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1.
Enzyme Microb Technol ; 162: 110140, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36272242

ABSTRACT

Developing a microbial chassis with efficient enzymes is key to the synthesis of products by metabolic engineering. The wide distribution of desired pathway enzymes across several species and categories is posing major challenges in screening and selection of the same for pathway reconstruction. One such key enzyme is isopropylmalate isomerase (IPMI) of leucine/isoleucine biosynthetic pathway. The enzymes reported earlier as citraconase and maleate hydratase in Arthrobacter sp. and Pseudomonas sp. respectively, were found to have the characteristics of IPMI. If a systematic study is undertaken to show that these orphan enzymes indeed are part of the aconitase family of enzymes, these reported ones will add to the repertoire of enzymes available for branch-chained amino acid pathway engineering. This work is focused on functional characterisation of the enzymes citraconase and maleate hydratase based on the properties of IPMI. The partially sequenced gene of maleate hydratase reported earlier served as a template to identify the respective genes in these organisms which is found to be that of IPMI with conserved regions in the active site. The native enzymes and the IPMI of A. globiformis and P. pseudoalcaligenes, expressed in E. coli acted upon all the substrates in the forward direction comprising of D-citramalate, citraconate & D-erythro-3-methylmalate. In the reverse direction all the enzymes converted citraconate to D-citramalate with high activity. The estimated equilibrium ratio was same for both the native enzyme and the over-expressed IPMI which is 96:1.5:2.5 for D-citramalate: citraconate: D-erythro-3-methylmalate. The iron requirement for both enzymes which is characteristic of IPMI is ascertained by chelation and reconstitution of the same. Therefore, this work elucidated the broad specificity and the reactions in equilibrium catalysed by these enzymes like that of IPMI, paving way for the integration of these two efficient candidates into aconitase family of enzymes facilitating pathway engineering.


Subject(s)
Aconitate Hydratase , Escherichia coli , Escherichia coli/genetics , Escherichia coli/metabolism , Aconitate Hydratase/chemistry , Aconitate Hydratase/genetics , Aconitate Hydratase/metabolism
2.
Microb Cell Fact ; 21(1): 20, 2022 Feb 05.
Article in English | MEDLINE | ID: mdl-35123481

ABSTRACT

BACKGROUND: During the recombinant protein expression, most heterologous proteins expressed in E. coli cell factories are generated as insoluble and inactive aggregates, which prohibit E. coli from being employed as an expression host despite its numerous advantages and ease of use. The yeast mitochondrial aconitase protein, which has a tendency to aggregate when expressed in E. coli cells in the absence of heterologous chaperones GroEL/ES was utilised as a model to investigate how the modulation of physiological stimuli in the host cell can increase protein solubility. The presence of folding modulators such as exogenous molecular chaperones or osmolytes, as well as process variables such as incubation temperature, inducer concentrations, growth media are all important for cellular folding and are investigated in this study. This study also investigated how the cell's stress response system activates and protects the proteins from aggregation. RESULTS: The cells exposed to osmolytes plus a pre-induction heat shock showed a substantial increase in recombinant aconitase activity when combined with modulation of process conditions. The concomitant GroEL/ES expression further assists the folding of these soluble aggregates and increases the functional protein molecules in the cytoplasm of the recombinant E. coli cells. CONCLUSIONS: The recombinant E. coli cells enduring physiological stress provide a cytosolic environment for the enhancement in the solubility and activity of the recombinant proteins. GroEL/ES-expressing cells not only aided in the folding of recombinant proteins, but also had an effect on the physiology of the expression host. The improvement in the specific growth rate and aconitase production during chaperone GroEL/ES co-expression is attributed to the reduction in overall cellular stress caused by the expression host's aggregation-prone recombinant protein expression.


