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Burgos A, Miranda E, Vilaprinyo E, Meza-Canales ID, Alves R. CAM Models: Lessons and Implications for CAM Evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:893095. [PMID: 35812979 PMCID: PMC9260309 DOI: 10.3389/fpls.2022.893095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The evolution of Crassulacean acid metabolism (CAM) by plants has been one of the most successful strategies in response to aridity. On the onset of climate change, expanding the use of water efficient crops and engineering higher water use efficiency into C3 and C4 crops constitute a plausible solution for the problems of agriculture in hotter and drier environments. A firm understanding of CAM is thus crucial for the development of agricultural responses to climate change. Computational models on CAM can contribute significantly to this understanding. Two types of models have been used so far. Early CAM models based on ordinary differential equations (ODE) reproduced the typical diel CAM features with a minimal set of components and investigated endogenous day/night rhythmicity. This line of research brought to light the preponderant role of vacuolar malate accumulation in diel rhythms. A second wave of CAM models used flux balance analysis (FBA) to better understand the role of CO2 uptake in flux distribution. They showed that flux distributions resembling CAM metabolism emerge upon constraining CO2 uptake by the system. We discuss the evolutionary implications of this and also how CAM components from unrelated pathways could have integrated along evolution.
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Affiliation(s)
- Asdrubal Burgos
- Laboratorio de Biotecnología, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
| | - Enoc Miranda
- Laboratorio de Biotecnología, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ester Vilaprinyo
- Institute of Biomedical Research of Lleida, IRBLleida, Lleida, Spain
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Iván David Meza-Canales
- Departamento de Ecología Aplicada, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
- Unidad de Biología Molecular, Genómica y Proteómica, ITRANS-CUCEI, Universidad de Guadalajara, Guadalajara, Mexico
| | - Rui Alves
- Institute of Biomedical Research of Lleida, IRBLleida, Lleida, Spain
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
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Harding CJ, Cadby IT, Moynihan PJ, Lovering AL. A rotary mechanism for allostery in bacterial hybrid malic enzymes. Nat Commun 2021; 12:1228. [PMID: 33623032 PMCID: PMC7902834 DOI: 10.1038/s41467-021-21528-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
Bacterial hybrid malic enzymes (MaeB grouping, multidomain) catalyse the transformation of malate to pyruvate, and are a major contributor to cellular reducing power and carbon flux. Distinct from other malic enzyme subtypes, the hybrid enzymes are regulated by acetyl-CoA, a molecular indicator of the metabolic state of the cell. Here we solve the structure of a MaeB protein, which reveals hybrid enzymes use the appended phosphotransacetylase (PTA) domain to form a hexameric sensor that communicates acetyl-CoA occupancy to the malic enzyme active site, 60 Å away. We demonstrate that allostery is governed by a large-scale rearrangement that rotates the catalytic subunits 70° between the two states, identifying MaeB as a new model enzyme for the study of ligand-induced conformational change. Our work provides the mechanistic basis for metabolic control of hybrid malic enzymes, and identifies inhibition-insensitive variants that may find utility in synthetic biology.
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Affiliation(s)
- Christopher John Harding
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Ian Thomas Cadby
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Patrick Joseph Moynihan
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Andrew Lee Lovering
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
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Pseudomonas putida Responds to the Toxin GraT by Inducing Ribosome Biogenesis Factors and Repressing TCA Cycle Enzymes. Toxins (Basel) 2019; 11:toxins11020103. [PMID: 30744127 PMCID: PMC6410093 DOI: 10.3390/toxins11020103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/29/2019] [Accepted: 02/07/2019] [Indexed: 11/21/2022] Open
Abstract
The potentially self-poisonous toxin-antitoxin modules are widespread in bacterial chromosomes, but despite extensive studies, their biological importance remains poorly understood. Here, we used whole-cell proteomics to study the cellular effects of the Pseudomonas putida toxin GraT that is known to inhibit growth and ribosome maturation in a cold-dependent manner when the graA antitoxin gene is deleted from the genome. Proteomic analysis of P. putida wild-type and ΔgraA strains at 30 °C and 25 °C, where the growth is differently affected by GraT, revealed two major responses to GraT at both temperatures. First, ribosome biogenesis factors, including the RNA helicase DeaD and RNase III, are upregulated in ΔgraA. This likely serves to alleviate the ribosome biogenesis defect of the ΔgraA strain. Secondly, proteome data indicated that GraT induces downregulation of central carbon metabolism, as suggested by the decreased levels of TCA cycle enzymes isocitrate dehydrogenase Idh, α-ketoglutarate dehydrogenase subunit SucA, and succinate-CoA ligase subunit SucD. Metabolomic analysis revealed remarkable GraT-dependent accumulation of oxaloacetate at 25 °C and a reduced amount of malate, another TCA intermediate. The accumulation of oxaloacetate is likely due to decreased flux through the TCA cycle but also indicates inhibition of anabolic pathways in GraT-affected bacteria. Thus, proteomic and metabolomic analysis of the ΔgraA strain revealed that GraT-mediated stress triggers several responses that reprogram the cell physiology to alleviate the GraT-caused damage.
