show full text]
  • Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
    Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6
    [Show full text]
  • Generated by SRI International Pathway Tools Version 25.0, Authors S
    Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000725805Cyc: Streptomyces xanthophaeus Cellular Overview Connections between pathways are omitted for legibility.
    [Show full text]
  • Generated by SRI International Pathway Tools Version 25.0, Authors S
    Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_001463765Cyc: Aureimonas sp. AU4 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari lipid II (meso diaminopimelate containing) FtsW HtpX MntH RS14400 lipid II (meso diaminopimelate containing) Hormone Biosynthesis Polyprenyl Biosynthesis Polymeric Aldehyde Degradation glutaminyl-tRNA gln Aminoacyl-tRNA Charging Macromolecule Modification tRNA-uridine 2-thiolation Compound N 6 -(3-methylbut- a [protein]- 4-methyl-5-(2- a [protein]-L- L-rhamnulose a [protein]-L- biosynthesis via transamidation and selenation (bacteria) Degradation a sulfurated + an L-cysteinyl- indole-3-acetate di-trans,poly-cis methylglyoxal degradation I 2-en-1-yl)- adenosylcobinamide a purine 2-oxoglutarate NADPH NAD a [glutamine- phosphooxyethyl) glutamate-O 5 L-aspartate ATP HMP-PP 1-phosphate Cys ATP methionine Tetrapyrrole Biosynthesis [sulfur carrier] 37 synthetase]- [tRNA ] biosynthesis -undecaprenyl muropeptide adenosine ribonucleoside thiazole -methyl-ester biotin peptide- cys 5'-triphosphate
    [Show full text]
  • Supplementary Information
    Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.
    [Show full text]
  • Fmicb-07-01854
    Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria Mayorga, O. L., Kingston-Smith, A. H., Kim, E. J., Allison, G. G., Wilkinson, T. J., Hegarty, M. J., Theodorou, M. K., Newbold, C. J., & Huws, S. A. (2016). Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria. Frontiers in Microbiology, 7, 1854. https://doi.org/10.3389/fmicb.2016.01854 Published in: Frontiers in Microbiology Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2017 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. Download date:07.
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Zheng Zhao, Delft University of Technology Marcel A. van den Broek, Delft University of Technology S. Aljoscha Wahl, Delft University of Technology Wilbert H. Heijne, DSM Biotechnology Center Roel A. Bovenberg, DSM Biotechnology Center Joseph J. Heijnen, Delft University of Technology An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Marco A. van den Berg, DSM Biotechnology Center Peter J.T. Verheijen, Delft University of Technology Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. PchrCyc: Penicillium rubens Wisconsin 54-1255 Cellular Overview Connections between pathways are omitted for legibility. Liang Wu, DSM Biotechnology Center Walter M. van Gulik, Delft University of Technology L-quinate phosphate a sugar a sugar a sugar a sugar multidrug multidrug a dicarboxylate phosphate a proteinogenic 2+ 2+ + met met nicotinate Mg Mg a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium UDP ammonium ammonium H O pro met amino acid a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K oxaloacetate L-carnitine L-carnitine L-carnitine 2 phosphate quinic acid brain-specific hypothetical hypothetical hypothetical hypothetical
    [Show full text]
  • B Number Gene Name Strand Orientation Protein Length Mrna
    list list sample) short list predicted B number Operon ID Gene name assignment Protein length mRNA present mRNA intensity Gene description Protein detected - Strand orientation Membrane protein detected (total list) detected (long list) membrane sample Proteins detected - detected (short list) # of tryptic peptides # of tryptic peptides # of tryptic peptides # of tryptic peptides # of tryptic peptides Functional category detected (membrane Protein detected - total Protein detected - long b0001 thrL + 21 1344 P 1 0 0 0 0 thr operon leader peptide Metabolism of small molecules 1 b0002 thrA + 820 13624 P 39 P 18 P 18 P 18 P(m) 2 aspartokinase I, homoserine dehydrogenase I Metabolism of small molecules 1 b0003 thrB + 310 6781 P 9 P 3 3 P 3 0 homoserine kinase Metabolism of small molecules 1 b0004 thrC + 428 15039 P 18 P 10 P 11 P 10 0 threonine synthase Metabolism of small molecules 1 b0005 b0005 + 98 432 A 5 0 0 0 0 orf, hypothetical protein Open reading frames 2 b0006 yaaA - 258 1047 P 11 P 1 2 P 1 0 orf, hypothetical protein Open reading frames 3 b0007 yaaJ - 476 342 P 8 0 0 0 0 MP-GenProt-PHD inner membrane transport protein Miscellaneous 4 b0008 talB + 317 20561 P 20 P 13 P 16 P 13 0 transaldolase B Metabolism of small molecules 5 b0009 mog + 195 1296 P 7 0 0 0 0 required for the efficient incorporation of molybdate into molybdoproteins Metabolism of small molecules 6 b0010 yaaH - 188 407 A 2 0 0 0 0 PHD orf, hypothetical protein Open reading frames 7 b0011 b0011 - 237 338 P 13 0 0 0 0 putative oxidoreductase Miscellaneous 8 b0012 htgA
    [Show full text]
  • O O2 Enzymes Available from Sigma Enzymes Available from Sigma
    COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc.