Subject(s)
Aconitate Hydratase/chemistry , Escherichia coli/metabolism , Iron-Regulatory Proteins/chemistry , Protein Folding , Recombinant Proteins/chemistry , Aconitate Hydratase/genetics , Aconitate Hydratase/metabolism , Escherichia coli/chemistry , Escherichia coli/genetics , Escherichia coli/growth & development , Iron-Regulatory Proteins/genetics , Iron-Regulatory Proteins/metabolism , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
3.
Biomolecules ; 11(9)2021 09 09.
Article in English | MEDLINE | ID: mdl-34572542

ABSTRACT

Maintaining iron homeostasis is fundamental for almost all living beings, and its deregulation correlates with severe and debilitating pathologies. The process is made more complicated by the omnipresence of iron and by its role as a fundamental component of a number of crucial metallo proteins. The response to modifications in the amount of the free-iron pool is performed via the inhibition of ferritin translation by sequestering consensus messenger RNA (mRNA) sequences. In turn, this is regulated by the iron-sensitive conformational equilibrium between cytosolic aconitase and IRP1, mediated by the presence of an iron-sulfur cluster. In this contribution, we analyze by full-atom molecular dynamics simulation, the factors leading to both the interaction with mRNA and the conformational transition. Furthermore, the role of the iron-sulfur cluster in driving the conformational transition is assessed by obtaining the related free energy profile via enhanced sampling molecular dynamics simulations.


Subject(s)
Aconitate Hydratase/metabolism , Cytosol/enzymology , Ferritins/metabolism , Hemostasis , Iron-Regulatory Proteins/metabolism , Iron/metabolism , Protein Biosynthesis , Aconitate Hydratase/chemistry , Animals , Chickens , Humans , Iron-Regulatory Proteins/chemistry , Molecular Dynamics Simulation , RNA, Messenger/genetics , RNA, Messenger/metabolism , Thermodynamics , Time Factors
4.
Commun Biol ; 4(1): 687, 2021 06 07.
Article in English | MEDLINE | ID: mdl-34099860

ABSTRACT

Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.


Subject(s)
Aconitate Hydratase/chemistry , Agrobacterium tumefaciens/enzymology , Thermococcus/enzymology , Agrobacterium tumefaciens/chemistry , Catalytic Domain , Crystallography, X-Ray , Evolution, Molecular , Models, Molecular , Protein Conformation , Thermococcus/chemistry
5.
Mol Cell Proteomics ; 19(11): 1860-1875, 2020 11.
Article in English | MEDLINE | ID: mdl-32839225

ABSTRACT

After ejaculation, mammalian spermatozoa must undergo a process known as capacitation in order to successfully fertilize the oocyte. Several post-translational modifications occur during capacitation, including sialylation, which despite being limited to a few proteins, seems to be essential for proper sperm-oocyte interaction. Regardless of its importance, to date, no single study has ever identified nor quantified which glycoproteins bearing terminal sialic acid (Sia) are altered during capacitation. Here we characterize sialylation during mouse sperm capacitation. Using tandem MS coupled with liquid chromatography (LC-MS/MS), we found 142 nonreductant peptides, with 9 of them showing potential modifications on their sialylated oligosaccharides during capacitation. As such, N-linked sialoglycopeptides from C4b-binding protein, endothelial lipase (EL), serine proteases 39 and 52, testis-expressed protein 101 and zonadhesin were reduced following capacitation. In contrast, mitochondrial aconitate hydratase (aconitase; ACO2), a TCA cycle enzyme, was the only protein to show an increase in Sia content during capacitation. Interestingly, although the loss of Sia within EL (N62) was accompanied by a reduction in its phospholipase A1 activity, a decrease in the activity of ACO2 (i.e. stereospecific isomerization of citrate to isocitrate) occurred when sialylation increased (N612). The latter was confirmed by N612D recombinant protein tagged with both His and GFP. The replacement of Sia for the negatively charged Aspartic acid in the N612D mutant caused complete loss of aconitase activity compared with the WT. Computer modeling show that N612 sits atop the catalytic site of ACO2. The introduction of Sia causes a large conformational change in the alpha helix, essentially, distorting the active site, leading to complete loss of function. These findings suggest that the switch from oxidative phosphorylation, over to glycolysis that occurs during capacitation may come about through sialylation of ACO2.


Subject(s)
Aconitate Hydratase/antagonists & inhibitors , Asparagine/metabolism , Glycolysis , N-Acetylneuraminic Acid/metabolism , Oxidative Phosphorylation , Sperm Capacitation , Spermatozoa/metabolism , Aconitate Hydratase/chemistry , Acrosome/enzymology , Acrosome/metabolism , Animals , Chromatography, Liquid , Glycoproteins/metabolism , HEK293 Cells , Humans , Immunohistochemistry , Lipase/metabolism , Male , Mice , Molecular Docking Simulation , N-Acetylneuraminic Acid/chemistry , Protein Processing, Post-Translational , Spermatozoa/enzymology , Tandem Mass Spectrometry
6.
Biochimie ; 170: 65-72, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31862235

