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Purification and Properties of Lactate Racemase from Lactobacillus Sake
The Journal of Biochemistry, Vol . 64, No. I, 1968 Purification and Properties of Lactate Racemase from Lactobacillus sake By TETSUG HIYAMA, SAKUzo FUKUI and KAKUO KITAHARA* (From the Institute of Applied Microbiology,University of Tokyo, Bunkyo-ku, Tokyo) (Received for publication, February 12, 1968) A lactate racemase [EC 5.1.2.1] was isolated and purified about 190 fold in specific activity from the sonic extract of Lactobacillus sake. The purified preparation was almost homogeneous by ultracentrifugal and electrophoretical analyses. Characteristic properties of the enzyme were as follows : (a) absorption spectrum showed a single peak at 274 my, (b) molecular weight was 25,000, (c) the enzyme did not require any additional cofactors and showed no activity of lactate dehydrogenase, (d) K, values were 1.7 •~ 10-2 M and 8.0 •~ 10-2 M for D and L-lactate, respectively, (e) optimal pH was 5.8-6.2, (f) an equilibrium point was at a molar ratio of 1/1 (L-isomer/D-isomer), (g) the enzyme activity was inhibited by atebrin, adenosine monosulfate, oxamate and some of Fe chelating agents, (h) pyruvate and acrylate were not incorporated into lactate during the reaction, and (i) exchange reaction of hydrogen between lactate and water did not occur during the reaction. Since the first observation on the enzy the addition of both NAD and pyridoxamine matic racemization of optical active lactate phosphate. In this paper we deal with the by lactic acid bacteria had been reported by purification and properties of the lactate KATAGIRI and KITAHARA in 1936 (1), racemases racemizing enzyme from the cells of L. -
A Web Tool for Hydrogenase Classification and Analysis Dan Søndergaard1, Christian N
www.nature.com/scientificreports OPEN HydDB: A web tool for hydrogenase classification and analysis Dan Søndergaard1, Christian N. S. Pedersen1 & Chris Greening2,3 H2 metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The Received: 24 June 2016 metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla Accepted: 09 September 2016 and are present in all major ecosystems. We developed a classification system and web tool, HydDB, Published: 27 September 2016 for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe], and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors’ algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea, and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical, and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at http://services.birc.au.dk/hyddb/ Microorganisms conserve energy by metabolizing H2. Oxidation of this high-energy fuel yields electrons that can be used for respiration and carbon-fixation. This diffusible gas is also produced in diverse fermentation and 1 anaerobic respiratory processes . H2 metabolism contributes to the growth and survival of microorganisms across the three domains of life, including chemotrophs and phototrophs, lithotrophs and heterotrophs, aerobes and 1,2 anaerobes, mesophiles and extremophiles alike . -
Hydrogenases of Methanogens
ANRV413-BI79-18 ARI 27 April 2010 21:0 Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage Rudolf K. Thauer, Anne-Kristin Kaster, Meike Goenrich, Michael Schick, Takeshi Hiromoto, and Seigo Shima Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; email: [email protected] Annu. Rev. Biochem. 2010. 79:507–36 Key Words First published online as a Review in Advance on H2 activation, energy-converting hydrogenase, complex I of the March 17, 2010 respiratory chain, chemiosmotic coupling, electron bifurcation, The Annual Review of Biochemistry is online at reversed electron transfer biochem.annualreviews.org This article’s doi: Abstract 10.1146/annurev.biochem.030508.152103 Most methanogenic archaea reduce CO2 with H2 to CH4. For the Copyright c 2010 by Annual Reviews. activation of H2, they use different [NiFe]-hydrogenases, namely All rights reserved energy-converting [NiFe]-hydrogenases, heterodisulfide reductase- 0066-4154/10/0707-0507$20.00 associated [NiFe]-hydrogenase or methanophenazine-reducing by University of Texas - Austin on 06/10/13. For personal use only. [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]- hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen. -
Nickel-Pincer Cofactor Biosynthesis Involves Larb-Catalyzed Pyridinium