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Bologna FP, Andreo CS, Drincovich MF. Escherichia coli malic enzymes: two isoforms with substantial differences in kinetic properties, metabolic regulation, and structure. J Bacteriol 2007; 189:5937-46. [PMID: 17557829 PMCID: PMC1952036 DOI: 10.1128/jb.00428-07] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malic enzymes (MEs) catalyze the oxidative decarboxylation of malate in the presence of a divalent metal ion. In eukaryotes, well-conserved cytoplasmic, mitochondrial, and plastidic MEs have been characterized. On the other hand, distinct groups can be detected among prokaryotic MEs, which are more diverse in structure and less well characterized than their eukaryotic counterparts. In Escherichia coli, two genes with a high degree of homology to ME can be detected: sfcA and maeB. MaeB possesses a multimodular structure: the N-terminal extension shows homology to ME, while the C-terminal extension shows homology to phosphotransacetylases (PTAs). In the present work, a detailed characterization of the products of E. coli sfcA and maeB was performed. The results indicate that the two MEs exhibit relevant kinetic, regulatory, and structural differences. SfcA is a NAD(P) ME, while MaeB is a NADP-specific ME highly regulated by key metabolites. Characterization of truncated versions of MaeB indicated that the PTA domain is not essential for the ME reaction. Nevertheless, truncated MaeB without the PTA domain loses most of its metabolic ME modulation and its native oligomeric state. Thus, the association of the two structural domains in MaeB seems to facilitate metabolic control of the enzyme. Although the PTA domain in MaeB is highly similar to the domains of proteins with PTA activity, MaeB and its PTA domain do not exhibit PTA activity. Determination of the distinct properties of recombinant products of sfcA and maeB performed in the present work will help to clarify the roles of MEs in prokaryotic metabolism.
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Affiliation(s)
- Federico P Bologna
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI)-Facultad Cs Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Argentina
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Wang J, Tan H, Zhao ZK. Over-expression, purification, and characterization of recombinant NAD-malic enzyme from Escherichia coli K12. Protein Expr Purif 2006; 53:97-103. [PMID: 17215140 DOI: 10.1016/j.pep.2006.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2006] [Revised: 11/27/2006] [Accepted: 11/29/2006] [Indexed: 11/25/2022]
Abstract
NAD(+)-dependent malic enzyme (NAD-ME) gene from Escherichia coli K12 was inserted into an expression vector pET24b(+) and transformed into E. coli BL21 (DE3). Recombinant NAD-ME was expressed upon IPTG induction, purified with affinity chromatography, and biochemically characterized. The results showed that recombinant NAD-ME could be produced mainly in a soluble form. The monomeric molecular weight of recombinant NAD-ME was about 65 kDa, whereas monomer, homotetramer, and homooctamer were formed in solution as revealed by nondenaturing polyacrylamide gel electrophoresis analysis. Finally, the K(m) values of NAD-ME for L-malate and NAD were determined as 0.420+/-0.174 and 0.097+/-0.038 mM, respectively, at pH 7.2. By using this over-expression and purification system, recombinant E. coli K12 NAD-ME can now be obtained in large quantity necessary for further biochemical characterization and applications.