ABSTRACT

We propose a new model for prochirality that satisfies all known examples: the prochiral plane. This plane contains the prochiral carbon and defines two separate faces for chemical modification. We extend this to enzyme catalysis, replacing the "three point attachment" hypothesis and its variants. Once a prochiral substrate is fixed on an enzyme surface, the asymmetry of the enzyme provides reactants exclusively on one side of the prochiral plane, producing an enantiomerically pure chiral product. The aconitase reaction is detailed as an example, using molecular modeling and its known enzymatic mechanism. We show that the prochiral substrate for this enzyme is not citrate, but rather cis-aconitate. The number of interaction points of cis-aconitate is not relevant to prochirality, but rather to substrate specificity. A second detailed example is the enzyme fumarase; here the substrate fumarate has only two binding sites, but is nonetheless fixed onto the enzyme and has a defined prochiral plane. We also provide a literature survey of more prochiral substrates, all of which have sp2 hybridized carbon and contain a prochiral plane. An example of a prochiral unnatural substrate for sphingosine kinase 2, fingolimod, has an sp3 hybridized prochiral carbon and also contains a prochiral plane. Finally, we provide an intuitive example of a prochiral physical object, a coffee cup, interacting with one hand and lip.


Subject(s)
Aconitate Hydratase/chemistry , Aconitate Hydratase/metabolism , Aconitic Acid/metabolism , Citrates/metabolism , Fumarate Hydratase/chemistry , Fumarate Hydratase/metabolism , Mycobacterium tuberculosis/enzymology , Binding Sites , Catalysis , Models, Molecular , Stereoisomerism , Substrate Specificity
7.
Inorg Chem ; 58(20): 13686-13695, 2019 Oct 21.
Article in English | MEDLINE | ID: mdl-31436962

ABSTRACT

Iron-sulfur (Fe-S) clusters are common prosthetic groups that are found within a variety of proteins responsible for functions that include electron transfer, regulation of gene expression, and substrate binding and activation. Acquisition of a [4Fe-4S] cluster is essential for the functionality of many such roles, and dysfunctions in Fe-S cluster synthesis and trafficking often result in human disease, such as multiple mitochondrial dysfunctions syndrome. While the topic of [2Fe-2S] cluster biosynthesis and trafficking has been relatively well studied, the understanding of such processes involving [4Fe-4S] centers is less developed. Herein, we focus on the mechanism of the assembly of [4Fe-4S] clusters on two members of the aconitase family, differing also in organelle placement (mitochondrion and cytosol) and biochemical function. Two mechanistic models are evaluated by a combination of kinetic and spectroscopic models, namely, a consecutive model (I), in which two [2Fe-2S] clusters are sequentially delivered to the target, and a prereaction equilibrium model (II), in which a [4Fe-4S] cluster transiently forms on a donor protein before transfer to the target. The paper also addresses the issue of cluster nuclearity for functionally active forms of ISCU, NFU, and ISCA trafficking proteins, each of which has been postulated to exist in both [2Fe-2S] and [4Fe-4S] bound states. By the application of kinetic assays and electron paramagnetic resonance spectroscopy to examine delivery pathways from a variety of potential [2Fe-2S] donor proteins to eukaryotic forms of both aconitase and iron regulatory protein, we conclude that a consecutive model following the delivery of [2Fe-2S] clusters from NFU1 is the most likely mechanism for these target proteins.


Subject(s)
Aconitate Hydratase/metabolism , Cytosol/metabolism , Eukaryota/metabolism , Iron-Sulfur Proteins/metabolism , Mitochondria/metabolism , Aconitate Hydratase/chemistry , Cytosol/chemistry , Electron Spin Resonance Spectroscopy , Eukaryota/chemistry , Humans , Iron-Sulfur Proteins/chemistry , Kinetics , Mitochondria/chemistry
8.
Acc Chem Res ; 52(9): 2609-2619, 2019 09 17.
Article in English | MEDLINE | ID: mdl-31287291

