A Racemizing Enzyme System of Lactobacill Us Plantar

Total Page:16

File Type:pdf, Size:1020Kb

A Racemizing Enzyme System of Lactobacill Us Plantar J. Gen. App!. Microbio!. Vol. 11, No. 1, 1965. A RACEMIZING ENZYME SYSTEM OF LACTOBACILL US PLANTAR UM TETSUO HIYAMA, SHOJI MIZUSHIMA and KAKUO KITAHARA Institute of Applied Microbiology, University of Tokyo, Tokyo ReceivedFebruary 15, 1965 It is well-known that the conversion of optically active lactate to the inactive form, racemization of lactate, can take place in some strains of bacteria such as the lactic acid bacteria and Clostridium sp. (1). In 1952, KITAHARAand coworkers obtained cell-free preparations of lactate racemase (trivial name " Recemiase," given by KATAGIRI and KITAHARA in 1937) from dried cells of Lactobacillus plantarum 11 which is one of the typical strains forming racemic lactate from glucose (2). Some enzymatic properties were reported with the partially purified " Racemiase " prepa- ration (3), and it was proved that nicotinamide adenine dinucleotide (NAD) is essential as a co-f actor to recover the activity with the preparation treated by active carbon or dialysis. It was difficult, however, to determine whether or not the racemization was catalyzed by a single enzyme because further purification was difficult due to its instability. In 1960, DENNIS and KAPLANdemonstrated the existence of NAD-depend- ent lactate dehydrogenases, each specific for the n(leavo)- or L(dextro)-isomer, in Lactobacillus plantarum ATCC 8041(4). It was proved in our laboratory that the formation of racemic lactate from glucose by resting cells of L. plantarum 11 is made possible by the cooperation of NAD-dependent D- and L-lactate dehydrogenases (5). This paper deals with the relationship between " Racemiase " and the lactate dehydrogenases in the organism, and discusses the mechanism of racemization. MATERIALS AND METHODS Materials Nicotinamide adenine dinucleotide (NAD) is a commercial product purchased from the Nutritional Biochemicals Corporation (Cleveland, Ohio). The reduced form of NAD was prepared by the method of RAFTER and COLOWICK(6), n- and L-lactic acids were prepared from the fermentation broths of Sporolactobacillus inulinus (7) and Lactobacillus casei TA, respec- tively. Lactic acid was neutralized by sodium or potassium hydroxide before use. Other materials were obtained commercially. Organism Lactobacillus plantarum 11 used in these experiments was from our own 51 52 HIYAMA, MIZUSHIMA and KITAHARA VOL. 11 culture collection and maintained on malt-bouillon agar. Cultivation of this organism was carried out exactly as described in the previous paper (5). Purification of lactate dehydrogenases As summarized in Table 1, the purification procedure was carried out according to the method described in the previous paper (5) with the following slight modification : for the D-enzyme, all buffers used throughout the procedure contained 0.01 M j3-mercaptoethanol to avoid loss of activity. D-Enzyme could be separated from L-enzyme by DEAE-cellulose chromato- Elution Volume (ml) Fig. 1. Elution patterns of crude "Racemiase" with DEAE-cellulose column. graphy (Fig. 1). It being difficult to separate the D-enzyme activity from the L-enzyme, the crude sonicate was heated at 50° for 3 minutes to inactivate the D-enzyme prior to the purification of the L-enzyme. For the details, see the previous report (5). Assays of enzyme activities The activity of lactate dehydrogenase was determined spectrophoto- metrically by the rate of NAD reduction or of NADH2 oxidation in the 1965 A Racemizing Enzyme System of Lactobacillus plantarum 53 Table 1. Purification procedures of D- and L-lactate dehydrogenases'. presence of lactate or pyruvate, respectively. Measurement was carried out at 340 mi and at 20° by the HITACHI EPU-2A spectrophotometer (Hitachi Ltd. Tokyo). Racemase activity was estimated by measuring the rate of D- or L-lactate formation from respective antipode. For the determination of optically active lactates, the manometrical method of KITAHARAand FUKUI (8 and 9) was used. When quick determination of racemase activity was required, D-lactate formed from L-isomer