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Affiliation(s)
- Jinxia Wang
- Dalian Institute of Chemical Physics, CAS, Dalian 116023, China
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Mitsch MJ, Voegele RT, Cowie A, Osteras M, Finan TM. Chimeric structure of the NAD(P)+- and NADP+-dependent malic enzymes of Rhizobium (Sinorhizobium) meliloti. J Biol Chem 1998; 273:9330-6. [PMID: 9535928 DOI: 10.1074/jbc.273.15.9330] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malic enzymes catalyze the oxidative decarboxylation of malate to pyruvate in conjunction with the reduction of a nicotinamide cofactor. We determined the DNA sequence and transcriptional start sites of the genes encoding the diphosphopyridine nucleotide-dependent malic enzyme (DME, EC 1.1.1.39) and the triphosphopyridine nucleotide-dependent malic enzyme (TME, EC 1.1.1. 40) of Rhizobium (Sinorhizobium) meliloti. The predicted DME and TME proteins contain 770 and 764 amino acids, respectively, and are approximately 320 amino acids larger than previously characterized prokaryotic malic enzymes. The increased size of DME and TME resides in the C-terminal extensions which are similar in sequence to phosphotransacetylase enzymes (EC 2.3.1.8). Modified DME and TME proteins which lack this C-terminal region retain malic enzyme activity but are unable to oligomerize into the native state. Data base searches have revealed that similar chimeric malic enzymes were uniquely present in Gram-negative bacteria. Thus DME and TME appear to be members of a new class of malic enzyme characterized by the presence of a phosphotransacetylase-like domain at the C terminus of the protein.
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Affiliation(s)
- M J Mitsch
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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Chang GG, Satterlee J, Hsu RY. Essential sulfhydryl group of malic enzyme from Escherichia coli. JOURNAL OF PROTEIN CHEMISTRY 1993; 12:7-10. [PMID: 8427636 DOI: 10.1007/bf01024907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The activity of malic enzyme from Escherichia coli was unaffected by the monovalent cations Na+ or Li+ at 10 mM. At 100 mM, Li+ or Na+ inhibited the enzyme activity by 88% and 83%, respectively. However, the enzyme activity was stimulated by 40-80-fold with 10 mM K+, Rb+, Cs+, or NH4+. Less stimulation was observed with 100 mM of these stimulating cations. The stimulatory effect was lost after the enzyme was dialyzed against Tris-Cl buffer, but was regained after incubating the dialyzed enzyme with dithiothreitol. The regenerated enzyme was inactivated by 5,5'-dithiobis(2-nitrobenzoic acid). The resulting inactive thionitrobenzoyl enzyme could be regenerated to the active thiol-enzyme by dithiothreitol or converted to the inactive thiocyanoylated enzyme by KCN. The thiocyanoylated enzyme was insensitive to K+ stimulation, which suggested the essentiality of the sulfhydryl groups of the E. coli malic enzyme.
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Affiliation(s)
- G G Chang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan, Republic of China
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Abstract
The bacteria having a unique ring-like morphology first isolated from nasal mucus by Weibel in 1887 were classified as a new genus Spirosoma by Migula in 1894. However, because these bacteria were not completely described for taxonomic purposes and their cultures were no longer available, the genus was deleted from the Bergey's Manual of Determinative Bacteriology, 6th edition, 1948. Orskov (1928) created a new genus "Microcyclus" (a name that has been found to be illegitimate and replaced with Ancylobacter by Raj 1983) to describe these nonmotile vibroid bacteria that occasionally formed ring-like structures. Several similar isolates found in many countries during the last 60 years were readily identified with this genus on the basis of the characteristic morphology alone. For the first time, these fascinating bacteria were extensively reviewed by Raj in 1977 and again in 1981. However, during the last decade, the systematics of these microcyclus bacteria has been reexamined and redefined. It has been shown that these Gram-negative ring-forming aerobic bacteria constitute a heterogeneous group of five genera: Ancylobacter, Cyclobacterium, Flectobacillus, Runella, and Spirosoma; the last four genera have been grouped into a family Spirosomaceace (reviving the old discarded name originally proposed by Migula 1894), thus separating them from the genus Ancylobacter which remains unaffiliated with any family yet (Bergey's Manual of Systematic Bacteriology, Vol. I, 9th ed., 1984). Also, this article reviews the recent studies reported on the ecology, morphogenesis, metabolism, and physiology of the picturesque bacteria.