ABSTRACT

Mammalian aconitases (mitochondrial and cytosolic isoenzymes) are unique iron-sulfur cluster-containing proteins in which the metallic center participates in the catalysis of a non-redox reaction. Within the cubane iron-sulfur cluster of aconitases only three of the four iron ions have cysteine thiolate ligands; the fourth iron ion (Feα) is solvent exposed within the active-site pocket and bound to oxygen atoms from either water or substrates to be dehydrated. The catalyzed reaction is the reversible isomerization of citrate to isocitrate with an intermediate metabolite, cis-aconitate. The cytosolic isoform of aconitase is a moonlighting enzyme; when intracellular iron is scarce, the complete disassembly of the iron-sulfur cluster occurs and apo-aconitase acquires the function of an iron responsive protein and regulates the translation of proteins involved in iron metabolism. In the late 1980s and during the 1990s, cumulative experimental evidence pointed out that aconitases are main targets of reactive oxygen and nitrogen species such as superoxide radical (O2•-), hydrogen peroxide (H2O2), nitric oxide (•NO), and peroxynitrite (ONOO-). These intermediates are capable of oxidizing the cluster, which leads to iron release and consequent loss of the catalytic activity of aconitase. As the reaction of the Fe-S cluster with O2•- is fast (∼107 M-1 s-1), quite specific, and reversible in vivo, quantification of active aconitase has been used to evaluate O2•- formation in cells. While •NO is modestly reactive with aconitase, its reaction with O2•- yields ONOO-, a strong oxidant that readily leads to the disruption of the Fe-S cluster. In the case of cytosolic aconitase, it has been seen that H2O2 and •NO promote activation of iron responsive protein activity in cells. Proteomic advances in the 2000s confirmed that aconitases are main targets of reactive species in cellular models and in vivo, and other post-translational oxidative modifications such as protein nitration and carbonylation have been detected. Herein, we (1) outline the particular structural features of aconitase that make these proteins specific targets of reactive species, (2) characterize the reactions of O2•-, H2O2, •NO, and ONOO- and related species with aconitases, (3) discuss how different oxidative post-translational modifications of aconitase impact the different functions of aconitases, and (4) argue how these proteins might function as redox sensors within different cellular compartments, regulating citrate concentration and efflux from mitochondria, iron availability in the cytosol, and cellular oxidant production.


Subject(s)
Aconitate Hydratase/metabolism , Hydrogen Peroxide/metabolism , Nitric Oxide/metabolism , Peroxynitrous Acid/metabolism , Superoxides/metabolism , Aconitate Hydratase/chemistry , Animals , Humans , Hydrogen Peroxide/chemistry , Mitochondria/enzymology , Models, Molecular , Nitric Oxide/chemistry , Peroxynitrous Acid/chemistry , Superoxides/chemistry
9.
Methods Mol Biol ; 1978: 355-368, 2019.
Article in English | MEDLINE | ID: mdl-31119674

ABSTRACT

Spectrophotometric analysis of metabolic enzyme activity from homogenized tissues is a valuable method for investigating mitochondrial content and capacity. Enzyme activity is normally measured in single cuvette spectrophotometers, requiring a large sample volume and low throughput. Here, we describe microplate assays for high-throughput analysis of mitochondrial enzymes citrate synthase, ß-hydroxyacyl CoA dehydrogenase, aconitase, and mitochondrial electron transport system (ETS) complexes I, II, III, and IV.


Subject(s)
Electron Transport Complex I/chemistry , Enzymes/chemistry , Mitochondria/enzymology , Spectrophotometry/methods , Aconitate Hydratase/chemistry , Electron Transport/genetics , Enzymes/metabolism , Mitochondria/chemistry
10.
Biotechnol Prog ; 35(3): e2799, 2019 05.
Article in English | MEDLINE | ID: mdl-30828994

ABSTRACT

Itaconic acid, which is a promising organic acid in synthetic polymers and some base-material production, has been produced by Aspergillus terreus fermentation at a high cost. The recombinant Escherichia coli that contained the cadA gene from A. terreus can produce itaconic acid but with low yield. By introducing the protein-protein scaffold between citrate synthesis, aconitase, and cis-aconitase decarboxylase, 5.7 g/L of itaconic acid was produced, which is 3.8-fold higher than that obtained with the strain without scaffold. The optimum pH and temperature for itaconic acid production were 8.5 and 30°C, respectively. When the competing metabolic network was inactivated by knock-out mutation, the itaconic acid concentration further increased, to 6.57 g/L.