    [Show full text]
  • Product Information Sheet for NR-19680
    Product Information Sheet for NR-19680 Vibrio cholerae Gateway® Clone Set, Growth Conditions: Media: Recombinant in Escherichia coli, Plate 2 LB broth or agar containing 50 µg/mL kanamycin Incubation: Catalog No. NR-19680 Temperature: E. coli, strain DH10B-T1 clones should be This reagent is the tangible property of the U.S. Government. grown at 37°C. Atmosphere: Aerobic For research use only. Not for human use. Propagation: 1. Scrape top of frozen well with a pipette tip and streak onto Contributor: agar plate. Pathogen Functional Genomics Resource Center at the J. 2. Incubate the plates at 37°C for 1 day. Craig Venter Institute Citation: Manufacturer: Acknowledgment for publications should read “The following BEI Resources reagent was obtained through BEI Resources, NIAID, NIH: ® Vibrio cholerae Gateway Clone Set, Recombinant in Product Description: Escherichia coli, Plate 2, NR-19680.” Production in the 96-well format has increased risk of cross- contamination between adjacent wells. Individual clones Biosafety Level: 1 should be purified (e.g. single colony isolation and purification Appropriate safety procedures should always be used with this using good microbiological practices) and sequence-verified material. Laboratory safety is discussed in the following prior to use. BEI Resources does not confirm or validate publication: U.S. Department of Health and Human Services, individual mutants provided by the contributor. Public Health Service, Centers for Disease Control and Prevention, and National Institutes of Health. Biosafety in The Vibrio cholerae (V. cholerae) Gateway® clone set Microbiological and Biomedical Laboratories. 5th ed. consists of 46 plates which contain 3813 sequence validated Washington, DC: U.S.
    [Show full text]
  • Endogenous Synthesis of Glycine From
    ENDOGENOUS SYNTHESIS OF GLYCINE FROM HYDROXYPROLINE IN NEONATAL PIGS A Dissertation by SHENGDI HU Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Guoyao Wu Committee Members, Fuller W. Bazer Yanan Tian Annie Newell-Fugate Head of Department, G. Cliff Lamb December 2017 Major Subject: Animal Science Copyright 2017 Shengdi Hu ABSTRACT This study was conducted to test the hypothesis that hydroxyproline is a novel and major substrate for endogenous synthesis of glycine in sow-reared pigs. At 0, 7, 14, and 21 days of age, neonatal piglets with a normal or low birth weight (BW) were sacrificed, and their tissue samples were obtained for metabolic studies, activities of glycine-synthetic enzymes, mRNA expression, and the localization of proteins for those enzymes. Moreover, normal and IUGR piglets received oral administration of glycine (0.2, 0.4, and 0.8 g/kg BW) between days 0 and 14 to evaluate a role for endogenous synthesis of glycine in the growth of piglets. Results from the studies of normal birth-weight piglets demonstrated that the activities of hydroxyproline oxidase (OH-POX), proline oxidase (POX), alanine:glyoxylate transaminase (AGT), and 4-hydroxy-2-oxoglutarate aldolase (HOA), key enzymes for glycine synthesis from hydroxyproline, decreased in the liver and kidneys between postnatal day 0 and day 21, but increased in the pancreas and small intestine over the same period of time (P < 0.05). Similar results were obtained for expression of mRNAs for those enzymes.
    [Show full text]
  • Chemoenzymatic Synthesis of 3-Ethyl-2,5
    ARTICLE https://doi.org/10.1038/s42004-021-00545-8 OPEN Chemoenzymatic synthesis of 3-ethyl-2,5- dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/ L-threonine aldolase ✉ Tomoharu Motoyama 1, Shogo Nakano 1,2 , Fumihito Hasebe 1, Ryo Miyata1, Shigenori Kumazawa1, ✉ Noriyuki Miyoshi1 & Sohei Ito 1 Pyrazines are typically formed from amino acids and sugars in chemical reactions such as the Maillard reaction. In this study, we demonstrate that 3-ethyl-2,5-dimethylpyrazine can be 1234567890():,; produced from L-Thr by a simple bacterial operon. We conclude that EDMP is synthesized chemoenzymatically from L-Thr via the condensation reaction of two molecules of aminoa- cetone and one molecule of acetaldehyde. Aminoacetone is supplied by L-threonine 3- dehydrogenase using L-Thr as a substrate via 2-amino-3-ketobutyrate. Acetaldehyde is supplied by 2-amino-3-ketobutyrate CoA ligase bearing threonine aldolase activity from L- Thr when CoA was at low concentrations. Considering the rate of EDMP production, the reaction intermediate is stable for a certain time, and moderate reaction temperature is important for the synthesis of EDMP. When the precursor was supplied from L-Thr by these enzymes, the yield of EDMP was increased up to 20.2%. Furthermore, we demonstrate that this reaction is useful for synthesizing various alkylpyrazines. 1 Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan. 2 PREST, Japan Science and Technology ✉ Agency, Tokyo, Japan. email: [email protected]; [email protected] COMMUNICATIONS CHEMISTRY | (2021) 4:108 | https://doi.org/10.1038/s42004-021-00545-8 | www.nature.com/commschem 1 ARTICLE COMMUNICATIONS CHEMISTRY | https://doi.org/10.1038/s42004-021-00545-8 yrazines are nitrogen-containing heterocyclic aromatic dehydrogenation of the side chain hydroxy group of L-Thr, compounds broadly found in nature, especially in foods converting L-Thr to 2-amino-3-ketobutyrate (AKB)18–20.
    [Show full text]