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Affiliation(s)
- H D Raj
- Department of Microbiology, California State University, Long Beach
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10
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Melville SB, Michel TA, Macy JM. Pathway and sites for energy conservation in the metabolism of glucose by Selenomonas ruminantium. J Bacteriol 1988; 170:5298-304. [PMID: 3141385 PMCID: PMC211604 DOI: 10.1128/jb.170.11.5298-5304.1988] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
On the basis of enzyme activities detected in extracts of Selenomonas ruminantium HD4 grown in glucose-limited continuous culture, at a slow (0.11 h-1) and a fast (0.52 h-1) dilution rate, a pathway of glucose catabolism to lactate, acetate, succinate, and propionate was constructed. Glucose was catabolized to phosphoenol pyruvate (PEP) via the Emden-Meyerhoff-Parnas pathway. PEP was converted to either pyruvate (via pyruvate kinase) or oxalacetate (via PEP carboxykinase). Pyruvate was reduced to L-lactate via a NAD-dependent lactate dehydrogenase or oxidatively decarboxylated to acetyl coenzyme A (acetyl-CoA) and CO2 by pyruvate:ferredoxin oxidoreductase. Acetyl-CoA was apparently converted in a single enzymatic step to acetate and CoA, with concomitant formation of 1 molecule of ATP; since acetyl-phosphate was not an intermediate, the enzyme catalyzing this reaction was identified as acetate thiokinase. Oxalacetate was converted to succinate via the activities of malate dehydrogenase, fumarase and a membrane-bound fumarate reductase. Succinate was then excreted or decarboxylated to propionate via a membrane-bound methylmalonyl-CoA decarboxylase. Pyruvate kinase was inhibited by Pi and activated by fructose 1,6-bisphosphate. PEP carboxykinase activity was found to be 0.054 mumol min-1 mg of protein-1 at a dilution rate of 0.11 h-1 but could not be detected in extracts of cells grown at a dilution rate of 0.52 h-1. Several potential sites for energy conservation exist in S. ruminantium HD4, including pyruvate kinase, acetate thiokinase, PEP carboxykinase, fumarate reductase, and methylmalonyl-CoA decarboxylase. Possession of these five sites for energy conservation may explain the high yields reported here (56 to 78 mg of cells [dry weight] mol of glucose-1) for S. ruminantium HD4 grown in glucose-limited continuous culture.
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Affiliation(s)
- S B Melville
- Department of Animal Science, University of California-Davis 95616
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11
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Saadalla V, Rassam MB. Regulation of aerobic fermentation in Leishmania donovani promastigotes by NADP+-dependent malic enzyme. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 1987; 81:687-92. [PMID: 3503645 DOI: 10.1080/00034983.1987.11812171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
NADP+-dependent malic enzyme (decarboxylating) was extracted from Leishmania donovani promastigotes with Triton X-100. The enzyme was specific for NADP+ and did not decarboxylate oxaloacetate (OA). The substrate activity relationship was hyperbolic for both L-malate and NADP+, and Km values were calculated as 0.18 and 0.12 mM, respectively. The enzyme exhibited a broad pH optimum of 7.5-8.0. Pyruvate, NADPH and OA inhibited the reaction in a competitive manner with apparent Ki values of 0.2, 0.04 and 0.04 mM, respectively, while oxalate inhibition was of the mixed type. The kinetic results obtained indicate that malic enzyme is involved in the regulation of carbon flow towards aerobic fermentation, complete oxidation of dicarboxylic acids or biosynthetic purposes.
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Affiliation(s)
- V Saadalla
- Chemistry Department, College of Science, University of Baghdad, Iraq
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12
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Zerez CR, Moul DE, Gomez EG, Lopez VM, Andreoli AJ. Negative modulation of Escherichia coli NAD kinase by NADPH and NADH. J Bacteriol 1987; 169:184-8. [PMID: 3025169 PMCID: PMC211751 DOI: 10.1128/jb.169.1.184-188.1987] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
NAD kinase was purified 93-fold from Escherichia coli. The enzyme was found to have a pH optimum of 7.2 and an apparent Km for NAD+, ATP, and Mg2+ of 1.9, 2.1, and 4.1 mM, respectively. Several compounds including quinolinic acid, nicotinic acid, nicotinamide, nicotinamide mononucleotide, AMP, ADP, and NADP+ did not affect NAD kinase activity. The enzyme was not affected by changes in the adenylate energy charge. In contrast, both NADH and NADPH were potent negative modulators of the enzyme, since their presence at micromolar concentrations resulted in a pronounced sigmoidal NAD+ saturation curve. In addition, the presence of a range of concentrations of the reduced nucleotides resulted in an increase of the Hill slope (nH) to 1.7 to 2.0 with NADH and to 1.8 to 2.1 with NADPH, suggesting that NAD kinase is an allosteric enzyme. These results indicate that NAD kinase activity is regulated by the availability of ATP, NAD+, and Mg2+ and, more significantly, by changes in the NADP+/NADPH and NAD+/NADH ratios. Thus, NAD kinase probably plays a role in the regulation of NADP turnover and pool size in E. coli.