Subject(s)
Aconitate Hydratase/genetics , Carboxy-Lyases/genetics , Citrate (si)-Synthase/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Fungal Proteins/genetics , Succinates/metabolism , Aconitate Hydratase/chemistry , Aconitate Hydratase/metabolism , Aspergillus niger/enzymology , Carboxy-Lyases/chemistry , Carboxy-Lyases/metabolism , Citrate (si)-Synthase/chemistry , Citrate (si)-Synthase/metabolism , Cloning, Molecular , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Metabolic Engineering
11.
PLoS One ; 12(11): e0188130, 2017.
Article in English | MEDLINE | ID: mdl-29145506

ABSTRACT

The 2-methylcitric acid cycle (2-MCC) is a common route of propionate catabolism in microorganisms. In Salmonella enterica, the prpBCDE operon encodes most of the 2-MCC enzymes. In other organisms, e.g., Shewanella oneidensis MR-1, two genes, acnD and prpF replace prpD, which encodes 2-methylcitrate dehydratase. We showed that together, S. oneidensis AcnD and PrpF (SoAcnD, SoPrpF) compensated for the absence of PrpD in a S. enterica prpD strain. We also showed that SoAcnD had 2-methylcitrate dehydratase activity and that PrpF has aconitate isomerase activity. Here we report in vitro evidence that the product of the SoAcnD reaction is an isomer of 2-methyl-cis-aconitate (2-MCA], the product of the SePrpD reaction. We show that the SoPrpF protein isomerizes the product of the AcnD reaction into the PrpD product (2-MCA], a known substrate of the housekeeping aconitase (AcnB]. Given that SoPrpF is an isomerase, that SoAcnD is a dehydratase, and the results from in vivo and in vitro experiments reported here, it is likely that 4-methylaconitate is the product of the AcnD enzyme. Results from in vivo studies using a S. enterica prpD strain show that SoPrpF variants with substitutions of residues K73 or C107 failed to support growth with propionate as the sole source of carbon and energy. High-resolution (1.22 Å) three-dimensional crystal structures of PrpFK73E in complex with trans-aconitate or malonate provide insights into the mechanism of catalysis of the wild-type protein.


Subject(s)
Aconitate Hydratase/metabolism , Bacterial Proteins/metabolism , Citrates/metabolism , Shewanella/metabolism , Aconitate Hydratase/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/classification , Catalysis , Crystallography, X-Ray , Genes, Bacterial , Isomerism , Mutagenesis, Site-Directed , Phylogeny , Protein Conformation , Shewanella/genetics
12.
Methods Enzymol ; 595: 83-106, 2017.
Article in English | MEDLINE | ID: mdl-28882209

ABSTRACT

MitoNEET is the first identified Fe-S protein anchored to mammalian outer mitochondrial membranes with the vast majority of the protein polypeptide located in the cytosol, including its [2Fe-2S] cluster-binding domain. The coordination of the cluster is unusual and involves three cysteines and one histidine. MitoNEET is capable of transferring its redox-active Fe-S cluster to a bacterial apo-ferredoxin in vitro even under aerobic conditions, unlike other Fe-S transfer proteins such as ISCU. This specificity suggests its possible involvement in Fe-S repair after oxidative and/or nitrosative stress. Recently, we identified cytosolic aconitase/iron regulatory protein 1 (IRP1) as the first physiological protein acceptor of the mitoNEET Fe-S cluster in an Fe-S repair process. This chapter describes methods to study in vitro mitoNEET Fe-S cluster transfer/repair to a bacterial ferredoxin used as a model aporeceptor and in a more comprehensive manner to cytosolic aconitase/IRP1 after a nitrosative stress using in vitro, in cellulo, and in vivo methods.


Subject(s)
Aconitate Hydratase/metabolism , Iron Regulatory Protein 1/metabolism , Iron-Sulfur Proteins/metabolism , Iron/metabolism , Mitochondrial Proteins/metabolism , Aconitate Hydratase/chemistry , Animals , Cysteine/metabolism , Cytosol/enzymology , Escherichia coli , Ferredoxins/metabolism , Histidine/metabolism , Humans , Iron/chemistry , Iron Regulatory Protein 1/chemistry , Iron-Sulfur Proteins/chemistry , Mitochondrial Membranes/metabolism , Nitrosative Stress , Oxidation-Reduction
13.
Biotechnol Bioeng ; 114(2): 457-462, 2017 02.
Article in English | MEDLINE | ID: mdl-27543843

