Design and in Vitro Realization of Carbon-Conserving Photorespiration
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Indications for a Central Role of Hexokinase Activity in Natural Variation of Heat Acclimation in Arabidopsis Thaliana
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 14 June 2020 doi:10.20944/preprints202006.0169.v1 Article Indications for a central role of hexokinase activity in natural variation of heat acclimation in Arabidopsis thaliana Vasil Atanasov §, Lisa Fürtauer § and Thomas Nägele * LMU Munich, Plant Evolutionary Cell Biology, Großhaderner Str. 2-4, 82152 Planegg, Germany § Authors contributed equally * Correspondence: [email protected] Abstract: Diurnal and seasonal changes of abiotic environmental factors shape plant performance and distribution. Changes of growth temperature and light intensity may vary significantly on a diurnal, but also on a weekly or seasonal scale. Hence, acclimation to a changing temperature and light regime is essential for plant survival and propagation. In the present study, we analyzed photosynthetic CO2 assimilation and metabolic regulation of the central carbohydrate metabolism in two natural accessions of Arabidopsis thaliana originating from Russia and south Italy during exposure to heat and a combination of heat and high light. Our findings indicate that it is hardly possible to predict photosynthetic capacities to fix CO2 under combined stress from single stress experiments. Further, capacities of hexose phosphorylation were found to be significantly lower in the Italian than in the Russian accession which could explain an inverted sucrose-to-hexose ratio. Together with the finding of significantly stronger accumulation of anthocyanins under heat/high light these observations indicate a central role of hexokinase activity in stabilization of photosynthetic capacities within a changing environment. Keywords: photosynthesis; carbohydrate metabolism; hexokinase; heat acclimation; environmental changes; natural variation; high light; combined stress. 1. Introduction Changes of growth temperature and light intensity broadly affect plant molecular, physiological and developmental processes. -
METABOLIC EVOLUTION in GALDIERIA SULPHURARIA By
METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA By CHAD M. TERNES Bachelor of Science in Botany Oklahoma State University Stillwater, Oklahoma 2009 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May, 2015 METABOLIC EVOLUTION IN GALDIERIA SUPHURARIA Dissertation Approved: Dr. Gerald Schoenknecht Dissertation Adviser Dr. David Meinke Dr. Andrew Doust Dr. Patricia Canaan ii Name: CHAD M. TERNES Date of Degree: MAY, 2015 Title of Study: METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA Major Field: PLANT SCIENCE Abstract: The thermoacidophilic, unicellular, red alga Galdieria sulphuraria possesses characteristics, including salt and heavy metal tolerance, unsurpassed by any other alga. Like most plastid bearing eukaryotes, G. sulphuraria can grow photoautotrophically. Additionally, it can also grow solely as a heterotroph, which results in the cessation of photosynthetic pigment biosynthesis. The ability to grow heterotrophically is likely correlated with G. sulphuraria ’s broad capacity for carbon metabolism, which rivals that of fungi. Annotation of the metabolic pathways encoded by the genome of G. sulphuraria revealed several pathways that are uncharacteristic for plants and algae, even red algae. Phylogenetic analyses of the enzymes underlying the metabolic pathways suggest multiple instances of horizontal gene transfer, in addition to endosymbiotic gene transfer and conservation through ancestry. Although some metabolic pathways as a whole appear to be retained through ancestry, genes encoding individual enzymes within a pathway were substituted by genes that were acquired horizontally from other domains of life. Thus, metabolic pathways in G. sulphuraria appear to be composed of a ‘metabolic patchwork’, underscored by a mosaic of genes resulting from multiple evolutionary processes. -