was calculated from the reduction rate of 2, 6-dichlorophenolindophenol with D-lactate dehydrogenase isolated from Lactobacillus casei (10). RESULTS Behavior of lactate dehydrogenases during purification of " racemiase ". The crude sonicate, which showed strong activity of lactate racemase in the presence of NAD, was fractionated by ammonium sulfate precipitation followed by column chromatographic fractionation with DEAE-cellulose. As summarized in Table 2, the second fractionation by DEAE-cellulose column chromatography caused an extreme loss of specific activity. Very active L-lactate dehydrogenase was detected in this fraction and only slight D-lactate dehydrogenase activity. The racemase activity was recovered by the addition of D-lactate dehydrogenase which had been purified separately. It is very likely that the loss of D-lactate dehydrogenase caused the inactivation of racemase activity due to less stability of the D-lactate dehydrogenase of this bacterium (5). Heat treatment, by which D-lactate dehydrogenase is inactivated (5), also caused inactivation of racemase activity. Fractionation of partially purified " Racemiase " by DEAE-cellulose column showed that the preparation contained NAD-dependent D- and L-lactate dehydrogenases (Fig. 1). Racemization of lactate by the mixture of dehydrogenases. The mixture 54 HIYAMA, MIzusHIMA and KITAHARA VOL. 11 Table 2. Purification of the racemase. Table 3. Activities of rasemase and dehydrogenases in crude sonicates. of n- and L-lactate dehydrogenases of L. plantarum, which were purified separately and had no racemase activity, could catalyze the racemization of lactate in the presence of NAD (Table 4). The data show that the rate of racemization, the n-lactate formation from L-lactate, nearly equals that of dehydrogenation, i.e., the pyruvate formation from L-lactate. Comparison of properties of "Racemiase " and dehydrogenases MICHAELIS'constants (Km) of L-lactate dehydrogenase for L-lactate and NAD were estimated by the method of LINEWEAVER-BURK'Splot. These 1965 A Racemizing Enzyme System of Lactobacillus plantarum 55 Table 4. Racemization by the mixture of two dehydrogenases. Table 5. Comparison of properties of "Racemiase " and L-dehydrogenase. values show good agreement with those of "Racemiase" reported by OBAYASHI et al. (3), using L-lactate as a substrate (Table 5). Racemase and dehydrogenase activities of crude extracts. The washed cells were suspended in 0.2 M-phosphate buffer, pH 7.0, and disrupted in a sonic disintegrator (Toyo-Riko, Ltd., Tokyo), 10-kc, 90-watt, for 30 minutes at 4°. The clear supernatant, obtained by centrifugation at 25,000 x g for 20 minutes, was used as a crude extract preparation. As shown in Table 3, the activity of the lactate dehydrogenase, from n-lactate and L-lactate to pyruvate, was 8.5 NM/mg cell/hr. Racemization, from L-lactate to n-lactate was 8.0 pM/mg cell/hr. This relationship between dehydrogenase and racemase activity was the same as found in the combined system of purified dehydrogenases shown in Table 4. The data show that the total activity of racemase comes from n- and L-lactate dehydrogenases in crude extracts which represents the total activity of the intact cell. The racemase activity of intact cells, however, was found to be several times lower than that of crude extracts. In the previous report it was shown that the backward reactions of n- and L-lactate dehydrogenases were inhibited by adenine nucleotides (5), as in the case of " Racemiase " reaction (3). It seemed reasonable, therefore, that the racemase activity was depressed in intact cells where concentrations of these substances were higher than in the 56 HIYAMA, MIZUSHIMA and KITAHARA VOL. 11 cell-free system. These observations were also supported by the fact that the activity of the lactate racemization in intact cells was further depressed under aerobic conditions where the intracellular concentration of pyruvate was increased by a lactate dehydrogenase-NADH2 oxidase system (15). Equilibria of dehydrogenase and racemase system. Equilibrium con- stants of D- and L-lactate dehvdrogenases were estimated from the concen- trations of substrates and