ABSTRACT

Here, we described a novel strategy for the production of itaconic acid in Escherichia coli by self-assembly of aconitase (ACO) and cis-aconitate decarboxylase (CAD) existing in the metabolic pathway of itaconic acid via the protein-peptide interactions of PDZ domain and PDZ ligand. Co-expression of ACO and CAD in E. coli (uCA) resulted in low levels of itaconate (117.25 mg/L) after 48 h fermentation while the itaconate titre was significantly improved up to 222.15 mg/L by self-assembly of ACO-PDZ (APd) and CAD-PDZlig (CPl) in E. coli (sPP) under the same conditions. To further confirm the effect of self-assembly, the itaconate catalyzed from sodium citrate was determined. The sPP was extra efficacious in the early catalytic period, showing approximately threefold itaconate yields increased after 2 h catalysis, when compared to uCA. Furthermore, the itaconate production of sPP was increased from 5 to 8.7 g/L after 30 h of reaction compared to uCA. This self-assembly strategy showed remarkable potential for the further improvement of itaconate production. Biotechnol. Bioeng. 2017;114: 457-462. © 2016 Wiley Periodicals, Inc.


Subject(s)
Aconitate Hydratase/metabolism , Carboxy-Lyases/metabolism , Escherichia coli/genetics , Metabolic Engineering/methods , Succinates/metabolism , Aconitate Hydratase/chemistry , Aconitate Hydratase/genetics , Aspergillus/enzymology , Aspergillus/genetics , Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , Escherichia coli/metabolism , Fermentation , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/metabolism , Protein Multimerization , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Succinates/analysis
14.
Methods Mol Biol ; 1511: 83-96, 2017.
Article in English | MEDLINE | ID: mdl-27730604

ABSTRACT

Mitochondria are the sites of a diverse set of essential biochemical processes in plants. In order to facilitate the analysis of these functions, this chapter presents protocols for the isolation of intact mitochondria from a range of plant tissues as well two workflows for fractionation into their four subcompartments; the inner and outer membranes and the two aqueous compartments, the inter membrane space and matrix. Protocols for the assessment of mitochondrial integrity and purity through enzymatic function and suggestions of commercially available compartment marker antibodies are provided.


Subject(s)
Arabidopsis Proteins/chemistry , Arabidopsis/chemistry , Cell Fractionation/methods , Intracellular Membranes/chemistry , Mitochondria/chemistry , Peroxisomes/chemistry , Protoplasts/chemistry , Aconitate Hydratase/chemistry , Biomarkers/chemistry , Catalase/chemistry , Cell Fractionation/instrumentation , Centrifugation, Density Gradient/instrumentation , Centrifugation, Density Gradient/methods , Culture Media/chemistry , Enzyme Assays , Fumarate Hydratase/chemistry , Intracellular Membranes/ultrastructure , Kinetics , Mitochondria/ultrastructure , Peroxisomes/ultrastructure , Phosphotransferases (Alcohol Group Acceptor)/chemistry , Povidone/chemistry , Protoplasts/ultrastructure , Silicon Dioxide/chemistry
15.
Sci Rep ; 6: 38720, 2016 12 08.
Article in English | MEDLINE | ID: mdl-27929065

ABSTRACT

In the aconitase superfamily, which includes the archetypical aconitase, homoaconitase, and isopropylmalate isomerase, only aconitase X is not functionally annotated. The corresponding gene (LhpI) was often located within the bacterial gene cluster involved in L-hydroxyproline metabolism. Screening of a library of (hydroxy)proline analogues revealed that this protein catalyzes the dehydration of cis-3-hydroxy-L-proline to Δ1-pyrroline-2-carboxylate. Furthermore, electron paramagnetic resonance and site-directed mutagenic analyses suggests the presence of a mononuclear Fe(III) center, which may be coordinated with one glutamate and two cysteine residues. These properties were significantly different from those of other aconitase members, which catalyze the isomerization of α- to ß-hydroxy acids, and have a [4Fe-4S] cluster-binding site composed of three cysteine residues. Bacteria with the LhpI gene could degrade cis-3-hydroxy-L-proline as the sole carbon source, and LhpI transcription was up-regulated not only by cis-3-hydroxy-L-proline, but also by several isomeric 3- and 4-hydroxyprolines.