Lecture 7 - the Calvin Cycle and the Pentose Phosphate Pathway
Lecture 7 - The Calvin Cycle and the Pentose Phosphate Pathway Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire 1 Introduction The Calvin cycle Text The dark reactions of photosynthesis in green plants Reduces carbon from CO2 to hexose (C6H12O6) Requires ATP for free energy and NADPH as a reducing agent. 2 2 Introduction NADH versus Text NADPH 3 3 Introduction The Pentose Phosphate Pathway Used in all organisms Glucose is oxidized and decarboxylated to produce reduced NADPH Used for the synthesis and degradation of pentoses Shares reactions with the Calvin cycle 4 4 1. The Calvin Cycle Source of carbon is CO2 Text Takes place in the stroma of the chloroplasts Comprises three stages Fixation of CO2 by ribulose 1,5-bisphosphate to form two 3-phosphoglycerate molecules Reduction of 3-phosphoglycerate to produce hexose sugars Regeneration of ribulose 1,5-bisphosphate 5 5 1. Calvin Cycle Three stages 6 6 1.1 Stage I: Fixation Incorporation of CO2 into 3-phosphoglycerate 7 7 1.1 Stage I: Fixation Rubisco: Ribulose 1,5- bisphosphate carboxylase/ oxygenase 8 8 1.1 Stage I: Fixation Active site contains a divalent metal ion 9 9 1.2 Rubisco Oxygenase Activity Rubisco also catalyzes a wasteful oxygenase reaction: 10 10 1.3 State II: Formation of Hexoses Reactions similar to those of gluconeogenesis But they take place in the chloroplasts And use NADPH instead of NADH 11 11 1.3 State III: Regeneration of Ribulose 1,5-Bisphosphosphate Involves a sequence of transketolase and aldolase reactions. 12 12 1.3 State III: -
New Nucleotide Sequence Data on the EMBL File Server
.=) 1991 Oxford University Press Nucleic Acids Research, Vol. 19, No. 2 413 New nucleotide sequence data on the EMBL File Server October 30, 1990 to November 13, 1990 New nucleotide sequence data, available from the EMBL File Server, (see Stoehr, P.J. and Omond, R.A. (1989) Nucleic Acids Res., 17 (16), 6763 -6764), are reported below. Availability of all the newest sequence data is the result of collaboration between.the EMBL Data Library and GenBank' , and data are supplied regularly by both groups. Updates to existing data are not reported here. This report has been prepared by the EMBL Data Library. PRIMATES: Human casein kinase II alpha subunit mRNA, complete cds. Human specific HS5 DNA Lozeman F.J., Litchfield D.W., Piening C., Takio K., Walsh Ueda S., Washio K., Kurosaki K.; K.A., Krebs E.G.; Genomics 8:7-12(1990). X17579 Biochemistry 29:8436-8447(1990). M55268 Human mRNA for heat shock protein HSP27 Human mRNA for actin-binding protein (ABP-280) Carper S.W., Rocheleau T.A., Storm F.K.; Gorlin J.B., Yamin R., Egan S., Stewart M., Stossel T.P., Nucleic Acids Res. 18:6457-6457(1990). X54079 Kwiatkowski D.J., Hartwig J.H.; J. Cell Biol. 111:1089-1105(1990). X53416 Human Ig germline H-chain D-region Dxpl and Dxp'1 genes, 3' Human amiloride-binding protein, complete cds. end. Barbry P., Champe M., Chassande O., Munemitsu S., Champigny Huang C., Stollar B.David.; G., Lingueglia E., Maes P., Frelin C., Tartar A., Ullrich A., Unpublished. M37485 Lazdunski M.; Proc. Natl. Acad. -
Supplementary Materials
Supplementary Materials Figure S1. Differentially abundant spots between the mid-log phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 3. Figure S2. Differentially abundant spots between the stationary phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 4. S2 Table S1. Summary of the non-polysaccharide degrading proteins identified in the B. proteoclasticus cytosol by 2DE/MALDI-TOF. Protein Locus Location Score pI kDa Pep. Cov. Amino Acid Biosynthesis Acetylornithine aminotransferase, ArgD Bpr_I1809 C 1.7 × 10−4 5.1 43.9 11 34% Aspartate/tyrosine/aromatic aminotransferase Bpr_I2631 C 3.0 × 10−14 4.7 43.8 15 46% Aspartate-semialdehyde dehydrogenase, Asd Bpr_I1664 C 7.6 × 10−18 5.5 40.1 17 50% Branched-chain amino acid aminotransferase, IlvE Bpr_I1650 C 2.4 × 10−12 5.2 39.2 13 32% Cysteine synthase, CysK Bpr_I1089 C 1.9 × 10−13 5.0 32.3 18 72% Diaminopimelate dehydrogenase Bpr_I0298 C 9.6 × 10−16 5.6 35.8 16 49% Dihydrodipicolinate reductase, DapB Bpr_I2453 C 2.7 × 10−6 4.9 27.0 9 46% Glu/Leu/Phe/Val dehydrogenase Bpr_I2129 C 1.2 × 10−30 5.4 48.6 31 64% Imidazole glycerol phosphate synthase Bpr_I1240 C 8.0 × 10−3 4.7 22.5 8 44% glutamine amidotransferase subunit Ketol-acid reductoisomerase, IlvC Bpr_I1657 C 3.8 × 10−16 -