Nickel-pincer cofactor biosynthesis involves LarB- catalyzed pyridinium carboxylation and LarE- dependent sacrificial sulfur insertion Benoît Desguina,b, Patrice Soumillionb, Pascal Holsb, and Robert P. Hausingera,1 aDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824; and bInstitute of Life Sciences, Université catholique de Louvain, B-1348 Louvain-La-Neuve, Belgium Edited by Tadhg P. Begley, Texas A&M University, College Station, TX, and accepted by the Editorial Board March 28, 2016 (received for review January 11, 2016) The lactate racemase enzyme (LarA) of Lactobacillus plantarum proteins) when incubated with ATP (1 mM), MgCl2 (12 mM), harbors a (SCS)Ni(II) pincer complex derived from nicotinic acid. and the other purified proteins, and the activity was stimulated Synthesis of the enzyme-bound cofactor requires LarB, LarC, and fivefold by inclusion of CoA (10 mM) (SI Appendix,Fig.S1A– LarE, which are widely distributed in microorganisms. The functions D). These results are consistent with the requirement of a small of the accessory proteins are unknown, but the LarB C terminus molecule produced by LarB being needed for development of resembles aminoimidazole ribonucleotide carboxylase/mutase, LarC Lar activity. To uncover the substrate of LarB, we replaced the binds Ni and could act in Ni delivery or storage, and LarE is a putative LarB-containing lysates in the LarA activation mixture with ATP-using enzyme of the pyrophosphatase-loop superfamily. Here, purified LarB and potential substrates. Because nicotinic acid is a precursor of the Lar cofactor (1) and LarB features partial we show that LarB carboxylates the pyridinium ring of nicotinic acid sequence identity with PurE, an aminoimidazole ribonucleotide adenine dinucleotide (NaAD) and cleaves the phosphoanhydride (AIR) mutase/carboxylase (4), we tested the possibility that bond to release AMP. -
A Web Tool for Hydrogenase Classification and Analysis
bioRxiv preprint doi: https://doi.org/10.1101/061994; this version posted September 16, 2016. 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. 1 HydDB: A web tool for hydrogenase 2 classification and analysis 3 Dan Søndergaarda, Christian N. S. Pedersena, Chris Greeningb, c* 4 5 a Aarhus University, Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus 6 DK-8000, Denmark 7 b The Commonwealth Scientific and Industrial Research Organisation, Land and 8 Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia 9 c Monash University, School of Biological Sciences, Clayton, VIC 2800, Australia 10 11 Correspondence: 12 Dr Chris Greening ([email protected]), Monash University, School of 13 Biological Sciences, Clayton, VIC 2800, Australia 14 Dan Søndergaard ([email protected]), Aarhus University, Bioinformatics Research 15 Centre, C.F. Møllers Allé 8, Aarhus DK-8000, Denmark 1 bioRxiv preprint doi: https://doi.org/10.1101/061994; this version posted September 16, 2016. 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. 16 Abstract 17 H2 metabolism is proposed to be the most ancient and diverse mechanism of 18 energy-conservation. The metalloenzymes mediating this metabolism, 19 hydrogenases, are encoded by over 60 microbial phyla and are present in all major 20 ecosystems. -
Nzvi Impacts Substrate Conversion and Microbiome Composition in Chain Elongation from D- and L-Lactate Substrates
fbioe-09-666582 June 9, 2021 Time: 17:45 # 1 ORIGINAL RESEARCH published: 15 June 2021 doi: 10.3389/fbioe.2021.666582 nZVI Impacts Substrate Conversion and Microbiome Composition in Chain Elongation From D- and L-Lactate Substrates Carlos A. Contreras-Dávila, Johan Esveld, Cees J. N. Buisman and David P. B. T. B. Strik* Environmental Technology, Wageningen University & Research, Wageningen, Netherlands Medium-chain carboxylates (MCC) derived from biomass biorefining are attractive biochemicals to uncouple the production of a wide array of products from the use of non-renewable sources. Biological conversion of biomass-derived lactate during secondary fermentation can be steered to produce a variety of MCC through chain Edited by: Caixia Wan, elongation. We explored the effects of zero-valent iron nanoparticles (nZVI) and University of Missouri, United States lactate enantiomers on substrate consumption, product formation and microbiome Reviewed by: composition in batch lactate-based chain elongation. In abiotic tests, nZVI supported Lan Wang, chemical hydrolysis of lactate oligomers present in concentrated lactic acid. In Institute of Process Engineering (CAS), China fermentation experiments, nZVI created favorable conditions for either chain-elongating Sergio Revah, or propionate-producing microbiomes in a dose-dependent manner. Improved lactate Metropolitan Autonomous University, · −1 Mexico conversion rates and n-caproate production were promoted at 0.5–2 g nZVI L while ≥ · −1 *Correspondence: propionate formation became relevant at 3.5 g nZVI L . Even-chain carboxylates David P. B. T. B. Strik (n-butyrate) were produced when using enantiopure and racemic lactate with lactate [email protected] conversion rates increased in nZVI presence (1 g·L−1). -
SI Appendix Index 1