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Holms W. Evolution of the glyoxylate bypass inEscherichia coliâ An hypothesis which suggests an alternative to the Krebs cycle. FEMS Microbiol Lett 1986. [DOI: 10.1111/j.1574-6968.1986.tb01390.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Holms WH. The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate. CURRENT TOPICS IN CELLULAR REGULATION 1986; 28:69-105. [PMID: 3098503 DOI: 10.1016/b978-0-12-152828-7.50004-4] [Citation(s) in RCA: 152] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Steinbüchel A, Schlegel HG. NAD-linked L(+)-lactate dehydrogenase from the strict aerobe alcaligenes eutrophus. 2. Kinetic properties and inhibition by oxaloacetate. EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 130:329-34. [PMID: 6825698 DOI: 10.1111/j.1432-1033.1983.tb07156.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The L(+)-lactate dehydrogenase (EC 1.1.1.27) of Alcaligenes eutrophus catalyzes the NADH-dependent reduction of pyruvate and a few other 2-oxoacids. The Km values for NADH, NAD, pyruvate and L(+)-lactate are 0.075 mM, 0.130 mM, 0.820 mM and 7.10 mM, respectively. The reaction follows a rapid equilibrium ordered bi-bi mechanism and involves the formation of a dead-end EBQ complex. The competitive inhibition of pyruvate reduction caused by NAD (with respect to NADH) is regarded to be of physiological importance. The enzyme is strongly inhibited by oxaloacetate, oxalate and to a less extent by oxamate. Oxaloacetate was found to be the most powerful inhibitor of the enzyme and exerts an almost complete inhibition of the reduction of pyruvate and some 2-oxoacids at concentrations of 1 microM and less. At 0.1 microM oxaloacetate the inhibition of pyruvate reduction is about 90%. The kinetics of pyruvate reduction in the presence of oxaloacetate is characterized by a burst phase followed by a decreased steady-state velocity. During the burst phase, which lasts from several seconds to some minutes, the enzyme undergoes transition to a less active enzyme form. The inhibition studies revealed the lactate dehydrogenase to be a hysteretic enzyme, due to its slow response to the ligand. The characteristics of the transient were examined. The inhibition of lactate dehydrogenase from A. eutrophus by oxaloacetate is considered to be of great physiological importance, allowing its function only at a low oxaloacetate concentration and consequently at high NADH/NAD ratios.
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AMP deaminase reaction as a control system of glycolysis in yeast. Activation of phosphofructokinase and pyruvate kinase by the AMP deaminase-ammonia system. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)81037-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Purification and characterization of the NADP-linked malate dehydrogenase (decarboxylating) from Mangifera indica. ACTA ACUST UNITED AC 1981. [DOI: 10.1016/0005-2744(81)90229-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Culture OH-75-B of Beggiatoa sp. differed significantly from any described previously in its utilization of organic carbon and reduced sulfur compounds. It deposited internal sulfur granules characteristic of Beggiatoa sp. with either sulfide or thiosulfate in the medium. This strain (OH-75-B, clone 2a) could be grown in agitated liquid cultures on mineral medium with acetate as the only source of organic carbon. The resultant growth yields and rates were comparable to those for typical heterotrophs. Of the other simple organic compounds tested, only pyruvate, lactate, or ethanol could singly support the growth of this strain. Single sugars or amino acids neither supported growth nor enhanced it when added to acetate-containing medium. In contrast, compounds of the tricarboxylic acid cycle enhanced growth yields when tested in concert with acetate. These and fluoroacetate inhibition results indicate that Beggiatoa sp. possesses a functional tricarboxylic acid cycle. Poor yields characterized the growth of this strain on dilute yeast extract medium, and higher concentrations of yeast extract proved inhibitory. The enzyme catalase, contrary to the findings of others, had no synergistic influence on growth yields when added to medium containing yeast extract or acetate or both.