Conversion of D-Ribulose 5-Phosphate to D-Xylulose 5-Phosphate: New Insights from Structural and Biochemical Studies on Human RPE
The FASEB Journal • Research Communication Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE Wenguang Liang,*,†,1 Songying Ouyang,*,1 Neil Shaw,* Andrzej Joachimiak,‡ Rongguang Zhang,* and Zhi-Jie Liu*,2 *National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; †Graduate University of Chinese Academy of Sciences, Beijing, China; and ‡Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA ABSTRACT The pentose phosphate pathway (PPP) such as erythrose 4-phosphate, glyceraldehyde 3-phos- confers protection against oxidative stress by supplying phate, and fructose 6-phosphate that are necessary for NADPH necessary for the regeneration of glutathione, the synthesis of aromatic amino acids and production which detoxifies H2O2 into H2O and O2. RPE functions of energy (Fig. 1) (3, 4). In addition, a majority of the in the PPP, catalyzing the reversible conversion of NADPH used by the human body for biosynthetic D-ribulose 5-phosphate to D-xylulose 5-phosphate and is purposes is supplied by the PPP (5). Interestingly, RPE an important enzyme for cellular response against has been shown to protect cells from oxidative stress via oxidative stress. Here, using structural, biochemical, its participation in PPP for the production of NADPH and functional studies, we show that human D-ribulose (6–8). The protection against reactive oxygen species is ؉ 5-phosphate 3-epimerase (hRPE) uses Fe2 for cataly- exerted by NADPH’s ability to reduce glutathione, sis. Structures of the binary complexes of hRPE with which detoxifies H2O2 into H2O (Fig. 1). -
Carbohydrates: Structure and Function
CARBOHYDRATES: STRUCTURE AND FUNCTION Color index: . Very important . Extra Information. “ STOP SAYING I WISH, START SAYING I WILL” 435 Biochemistry Team *هذا العمل ﻻ يغني عن المصدر المذاكرة الرئيسي • The structure of carbohydrates of physiological significance. • The main role of carbohydrates in providing and storing of energy. • The structure and function of glycosaminoglycans. OBJECTIVES: 435 Biochemistry Team extra information that might help you 1-synovial fluid: - It is a viscous, non-Newtonian fluid found in the cavities of synovial joints. - the principal role of synovial fluid is to reduce friction between the articular cartilage of synovial joints during movement O 2- aldehyde = terminal carbonyl group (RCHO) R H 3- ketone = carbonyl group within (inside) the compound (RCOR’) 435 Biochemistry Team the most abundant organic molecules in nature (CH2O)n Carbohydrates Formula *hydrate of carbon* Function 1-provides important part of energy Diseases caused by disorders of in diet . 2-Acts as the storage form of energy carbohydrate metabolism in the body 3-structural component of cell membrane. 1-Diabetesmellitus. 2-Galactosemia. 3-Glycogen storage disease. 4-Lactoseintolerance. 435 Biochemistry Team Classification of carbohydrates monosaccharides disaccharides oligosaccharides polysaccharides simple sugar Two monosaccharides 3-10 sugar units units more than 10 sugar units Joining of 2 monosaccharides No. of carbon atoms Type of carbonyl by O-glycosidic bond: they contain group they contain - Maltose (α-1, 4)= glucose + glucose -Sucrose (α-1,2)= glucose + fructose - Lactose (β-1,4)= glucose+ galactose Homopolysaccharides Heteropolysaccharides Ketone or aldehyde Homo= same type of sugars Hetero= different types Ketose aldose of sugars branched unBranched -Example: - Contains: - Contains: Examples: aldehyde group glycosaminoglycans ketone group. -
Taming the Wild Rubisco: Explorations in Functional Metagenomics