SI Appendix Index Calculating chemical attributes using EC-BLAST ................................................................................ 2 Chemical attributes in isomerase reactions ............................................................................................ 3 Bond changes …..................................................................................................................................... 3 Reaction centres …................................................................................................................................. 5 Substrates and products …..................................................................................................................... 6 Comparative analysis …........................................................................................................................ 7 Racemases and epimerases (EC 5.1) ….................................................................................................. 7 Intramolecular oxidoreductases (EC 5.3) …........................................................................................... 8 Intramolecular transferases (EC 5.4) ….................................................................................................. 9 Supporting references …....................................................................................................................... 10 Fig. S1. Overview …............................................................................................................................ -
Unravelling Lactate‐Acetate and Sugar Conversion Into Butyrate By
Environmental Microbiology (2020) 22(11), 4863–4875 doi:10.1111/1462-2920.15269 Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics Sudarshan A. Shetty ,1 Sjef Boeren,2 study demonstrates that A. soehngenii and several Thi P. N. Bui,1,3 Hauke Smidt1 and Willem M. de Vos 1,4* related Anaerobutyricum and Anaerostipes spp. are 1Laboratory of Microbiology, Wageningen University and highly adapted for a lifestyle involving lactate plus Research, Wageningen, The Netherlands. acetate utilization in the human intestinal tract. 2Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands. Introduction 3No Caelus Pharmaceuticals, Armsterdam, The Netherlands. The major fermentation end products in anaerobic colonic sugar fermentations are the short chain fatty acids 4Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. (SCFAs) acetate, propionate and butyrate. While all these SCFAs confer health benefits, butyrate is used to fuel colonic enterocytes and has been shown to inhibit Summary the proliferation and to induce apoptosis of tumour cells The D- and L-forms of lactate are important fermenta- (McMillan et al., 2003; Thangaraju et al., 2009; Topping tion metabolites produced by intestinal bacteria but and Clifton, 2001). Butyrate is also suggested to play a are found to negatively affect mucosal barrier func- role in gene expression as it is a known inhibitor of his- tion and human health. Both enantiomers of lactate tone deacetylases, and recently it was demonstrated that can be converted with acetate into the presumed ben- butyrate promotes histone crotonylation in vitro eficial butyrate by a phylogenetically related group of (Davie, 2003; Fellows et al., 2018). -
Effects of High Forage/Concentrate Diet on Volatile Fatty Acid
animals Article Effects of High Forage/Concentrate Diet on Volatile Fatty Acid Production and the Microorganisms Involved in VFA Production in Cow Rumen Lijun Wang 1,2, Guangning Zhang 2, Yang Li 2 and Yonggen Zhang 2,* 1 College of Animal Science and Technology, Qingdao Agricultural university, No. 700 of Changcheng Road, Qingdao 266000, China; [email protected] 2 College of Animal Science and Technology, Northeast Agricultural University, No. 600 of Changjiang Road, Harbin 150030, China; [email protected] (G.Z.); [email protected] (Y.L.) * Correspondence: [email protected]; Tel./Fax: +86-451-5519-0840 Received: 15 January 2020; Accepted: 28 January 2020; Published: 30 January 2020 Simple Summary: The rumen is well known as a natural bioreactor for highly efficient degradation of fibers, and rumen microbes play an important role on fiber degradation. Carbohydrates are fermented by a variety of bacteria in the rumen and transformed into volatile fatty acids (VFAs) by the corresponding enzymes. However, the content of forage in the diet affects the metabolism of cellulose degradation and VFA production. Therefore, we combine metabolism and metagenomics to explore the effects of High forage/concentrate diets and sampling time on enzymes and microorganisms involved in the metabolism of fiber and VFA in cow rumen. This study showed that propionate formation via the succinic pathway, in which succinate CoA synthetase (EC 6.2.1.5) and propionyl CoA carboxylase (EC 2.8.3.1) were key enzymes. Butyrate formation via the succinic pathway, in which phosphate butyryltransferase (EC 2.3.1.19), butyrate kinase (EC 2.7.2.7) and pyruvate ferredoxin oxidoreductase (EC 1.2.7.1) are the important enzymes. -