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19
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Brown DA, Cook RA. Role of metal cofactors in enzyme regulation. Differences in the regulatory properties of the Escherichia coli nicotinamide adenine dinucleotide phosphate specific malic enzyme, depending on whether magnesium ion or manganese ion serves as divalent cation. Biochemistry 1981; 20:2503-12. [PMID: 7016178 DOI: 10.1021/bi00512a022] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A number of differences in the kinetic and physical properties of the Escherichia coli nicotinamide adenine dinucleotide phosphate (NADP+) dependent malic enzyme have been found, depending upon whether Mg2+ or Mn2+ served to fulfill the divalent cation requirement. The velocity-NADP+ and velocity-cation saturation curves exhibit a simple hyperbolic response in the presence of either metal cofactor, but the affinity for NADP+ (and malate) as well as the Vmax is increased in the presence of Mn2+. The high affinity of the enzyme for Mn2+ coupled with the increased affinity for substrates indicates that Mn2+ is the preferred cofactor in vitro. With either Mg2+ or Mn2+ as cation, the velocity-malate saturation curves in the absence of effectors are complex at pH 7.45, indicating varying combinations of apparent positive and negative cooperative behavior. Greater initial positive cooperative behavior between malate binding sites is observed with Mg2+ as cation. The enzyme appears to be equally sensitive to inhibition by the allosteric inhibitors reduced nicotinamide adenine dinucleotide (NADH) and oxaloacetic acid (OAA) in the presence of either cation, but the interaction between malate binding sites, in the presence of effectors, varies significantly with the choice of metal cofactor. The inhibitor NADH increases the interaction between malate binding sites in the presence of Mn2+ but has little effect on subunit interaction in the presence of Mg2+. The inhibitor OAA increases the interaction between malate binding sites in the presence of both cations, with increased positive cooperativity observed with Mn2+ but increased negative cooperativity with Mg2+. The kinetic data can be explained by a model involving sequential ligand-induced conformational changes of the enzyme, resulting in a mixture of apparent positive and negative cooperative behavior. Alternative explanations involving different classes of noninteracting binding sites or different enzyme forms are also considered. The metal cofactors, Mg2+ and Mn2+, appear to stabilize two distinct conformational states of the enzyme which differ in response to varying substrate and effector concentrations. Altered conformational states of the enzyme in the presence of the two cations are further substantiated by proteolytic digestion studies with the homogeneous enzyme. The results are strikingly similar to previous results reported on the nicotinamide adenine dinucleotide (NAD+) dependent malic enzyme and the NAD+-dependent isocitrate dehydrogenase, supporting the suggestion that metal cofactors function as regulatory entities.
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Abstract
Malic enzyme of the phototropic bacterium Chromatium vinosum strain D that lacks malate dehydrogenase was partially purified yielding a specific activity of 55 units/mg protein. The constitutive enzyme with a molecular weight of 110,000 and a pH optimum of 8.0 was absolutely dependent on the presence of a monovalent cation (NH4+, K+, Cs+, or Rb+) as well as a divalent cation (Mn2+, or Mg2+). The enzyme was inhibited by oxaloacetate, glyoxyate, and NADPH. The K0.5 value for L-malate and the inhibition constants for oxaloacetate and glyoxylate are dependent on the concentration of the monovalent cation, whereas the Km value for NADP (18 microM) and the KI value for NADPH (42 microM) are independent. Throughout all kinetic measurements hyperbolic saturation curves and linear double reciprocal plots were obtained.
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Macy JM, Ljungdahl LG, Gottschalk G. Pathway of succinate and propionate formation in Bacteroides fragilis. J Bacteriol 1978; 134:84-91. [PMID: 148460 PMCID: PMC222221 DOI: 10.1128/jb.134.1.84-91.1978] [Citation(s) in RCA: 198] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cell suspensions of Bacteroides fragilis were allowed to ferment glucose and lactate labeled with (14)C in different positions. The fermentation products, propionate and acetate, were isolated, and the distribution of radioactivity was determined. An analysis of key enzymes of possible pathways was also made. The results of the labeling experiments showed that: (i) B. fragilis ferments glucose via the Embden-Meyerhof pathway; and (ii) there was a randomization of carbons 1, 2, and 6 of glucose during conversion to propionate, which is in accordance with propionate formation via fumarate and succinate. The enzymes 6-phosphofrucktokinase (pyrophosphate-dependent), fructose-1,6-diphosphate aldolase, phosphoenolpyruvate carboxykinase, malate dehydrogenase, fumarate reductase, and methylmalonyl-coenzyme A mutase could be demonstrated in cell extracts. Their presence supported the labeling results and suggested that propionate is formed from succinate via succinyl-, methylmalonyl-, and propionyl-coenzyme A. From the results it also is clear that CO(2) is necessary for growth because it is needed for the formation of C4 acids. There was also a randomization of carbons 1, 2, and 6 of glucose during conversion to acetate, which indicated that pyruvate kinase played a minor role in pyruvate formation from phosphoenolpyruvate. Phosphoenolpyruvate carboxykinase, oxaloacetate decarboxylase, and malic enzyme (nicotinamide adenine dinucleotide phosphate-dependent) were present in cell extracts of B. fragilis, and the results of the labeling experiments agreed with pyruvate synthesis via oxaloacetate and malate if these acids are in equilibrium with fumarate. The conversion of [2-(14)C]- and [3-(14)C]lactate to acetate was not associated with a randomization of radioactivity.