products at the equilibrium points. The reaction was initiated from lactate and NAD. Formed NADH2 was determined spectrophotometrically Time (hr) Fig. 3. Time curves of reacemizing reaction. Time(min) Fig. 2. Equilibria of D- and L-lactate dehydrogenases. Reaction mixture is as follows: For D-reaction, 7.7 x 10-2 M D-lactate, 3.8 x 10-4 M NAD, D-lactate dehydrogenase (14~amoles/hr.) and 0.2M phosphate buffer, pH 7.2. For L-reaction, the same consti- tuents with exceptions of 7.7 x 10-2 M L-lactate and L-lactate dehydrogenase (16 p moles/hr.) (Fig. 2). From the results obtained the constants were calculated to be 2.4x 10.12 and 2.5 x 1012 at 20° for D- and L-lactate dehydrogenase, respec- tively. This explains the fact that the racemizing reaction in the present system reaches equilibrium where the D : L-ratio of lactate is 1:1, i .e., com- plete racemization. Figure 3 shows the time curves of the racemizing reaction by mixture of the dehydrogenases. The reactions were equilibrated at D : L=1:1 both from D- and L-isomers. The imbalance of the activities 1965 A Racemizing Enzyme System of Lactobacillus plantarum 57 Table 6. The activity of acetone dried cells. ATATI Fig. 4. Paper electrophoretic patterns of D- and L-lactate dehydrogenases, 0.01 M Tris-HC1 buffer containing 0.01 M jS-mercaptoe- of dehydrogenases (D: L=23 :14) has no influence on the final equilibrium point (D : L=1:1) as shown in Fig. 3. Other lactate dehydrogenases. As shown in Table 6, acetone treated cells do not show any dependency on NAD in the reduction of indophenol by D-lactate. The data suggest the presence of a D-lactate dehydrogenase which is independent of NAD and phrhaps has a flavin nucleotide as a prosthetic group. No further experiments to investigate this enzyme or to detect flavoprotein L-lactate dehydrogenases have been done.
Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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 …............................................................................................................................
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]
  • Perspectives
    PERSPECTIVES in a number of enzymes such as [FeFe]- hydrogenase, [FeNi]-hydrogenase, Natural inspirations for metal–ligand [Fe]-hydrogenase, lactate racemase and alcohol dehydrogenase. In this Perspective, cooperative catalysis we discuss these examples of biological cooperative catalysis and how, inspired by these naturally occurring systems, chemists Matthew D. Wodrich and Xile Hu have sought to create functional analogues. Abstract | In conventional homogeneous catalysis, supporting ligands act as We also speculate that cooperative catalysis spectators that do not interact directly with substrates. However, in metal–ligand may be at play in [NiFe]-carbon monoxide cooperative catalysis, ligands are involved in facilitating reaction pathways that dehydrogenase ([NiFe]-CODHase), which may inspire the design of synthetic CO2 would be less favourable were they to occur solely at the metal centre. This reduction catalysts making use of these catalysis paradigm has been known for some time, in part because it is at play motifs. Each section in the following in enzyme catalysis. For example, studies of hydrogenative and dehydrogenative discussion is devoted to an enzyme and its enzymes have revealed striking details of metal–ligand cooperative catalysis synthetic models. that involve functional groups proximal to metal active sites. In addition to [FeFe]- and [NiFe]-hydrogenase the more well-known [FeFe]-hydrogenase and [NiFe]-hydrogenase enzymes, Hydrogenases are enzymes that catalyse [Fe]-hydrogenase, lactate racemase and alcohol dehydrogenase each makes use (REF. 5) the production and utilization of H2 . of cooperative catalysis. This Perspective highlights these enzymatic examples of Three variants of hydrogenase enzymes exist metal–ligand cooperative catalysis and describes functional bioinspired which are named [FeFe]-, [NiFe]- and [Fe]-hydrogenase because their active molecular catalysts that also make use of these motifs.
    [Show full text]
  • 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.