Subject(s)
Aconitate Hydratase/chemistry , Bacteria/enzymology , Hydro-Lyases/chemistry , Iron-Sulfur Proteins/chemistry , Aconitate Hydratase/genetics , Aconitate Hydratase/metabolism , Bacteria/genetics , Catalytic Domain , Hydro-Lyases/genetics , Hydro-Lyases/metabolism , Hydroxyproline/chemistry , Hydroxyproline/genetics , Hydroxyproline/metabolism , Iron-Sulfur Proteins/genetics , Iron-Sulfur Proteins/metabolism
16.
ACS Chem Biol ; 11(10): 2847-2853, 2016 10 21.
Article in English | MEDLINE | ID: mdl-27556423

ABSTRACT

Supramolecular assembly of enzymes into metabolon structures is thought to enable efficient transport of reactants between active sites via substrate channeling. Recombinant versions of porcine citrate synthase (CS), mitochondrial malate dehydrogenase (mMDH), and aconitase (Aco) were found to adopt a homogeneous native-like metabolon structure in vitro. Site-directed mutagenesis performed on highly conserved arginine residues located in the positively charged channel connecting mMDH and CS active sites led to the identification of CS(R65A) which retained high catalytic efficiency. Substrate channeling between the CS mutant and mMDH was severely impaired and the overall channeling probability decreased from 0.99 to 0.023. This work provides direct mechanistic evidence for the channeling of reaction intermediates, and disruption of this interaction would have important implications on the control of flux in central carbon metabolism.


Subject(s)
Aconitate Hydratase/metabolism , Citrate (si)-Synthase/metabolism , Citric Acid Cycle , Malate Dehydrogenase/metabolism , Aconitate Hydratase/chemistry , Arginine/genetics , Catalysis , Citrate (si)-Synthase/chemistry , Citrate (si)-Synthase/genetics , Kinetics , Malate Dehydrogenase/chemistry , Malate Dehydrogenase/genetics , Mutagenesis, Site-Directed , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Static Electricity , Substrate Specificity
17.
J Biol Inorg Chem ; 21(3): 305-17, 2016 06.
Article in English | MEDLINE | ID: mdl-26837749

ABSTRACT

Smokers have an elevated risk of cardiovascular disease, but the origin(s) of this increased risk are incompletely defined. Evidence supports an accumulation of the oxidant-generating enzyme myeloperoxidase (MPO) in the inflamed artery wall, and smokers have high levels of SCN(-), a preferred MPO substrate, with this resulting in HOSCN formation. We hypothesised that HOSCN, a thiol-specific oxidant may target the iron-sulphur cluster of aconitase (both isolated, and within primary human coronary artery endothelial cells; HCAEC) resulting in enzyme dysfunction, release of iron, and conversion of the cytosolic isoform to iron response protein-1, which regulates intracellular iron levels. We show that exposure of isolated aconitase to increasing concentrations of HOSCN releases iron from the aconitase [Fe-S]4 cluster, and decreases enzyme activity. This is associated with protein thiol loss and modification of specific Cys residues in, and around, the [Fe-S]4 cluster. Exposure of HCAEC to HOSCN resulted in increased intracellular levels of chelatable iron, loss of aconitase activity and increased iron response protein-1 (IRP-1) activity. These data indicate HOSCN, an oxidant associated with oxidative stress in smokers, can induce aconitase dysfunction in human endothelial cells via Cys oxidation, damage to the [Fe-S]4 cluster, iron release and generation of IRP-1 activity, which modulates ferritin protein levels and results in dysregulation of iron metabolism. These data may rationalise, in part, the presence of increased levels of iron in human atherosclerotic lesions and contribute to increased oxidative damage and endothelial cell dysfunction in smokers. Similar reactions may occur at other sites of inflammation.


Subject(s)
Aconitate Hydratase/metabolism , Iron Deficiencies , Iron-Regulatory Proteins/metabolism , Oxidants/metabolism , Smoking/metabolism , Aconitate Hydratase/chemistry , Cells, Cultured , Coronary Vessels/cytology , Coronary Vessels/drug effects , Coronary Vessels/metabolism , Dose-Response Relationship, Drug , Endothelial Cells/drug effects , Endothelial Cells/metabolism , Humans , Hypochlorous Acid/pharmacology , Iron/metabolism , Oxidants/chemistry , Structure-Activity Relationship , Thiocyanates/pharmacology
18.
Molecules ; 20(7): 12599-622, 2015 Jul 10.
Article in English | MEDLINE | ID: mdl-26184143

ABSTRACT

Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spectra are fitted simultaneously. Our approach, which we name co-fitting, leads to a more reliable modelling of the experimental data because it uses more spectral information than the standard approach of fitting only the absorption spectrum. It also avoids that the fitting routine becomes trapped in local minima. We have tested the proposed approach using infrared absorption spectra of three mixed α/ß proteins with different degrees of spectral overlap in the amide I region: ribonuclease A, pyruvate kinase, and aconitase.


