Physiological Functions of Threonine in Animals: Beyond Nutrition Metabolism
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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. -
GCAT|Panel, a Comprehensive Structural Variant Haplotype Map of the Iberian Population from High-Coverage Whole-Genome Sequencing
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.20.453041; this version posted July 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing Jordi Valls-Margarit1,#, Iván Galván-Femenía2,3,#, Daniel Matías-Sánchez1,#, Natalia Blay2, Montserrat Puiggròs1, Anna Carreras2, Cecilia Salvoro1, Beatriz Cortés2, Ramon Amela1, Xavier Farre2, Jon Lerga- Jaso4, Marta Puig4, Jose Francisco Sánchez-Herrero5, Victor Moreno6,7,8,9, Manuel Perucho10,11, Lauro Sumoy5, Lluís Armengol12, Olivier Delaneau13,14, Mario Cáceres4,15, Rafael de Cid2,*,† & David Torrents1,15,* 1. Life sciences dept, Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain. 2. Genomes for Life-GCAT lab Group, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, 08916, Spain. 3. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain (current affiliation). 4. Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain. 5. High Content Genomics and Bioinformatics Unit, Institute for Health Science Research Germans Trias i Pujol (IGTP), 08916, Badalona, Spain. 6. Catalan Institute of Oncology, Hospitalet del Llobregat, 08908, Spain. 7. Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet del Llobregat, 08908, Spain. 8. CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, 28029, Spain. 9. Universitat de Barcelona (UB), Barcelona, 08007, Spain. -
GCAT (NM 014291) Human Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RG204870 GCAT (NM_014291) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: GCAT (NM_014291) Human Tagged ORF Clone Tag: TurboGFP Symbol: GCAT Synonyms: KBL Vector: pCMV6-AC-GFP (PS100010) E. coli Selection: Ampicillin (100 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RG204870 representing NM_014291 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGTGGCCTGGGAACGCCTGGCGCGCCGCACTCTTCTGGGTGCCCCGCGGCCGCCGCGCACAGTCAGCGC TGGCCCAGCTGCGTGGCATTCTGGAGGGGGAGCTGGAAGGCATCTGCGGAGCTGGCACTTGGAAGAGTGA GCGGGTCATCACGTCCCGTCAGGGGCCGCACATCCGCGTGGACGGCGTCTCCGGAGGAATCCTTAACTTC TGTGCCAACAACTACCTGGGCCTGAGCAGCCACCCTGAGGTGATCCAGGCAGGTCTGCAGGCTCTGGAGG AGTTTGGAGCTGGCCTCAGCTCTGTCCGCTTTATCTGTGGAACCCAGAGCATCCACAAGAATCTAGAAGC AAAAATAGCCCGCTTCCACCAGCGGGAGGATGCCATCCTCTATCCCAGCTGTTATGACGCCAACGCCGGC CTCTTTGAGGCCCTGCTGACCCCAGAGGACGCAGTCCTGTCGGACGAGCTGAACCATGCCTCCATCATCG ACGGCATCCGGCTGTGCAAGGCCCACAAGTACCGCTATCGCCACCTGGACATGGCCGACCTAGAAGCCAA GCTGCAGGAGGCCCAGAAGCATCGGCTGCGCCTGGTGGCCACTGATGGGGCCTTTTCCATGGATGGCGAC ATCGCACCCCTGCAGGAGATCTGCTGCCTCGCCTCTAGATATGGTGCCCTGGTCTTCATGGATGAATGCC ATGCCACTGGCTTCCTGGGGCCCACAGGACGGGGCACAGATGAGCTGCTGGGTGTGATGGACCAGGTCAC CATCATCAACTCCACCCTGGGGAAGGCCCTGGGTGGAGCATCAGGGGGCTACACGACAGGGCCTGGGCCC CTGGTGTCCCTGCTGCGGCAGCGCGCCCGGCCATACCTCTTCTCCAACAGTCTGCCACCTGCTGTCGTTG -
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 -
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. -
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 -
Epigenetic Regulation of the Nuclear-Coded GCAT and SHMT2
www.nature.com/scientificreports OPEN Epigenetic regulation of the nuclear-coded GCAT and SHMT2 genes confers human Received: 29 October 2014 Accepted: 14 April 2015 age-associated mitochondrial Published: 22 May 2015 respiration defects Osamu Hashizume1,*, Sakiko Ohnishi1,*, Takayuki Mito1,*, Akinori Shimizu1, Kaori Ishikawa1, Kazuto Nakada1,2, Manabu Soda3, Hiroyuki Mano3, Sumie Togayachi4, Hiroyuki Miyoshi4,5, Keisuke Okita6 & Jun-Ichi Hayashi1,2,7 Age-associated accumulation of somatic mutations in mitochondrial DNA (mtDNA) has been proposed to be responsible for the age-associated mitochondrial respiration defects found in elderly human subjects. We carried out reprogramming of human fibroblast lines derived from elderly subjects by generating their induced pluripotent stem cells (iPSCs), and examined another possibility, namely that these aging phenotypes are controlled not by mutations but by epigenetic regulation. Here, we show that reprogramming of elderly fibroblasts restores age-associated mitochondrial respiration defects, indicating that these aging phenotypes are reversible and are similar to differentiation phenotypes in that both are controlled by epigenetic regulation, not by mutations in either the nuclear or the mitochondrial genome. Microarray screening revealed that epigenetic downregulation of the nuclear-coded GCAT gene, which is involved in glycine production in mitochondria, is partly responsible for these aging phenotypes. Treatment of elderly fibroblasts with glycine effectively prevented the expression of these -
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. -
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. -
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. -
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 -
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