    [Show full text]
  • The Chemistry and Evolution of Enzyme Function
    The Chemistry and Evolution of Enzyme Function: Isomerases as a Case Study Sergio Mart´ınez Cuesta EMBL - European Bioinformatics Institute Gonville and Caius College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 31st July 2014 This dissertation is the result of my own work and contains nothing which is the outcome of work done in collaboration except where specifically indicated in the text. No part of this dissertation has been submitted or is currently being submitted for any other degree or diploma or other qualification. This thesis does not exceed the specified length limit of 60.000 words as defined by the Biology Degree Committee. This thesis has been typeset in 12pt font using LATEX according to the specifications de- fined by the Board of Graduate Studies and the Biology Degree Committee. Cambridge, 31st July 2014 Sergio Mart´ınezCuesta To my parents and my sister Contents Abstract ix Acknowledgements xi List of Figures xiii List of Tables xv List of Publications xvi 1 Introduction 1 1.1 Chemistry of enzymes . .2 1.1.1 Catalytic sites, mechanisms and cofactors . .3 1.1.2 Enzyme classification . .5 1.2 Evolution of enzyme function . .6 1.3 Similarity between enzymes . .8 1.3.1 Comparing sequences and structures . .8 1.3.2 Comparing genomic context . .9 1.3.3 Comparing biochemical reactions and mechanisms . 10 1.4 Isomerases . 12 1.4.1 Metabolism . 13 1.4.2 Genome . 14 1.4.3 EC classification . 15 1.4.4 Applications . 18 1.5 Structure of the thesis . 20 2 Data Resources and Methods 21 2.1 Introduction .
    [Show full text]
  • Methane-Yielding Microbial Communities Processing Lactate-Rich Medium to Methane M1A M1B
    Detman et al. Biotechnol Biofuels (2018) 11:116 https://doi.org/10.1186/s13068-018-1106-z Biotechnology for Biofuels RESEARCH Open Access Methane‑yielding microbial communities processing lactate‑rich substrates: a piece of the anaerobic digestion puzzle Anna Detman1, Damian Mielecki1, Łukasz Pleśniak1, Michał Bucha2, Marek Janiga3, Irena Matyasik3, Aleksandra Chojnacka1, Mariusz‑Orion Jędrysek4, Mieczysław K. Błaszczyk5 and Anna Sikora1* Abstract Background: Anaerobic digestion, whose fnal products are methane and carbon dioxide, ensures energy fow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Efective utilization of lactate has been observed in many experimen‑ tal approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors. Results: Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artifcial lactate-rich media to methane and carbon dioxide in up-fow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Efective utilization of lactate and biogas production was observed. 16S rRNA profling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated.
    [Show full text]
  • All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
    All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA
    [Show full text]
  • Application-Oriented Marine Isomerases in Biocatalysis
    marine drugs Review Application-Oriented Marine Isomerases in Biocatalysis Antonio Trincone Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy; [email protected] Received: 3 November 2020; Accepted: 20 November 2020; Published: 21 November 2020 Abstract: The class EC 5.xx, a group of enzymes that interconvert optical, geometric, or positional isomers are interesting biocatalysts for the synthesis of pharmaceuticals and pharmaceutical intermediates. This class, named “isomerases,” can transform cheap biomolecules into expensive isomers with suitable stereochemistry useful in synthetic medicinal chemistry, and interesting cases of production of l-ribose, d-psicose, lactulose, and d-phenylalanine are known. However, in two published reports about potential biocatalysts of marine origin, isomerases are hardly mentioned. Therefore, it is of interest to deepen the knowledge of these biocatalysts from the marine environment with this specialized in-depth analysis conducted using a literature search without time limit constraints. In this review, the focus is dedicated mainly to example applications in biocatalysis that are not numerous confirming the general view previously reported. However, from this overall literature analysis, curiosity-driven scientific interest for marine isomerases seems to have been long-standing. However, the major fields in which application examples are framed are placed at the cutting edge of current biotechnological development. Since these enzymes can offer properties of industrial interest, this will act as a promoter for future studies of marine-originating isomerases in applied biocatalysis. Keywords: marine enzymes; biocatalysis; marine biotechnology 1. Introduction In 2010, one of the first comprehensive review articles about enzymes of marine origin especially suitable for future applications in biocatalysis reported an account of the knowledge in the field.
    [Show full text]