Reconstitution of [Fe]-Hydrogenase Using Model Complexes
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Infoscience - École polytechnique fédérale de Lausanne Reconstitution of [Fe]-hydrogenase using model complexes Seigo Shima1,2,*, Dafa Chen3, Tao Xu4, Matthew D. Wodrich4,5, Takashi Fujishiro1, Katherine M. Schultz4, Jörg Kahnt1, Kenichi Ataka6 & Xile Hu4,* 1Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany. 2PRESTO, Japan Science and Technology Agency (JST), 332-0012 Saitama, Japan. 3School of Chemical Engineering and Technology, Harbin Institute of Technology, 150001 Harbin, China. 4Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. 5Laboratory for Computational Molecular Design, Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. 6Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany. 1 Abstract. [Fe]-Hydrogenase catalyzes the reversible hydrogenation of a methenyl- tetrahydromethanopterin substrate, which is an intermediate step during methanogenesis from CO2 and H2. The active site contains an iron-guanylylpyridinol (FeGP) cofactor, in which Fe2+ is coordinated by two CO ligands, as well as an acyl carbon atom and a pyridinyl nitrogen atom from a 3,4,5,6-substituted 2-pyridinol ligand. However, the mechanism of H2 activation by [Fe]-hydrogenase is unclear. Here, we report reconstitution of [Fe]-hydrogenase from an apoenzyme using two FeGP cofactor mimics to create semi-synthetic enzymes. The small molecule mimics reproduce the ligand environment of the active site, but are inactive towards H2 binding and activation on their own. We show that reconstituting the enzyme using a mimic containing a 2-hydroxy pyridine group restores activity, whilst an analogous experiment with a 2-methoxy-pyridine complex was essentially inactive. -
Uncovering a Superfamily of Nickel-Dependent Hydroxyacid
www.nature.com/scientificreports OPEN Uncovering a superfamily of nickel‑dependent hydroxyacid racemases and epimerases Benoît Desguin 1*, Julian Urdiain‑Arraiza1, Matthieu Da Costa2, Matthias Fellner 3,4, Jian Hu4,5, Robert P. Hausinger 4,6, Tom Desmet 2, Pascal Hols 1 & Patrice Soumillion 1 Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L‑ and D‑lactate, is composed of the LarA protein and a nickel‑containing cofactor, the nickel‑pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many diferent enzymes. We overexpressed and purifed 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of diferent substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one α‑hydroxyglutarate racemase, two D‑gluconate 2‑epimerases, and one short‑chain aliphatic α‑hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D‑gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of α‑hydroxyacid racemases and epimerases, widely expanding the scope of NPN‑dependent enzymes. Chemical isomers exhibit subtle changes in their structures, yet can show dramatic diferences in biological properties1. Interconversions of isomers by isomerases are important in the metabolism of living organisms and have many applications in biocatalysis, biotechnology, and drug discovery2. Tese enzymes are divided into 6 classes, depending on the type of reaction catalyzed: racemases and epimerases, cis–trans isomerases, intramo- lecular oxidoreductases, intramolecular transferases, intramolecular lyases, and other isomerases3. -
Hydrogenase and Ferredoxin:NADP -Oxidoreductase (FNR)
Photosynthetic electron partitioning between [FeFe]- hydrogenase and ferredoxin:NADPþ-oxidoreductase (FNR) enzymes in vitro Iftach Yacobya,1, Sergii Pochekailova, Hila Toporikb, Maria L. Ghirardic, Paul W. Kingc,1, and Shuguang Zhanga,1 aCenter for Biomedical Engineering NE47-379, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307; cBiosciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401-3305; and bDepartment of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel Edited by Alan R. Fersht, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom, and approved April 28, 2011 (receivedfor review March 5, 2011) Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its commercialization. Here we provide evi- dence that, under the anaerobic conditions that support hydrogen production, there is a significant loss of photosynthetic electrons toward NADPH production in vitro. To elucidate the basis for com- petition, we bioengineered a ferredoxin-hydrogenase fusion and characterized hydrogen production kinetics in the presence of Fd, ferredoxin:NADPþ-oxidoreductase (FNR), and NADPþ. Replacing the hydrogenase with a ferredoxin-hydrogenase fusion switched the bias of electron transfer from FNR to hydrogenase and resulted in an increased rate of hydrogen photoproduction. These results suggest a new direction for improvement of biohydrogen produc- tion and a means to further resolve the mechanisms that control partitioning of photosynthetic electron transport.