Subject(s)
Aconitate Hydratase/chemistry , Pyruvate Kinase/chemistry , Ribonuclease, Pancreatic/chemistry , Spectroscopy, Fourier Transform Infrared/statistics & numerical data , Aconitate Hydratase/isolation & purification , Animals , Buffers , Cattle , Muscle, Skeletal/chemistry , Muscle, Skeletal/enzymology , Myocardium/chemistry , Myocardium/enzymology , Pancreas/chemistry , Pancreas/enzymology , Protein Structure, Secondary , Pyruvate Kinase/isolation & purification , Rabbits , Ribonuclease, Pancreatic/isolation & purification , Solutions , Swine
19.
Biochemistry ; 54(25): 4008-18, 2015 Jun 30.
Article in English | MEDLINE | ID: mdl-26061789

ABSTRACT

High-throughput proteomics studies have identified several thousand acetylation sites on more than 1000 proteins. Mitochondrial aconitase, the Krebs cycle enzyme that converts citrate to isocitrate, has been identified in many of these reports. Acetylated mitochondrial aconitase has also been identified as a target for sirtuin 3 (SIRT3)-catalyzed deacetylation. However, the functional significance of mitochondrial aconitase acetylation has not been determined. Using in vitro strategies, mass spectrometric analyses, and an in vivo mouse model of obesity, we found a significant acetylation-dependent activation of aconitase. Isolated heart mitochondria subjected to in vitro chemical acetylation with either acetic anhydride or acetyl-coenzyme A resulted in increased aconitase activity that was reversed with SIRT3 treatment. Quantitative mass spectrometry was used to measure acetylation at 21 lysine residues and revealed significant increases with both in vitro treatments. A high-fat diet (60% of kilocalories from fat) was used as an in vivo model and also showed significantly increased mitochondrial aconitase activity without changes in protein level. The high-fat diet also produced an increased level of aconitase acetylation at multiple sites as measured by the quantitative mass spectrometry assays. Treatment of isolated mitochondria from these mice with SIRT3 abolished the high-fat diet-induced activation of aconitase and reduced acetylation. Finally, kinetic analyses found that the increase in activity was a result of increased maximal velocity, and molecular modeling suggests the potential for acetylation at K144 to perturb the tertiary structure of the enzyme. The results of this study reveal a novel activation of mitochondrial aconitase by acetylation.


Subject(s)
Aconitate Hydratase/metabolism , Lysine/metabolism , Mitochondria/enzymology , Myocardium/enzymology , Acetylation , Aconitate Hydratase/chemistry , Aconitate Hydratase/genetics , Amino Acid Motifs , Animals , Lysine/chemistry , Male , Mass Spectrometry , Mice , Mice, Inbred C57BL , Mitochondria/chemistry , Myocardium/chemistry , Myocardium/metabolism , Sirtuin 3/genetics , Sirtuin 3/metabolism
20.
Bioresour Technol ; 182: 368-372, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25708541

ABSTRACT

Thermochemical processes developed for carbon capture and storage (CCS) offer high carbon capture capacities, but are generally hampered by low energy efficiency. Reversible cascade enzyme reactions are examined in this work for energy-efficient carbon sequestration. By integrating the reactions of two key enzymes of RTCA cycle, isocitrate dehydrogenase and aconitase, we demonstrate that intensified carbon capture can be realized through such cascade enzymatic reactions. Experiments show that enhanced thermodynamic driving force for carbon conversion can be attained via pH control under ambient conditions, and that the cascade reactions have the potential to capture 0.5 mol carbon at pH 6 for each mole of substrate applied. Overall it manifests that the carbon capture capacity of biocatalytic reactions, in addition to be energy efficient, can also be ultimately intensified to approach those realized with chemical absorbents such as MEA.


Subject(s)
Carbon Sequestration , Enzymes/chemistry , Thermodynamics , Aconitate Hydratase/chemistry , Aconitate Hydratase/metabolism , Biocatalysis , Carbon/chemistry , Carbon/metabolism , Hydrogen-Ion Concentration , Isocitrate Dehydrogenase/chemistry , Isocitrate Dehydrogenase/metabolism
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