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Dolin MI, Juni E. Utilization of oxalacetate by Acinetobacter calcoaceticus: evidence for coupling between malic enzyme and malic dehydrogenase. J Bacteriol 1978; 133:786-93. [PMID: 627536 PMCID: PMC222089 DOI: 10.1128/jb.133.2.786-793.1978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Growth of Acinetobacter calcoaceticus strain BD413 in malate-mineral medium resulted in the excretion of large quantities of oxalacetate. Malate was virtually depleted by the time the cell density reached 60% of its final value; most of the remaining growth took place at the expense of oxalacetate. Experiments in which oxalacetate was used as the initial substrate showed that pyruvate was not utilized until most of the oxalacetate disappeared. The generation time for growth on malate or oxalacetate was approximately 40 min; the generation time for growth on pyruvate was 62 min, which implies that pyruvate transport may be rate limiting. Oxalacetate and pyruvate, however, supported approximately the same growth yield. These observations suggested that the first step in the utilization of oxalacetate as an energy source consisted of an enzymatic decarboxylation of the keto acid to pyruvate and CO(2). Three enzyme reactions that carry out this decarboxylation have been detected in extracts of A. calcoaceticus. The first, which functioned maximally at pH 4.8, was attributable to the oxalacetate decarboxylase activity of oxidized diphosphopyridine nucleotide-malic enzyme. The second and third, which functioned in the neutral pH range, resulted from coupling of oxidized diphosphopyridine nucleotide-malic enzyme to reduced diphosphopyridine nucleotide-dependent malic dehydrogenase, and oxidized triphosphopyridine nucleotide-malic enzyme to a reduced triphosphopyridine nucleotide-dependent malic dehydrogenase. The efficiency of these coupled reactions was high enough so that the overall reaction could be physiologically significant.
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Slabas AR, Whatley FR. Metabolic regulation of malic enzyme activity from Paracoccus denitrificans by glyoxylate and acetylCoA. Biochem Biophys Res Commun 1977; 74:1116-24. [PMID: 14633 DOI: 10.1016/0006-291x(77)91634-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Vidal MC, Cazzulo JJ. On the regulatory properties of a halophilic malic enzyme from Halobacterium cutirubrum. EXPERIENTIA 1976; 32:441-2. [PMID: 5287 DOI: 10.1007/bf01920783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The NADP-linked malic enzyme from Halobacterium cutirubrum is strongly inhibited by acetyl-CoA and NADH, and rather weakly inhibited by oxaloacetate and glyoxylate, in the presence of very high KCl concentrations (3 M), considered physiological for the extremely halophilic bacteria.