Taming the Wild RubisCO: Explorations in Functional Metagenomics DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Brian Hurin Witte, M.S. Graduate Program in Microbiology The Ohio State University 2012 Dissertation Committee : F. Robert Tabita, Advisor Joseph Krzycki Birgit E. Alber Paul Fuerst Copyright by Brian Hurin Witte 2012 Abstract Ribulose bisphosphate carboxylase/oxygenase (E.C. 4.1.1.39) (RubisCO) is the most abundant protein on Earth and the mechanism by which the vast majority of carbon enters the planet’s biosphere. Despite decades of study, many significant questions about this enzyme remain unanswered. As anthropogenic CO2 levels continue to rise, understanding this key component of the carbon cycle is crucial to forecasting feedback circuits, as well as to engineering food and fuel crops to produce more biomass with few inputs of increasingly scarce resources. This study demonstrates three means of investigating the natural diversity of RubisCO. Chapter 1 builds on existing DNA sequence-based techniques of gene discovery and shows that RubisCO from uncultured organisms can be used to complement growth in a RubisCO-deletion strain of autotrophic bacteria. In a few short steps, the time-consuming work of bringing an autotrophic organism in to pure culture can be circumvented. Chapter 2 details a means of entirely bypassing the bias inherent in sequence-based gene discovery by using selection of RubisCO genes from a metagenomic library. Chapter 3 provides a more in-depth study of the RubisCO from the methanogenic archaeon Methanococcoides burtonii. -
PENTOSE PHOSPHATE PATHWAY — Restricted for Students Enrolled in MCB102, UC Berkeley, Spring 2008 ONLY
Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Bryan Krantz: University of California, Berkeley MCB 102, Spring 2008, Metabolism Lecture 5 Reading: Ch. 14 of Principles of Biochemistry, “Glycolysis, Gluconeogenesis, & Pentose Phosphate Pathway.” PENTOSE PHOSPHATE PATHWAY This pathway produces ribose from glucose, and it also generates 2 NADPH. Two Phases: [1] Oxidative Phase & [2] Non-oxidative Phase + + Glucose 6-Phosphate + 2 NADP + H2O Ribose 5-Phosphate + 2 NADPH + CO2 + 2H ● What are pentoses? Why do we need them? ◦ DNA & RNA ◦ Cofactors in enzymes ● Where do we get them? Diet and from glucose (and other sugars) via the Pentose Phosphate Pathway. ● Is the Pentose Phosphate Pathway just about making ribose sugars from glucose? (1) Important for biosynthetic pathways using NADPH, and (2) a high cytosolic reducing potential from NADPH is sometimes required to advert oxidative damage by radicals, e.g., ● - ● O2 and H—O Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Two Phases of the Pentose Pathway Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY NADPH vs. NADH Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Oxidative Phase: Glucose-6-P Ribose-5-P Glucose 6-phosphate dehydrogenase. First enzymatic step in oxidative phase, converting NADP+ to NADPH. Glucose 6-phosphate + NADP+ 6-Phosphoglucono-δ-lactone + NADPH + H+ Mechanism. Oxidation reaction of C1 position. Hydride transfer to the NADP+, forming a lactone, which is an intra-molecular ester. -
Enzymatic Synthesis of L-Fucose from L-Fuculose Using a Fucose Isomerase
Kim et al. Biotechnol Biofuels (2019) 12:282 https://doi.org/10.1186/s13068-019-1619-0 Biotechnology for Biofuels RESEARCH Open Access Enzymatic synthesis of L-fucose from L-fuculose using a fucose isomerase from Raoultella sp. and the biochemical and structural analyses of the enzyme In Jung Kim1†, Do Hyoung Kim1†, Ki Hyun Nam1,2 and Kyoung Heon Kim1* Abstract Background: L-Fucose is a rare sugar with potential uses in the pharmaceutical, cosmetic, and food industries. The enzymatic approach using L-fucose isomerase, which interconverts L-fucose and L-fuculose, can be an efcient way of producing L-fucose for industrial applications. Here, we performed biochemical and structural analyses of L-fucose isomerase identifed from a novel species of Raoultella (RdFucI). Results: RdFucI exhibited higher enzymatic activity for L-fuculose than for L-fucose, and the rate for the reverse reaction of converting L-fuculose to L-fucose was higher than that for the forward reaction of converting L-fucose to L-fuculose. In