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Kleber HP, Aurich H. [Regulation of the malic enzyme activity of Acinetobacter by organic acids]. ZEITSCHRIFT FUR ALLGEMEINE MIKROBIOLOGIE 1976; 16:91-5. [PMID: 9741 DOI: 10.1002/jobm.3630160202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Hansen EJ, Juni E. Isolation of mutants of Escherichia coli lacking NAD- and NADP-linked malic. Biochem Biophys Res Commun 1975; 65:559-66. [PMID: 238534 DOI: 10.1016/s0006-291x(75)80183-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kleber HP. Hemmung des Malatenzyms ausAcinetobacter calcoaceticus durch Acetyl-CoA. ACTA ACUST UNITED AC 1975. [DOI: 10.1002/jobm.3630150104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Frenkel R. Regulation and physiological functions of malic enzymes. CURRENT TOPICS IN CELLULAR REGULATION 1975; 9:157-81. [PMID: 235406 DOI: 10.1016/b978-0-12-152809-6.50012-3] [Citation(s) in RCA: 131] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Park SL, Guttman HN. Purification and properties of Lactobacillus plantarum inducible malic enzyme. J Bacteriol 1973; 116:263-70. [PMID: 4355483 PMCID: PMC246417 DOI: 10.1128/jb.116.1.263-270.1973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Inducible malic enzyme (l-malate:NAD oxidoreductase [decarboxylating], EC 1.1.1.39) was isolated from Lactobacillus plantarum and purified about 100-fold with 27% yield of the original activity. Kinetic studies with the purified malic enzyme yielded the following results: pH optimum, 7.6 to 8.0; K(m) for l-malate, 0.38 mM; K(m) for NAD, 0.072 mM; and K(m) for MnCl(2), 0.048 mM. It was shown that this enzyme was inhibited by high concentrations of substrate and nicotinamide adenine dinucleotide (NAD), indicating it may be regulated by substrate or NAD. Molecular weight of 130,000 +/- 10,000 was determined by Sephadex gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isoelectric point, determined by isoelectrofocusing, was 4.3 at 7 C. Isoelectrofocusing also resolved three active peaks which focused at pH 4.19, 4.31, and 4.40.
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Abstract
Cell-free extract supernatant fluids of Pseudomonas aeruginosa were shown to lack malic dehydrogenase but possess a nicotinamide adenine dinucleotide (NAD)- or NAD phosphate (NADP)-dependent enzymatic activity, with properties suggesting a malic enzyme (malate + NAD (NADP) --> pyruvate + reduced NAD (NADH) (reduced NADP [NADPH] + CO(2)), in agreement with earlier findings. This was confirmed by determining the nature and stoichiometry of the reaction products. Differences in heat stability and partial purification of these activities demonstrated the existence of two malic enzymes, one specific for NAD and the other for NADP. Both enzymes require bivalent metal cations for activity, Mn(2+) being more effective than Mg(2+). The NADP-dependent enzyme is activated by K(+) and low concentrations of NH(4) (+). Both reactions are reversible, as shown by incubation with pyruvate, CO(2), NADH, or NADPH and Mn(2+). The molecular weights of the enzymes were estimated by gel filtration (270,000 for the NAD enzyme and 68,000 for the NADP enzyme) and by sucrose density gradient centrifugation (about 200,000 and 90,000, respectively).
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Cavalieri RL, Sable HZ, With the technical assistance of Judith Dogin. Enzymes of Pentose Biosynthesis. J Biol Chem 1973. [DOI: 10.1016/s0021-9258(19)44079-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Marr JJ. Regulations of aerobic fermentation in protozoans. II. Allosteric inhibition of the malic enzyme. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1973; 44:701-10. [PMID: 4145455 DOI: 10.1016/0305-0491(73)90219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Fodge DW, Gracy RW, Harris BG. Studies on enzymes from parasitic helminths. I. Purification and physical properties of malic enzyme from the muscle tissue of Ascaris suum. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 268:271-84. [PMID: 4402077 DOI: 10.1016/0005-2744(72)90322-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Affiliation(s)
- J J. Cazzulo
- Departamento de Bioquímica, Facultad de Ciencias Bioquímicas, Universidad Nacional de Rosario, Suipacha 570, Rosario, República Argentina
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Kanazawa T, Kirk MR, Bassham JA. Regulatory effects of ammonia on carbon metabolism in photosynthesizing Chlorella pyrenoidosa. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 205:401-8. [PMID: 5471291 DOI: 10.1016/0005-2728(70)90106-4] [Citation(s) in RCA: 98] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Sanwal B. Regulatory Mechanisms Involving Nicotinamide Adenine Nucleotides As Allosteric Effectors. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(19)77138-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Regulatory Characteristics of the Diphosphopyridine Nucleotide-specific Malic Enzyme of Escherichia coli. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)63309-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Sanwal BD, Smando R. Regulatory roles of cyclic 3',5'-AMP in bacteria: control of malic enzyme of Escherichia coli. Biochem Biophys Res Commun 1969; 35:486-91. [PMID: 4389228 DOI: 10.1016/0006-291x(69)90372-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Wright JA, Sanwal BD. Regulatory Mechanisms Involving Nicotinamide Adenine Nucleotides as Allosteric Effectors. J Biol Chem 1969. [DOI: 10.1016/s0021-9258(18)91758-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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