the equilibrium mixture, a much higher proportion of L-fucose (~ ninefold) was achieved at 30 °C and pH 7, indicating that the enzyme-catalyzed reaction favors the formation of L-fucose from L-fuculose. When biochemical analysis was conducted using L-fuculose as the substrate, the optimal conditions for RdFucI activity were determined to be 40 °C and pH 10. However, the equilibrium composition was not afected by reaction temperature in the range 2 of 30 to 50 °C. Furthermore, RdFucI was found to be a metalloenzyme requiring Mn + as a cofactor. The comparative crystal structural analysis of RdFucI revealed the distinct conformation of α7–α8 loop of RdFucI. -
( 12 ) United States Patent ( 10 ) Patent No .: US 11,019,776 B2 Klessig Et Al
US011019776B2 ( 12 ) United States Patent ( 10 ) Patent No .: US 11,019,776 B2 Klessig et al . ( 45 ) Date of Patent : * Jun . 1 , 2021 ( 54 ) COMPOSITIONS AND METHODS FOR AOIN 43/38 ( 2006.01 ) MODULATING IMMUNITY IN PLANTS AOIN 63/10 ( 2020.01 ) ( 52 ) U.S. CI . ( 71 ) Applicant: Boyce Thompson Institute for Plant CPC A01H 3/04 ( 2013.01 ) ; A01N 43/16 Research , Inc. , Ithaca , NY ( US ) ( 2013.01 ) ; AOIN 43/38 ( 2013.01 ) ; AOIN 63/10 ( 2020.01 ) ; C12N 15/8281 ( 2013.01 ) ; ( 72 ) Inventors : Daniel Klessig , Dryden , NY ( US ) ; C12N 15/8282 ( 2013.01 ) ; C12N 15/8283 Frank Schroeder , Ithaca , NY ( US ) ; ( 2013.01 ) ; C12N 15/8285 ( 2013.01 ) Patricia Manosalva, Ithaca, NY ( US ) ( 58 ) Field of Classification Search CPC C12N 15/8282 ; C12N 15/8281 ( 73 ) Assignee : BOYCE THOMPSON INSTITUTE See application file for complete search history. FOR PLANT RESEARCH , INC . , Ithaca , NY (US ) ( 56 ) References Cited ( * ) Notice: Subject to any disclaimer , the term of this U.S. PATENT DOCUMENTS patent is extended or adjusted under 35 U.S.C. 154 ( b ) by 26 days. 8,318,146 B1 11/2012 Teal et al . This patent is subject to a terminal dis FOREIGN PATENT DOCUMENTS claimer . WO 2010/009241 A2 1/2010 WO 2010/146062 A2 12/2010 ( 21 ) Appl. No .: 16 / 161,252 WO 2012/084858 A2 6/2012 WO 2013/022985 A2 2/2013 ( 22 ) Filed : Oct. 16 , 2018 WO 2013/022997 A2 2/2013 ( Continued ) ( 65 ) Prior Publication Data US 2019/0053451 A1 Feb. 21 , 2019 OTHER PUBLICATIONS Hsueh , Y.-P. et al 2013. -
Inhibition of Spinach Phosphoribulokinase by DL-Glyceraldehyde by ANTONI R
Biochem. J. (1976) 153, 613-619 613 Printed in Great Britain Inhibition of Spinach Phosphoribulokinase by DL-Glyceraldehyde By ANTONI R. SLABAS and DAVID A. WALKER Department ofBotany, University ofSheffield, Sheffield S1O 2TN, U.K. (Received 10 September 1975) Spinach chloroplast phosphoribulokinase is inhibited by DL-glyceraldehyde. The in- hibition is non-competitive with respect to ribulose 5-phosphate (Ki 19mM) and ATP (Ki 20mM). The inhibition is discussed in relation to a previously reported inhibition of CO2 assimilation in intact and envelope-free chloroplasts by DL-glyceraldehyde. It is concluded that the inhibition of phosphoribulokinase is insufficient to account for the inhibition, by DL-glyceraldehyde, of 02 evolution with ribose 5-phosphate as substrate and that a further site of inhibition is also present in this system. DL-Glyceraldehyde inhibits photosynthetic carbon glycylglycine buffer, pH7.4, in a total volume of assiniilation by intact chloroplasts and by the re- 13 ml. The reaction was terminated by the addition constituted chloroplast system (Stokes & Walker, of 2ml of 50 % (w/v) trichloroacetic acid and the pH 1972). The inhibition is most pronounced with intact was adjusted to pH8.0 with KOH. After the addition chloroplasts, a concentration of 1OmM being sufficient of Sml of 1.OM-barium acetate the solution was to suppress 02 evolution completely. It is important centrifuged and the precipitate discarded after because DL-glyceraldehyde is the only known inhibi- washing with Sml of water. Cold ethanol (4vol.) was tor of photosynthesis that is entirely without detect- added to the combined supernatants (total volume able effect on photophosphorylation or photo- 25.4ml); the new precipitate was recovered by synthetic electron transport.