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1.
Microbiol Spectr ; : e0415223, 2024 Jul 16.
Article in English | MEDLINE | ID: mdl-39012110

ABSTRACT

Staphylococcus aureus is an opportunistic pathogen that has emerged as a major public health threat due to the increased incidence of its drug resistance. S. aureus presents a remarkable capacity to adapt to different niches due to the plasticity of its energy metabolism. In this work, we investigated the energy metabolism of S. aureus, focusing on the alternative NADH:quinone oxidoreductases, NDH-2s. S. aureus presents two genes encoding NDH-2s (NDH-2A and NDH-2B) and lacks genes coding for Complex I, the canonical respiratory NADH:quinone oxidoreductase. This observation makes the action of NDH-2s crucial for the regeneration of NAD+ and, consequently, for the progression of metabolism. Our study involved the comprehensive biochemical characterization of NDH-2B and the exploration of the cellular roles of NDH-2A and NDH-2B, utilizing knockout mutants (Δndh-2a and Δndh-2b). We show that NDH-2B uses NADPH instead of NADH, does not establish a charge-transfer complex in the presence of NADPH, and its reduction by this substrate is the catalytic rate-limiting step. In the case of NDH-2B, the reduction of the flavin is inherently slow, and we suggest the establishment of a charge transfer complex between NADP+ and FADH2, as previously observed for NDH-2A, to slow down quinone reduction and, consequently, prevent the overproduction of reactive oxygen species, which is potentially unnecessary. Furthermore, we observed that the lack of NDH-2A or NDH-2B impacts cell growth, volume, and division differently. The absence of these enzymes results in distinct metabolic phenotypes, emphasizing the unique cellular roles of each NDH-2 in energy metabolism.IMPORTANCEStaphylococcus aureus is an opportunistic pathogen, posing a global challenge in clinical medicine due to the increased incidence of its drug resistance. For this reason, it is essential to explore and understand the mechanisms behind its resistance, as well as the fundamental biological features such as energy metabolism and the respective players that allow S. aureus to live and survive. Despite its prominence as a pathogen, the energy metabolism of S. aureus remains underexplored, with its respiratory enzymes often escaping thorough investigation. S. aureus bioenergetic plasticity is illustrated by its ability to use different respiratory enzymes, two of which are investigated in the present study. Understanding the metabolic adaptation strategies of S. aureus to bioenergetic challenges may pave the way for the design of therapeutic approaches that interfere with the ability of the pathogen to successfully adapt when it invades different niches within its host.

2.
Biochim Biophys Acta Bioenerg ; 1864(3): 148983, 2023 08 01.
Article in English | MEDLINE | ID: mdl-37127243

ABSTRACT

Rhodothermus marinus is a thermohalophilic organism that has optimized its microaerobic metabolism at 65 °C. We have been exploring its respiratory chain and observed the existence of a quinone:cytochrome c oxidoreductase complex, named Alternative Complex III, structurally different from the bc1 complex. In the present work, we took profit from nanodiscs and liposomes technology to investigate ACIII activity in membrane-mimicking systems. In addition, we studied the interaction of ACIII with menaquinone, its potential electron acceptors (HiPIP and cytochrome c) and the caa3 oxygen reductase.


Subject(s)
Cytochromes c , Electron Transport Complex III , Electron Transport , Oxidoreductases
3.
Biochim Biophys Acta Bioenerg ; 1864(2): 148958, 2023 04 01.
Article in English | MEDLINE | ID: mdl-36758662

ABSTRACT

Pyruvate:quinone oxidoreductases (PQOs) catalyse the oxidative decarboxylation of pyruvate to acetate and concomitant reduction of quinone to quinol with the release of CO2. They are thiamine pyrophosphate (TPP) and flavin-adenine dinucleotide (FAD) containing enzymes, which interact with the membrane in a monotopic way. PQOs are considered as part of alternatives to most recognized pyruvate catabolizing pathways, and little is known about their taxonomic distribution and structural/functional relationship. In this bioinformatics work we tackled these gaps in PQO knowledge. We used the KEGG database to identify PQO coding genes, performed a multiple sequence analysis which allowed us to study the amino acid conservation on these enzymes, and looked at their possible cellular function. We observed that PQOS are enzymes exclusively present in prokaryotes with most of the sequences identified in bacteria. Regarding the amino acid sequence conservation, we found that 75 amino acid residues (out of 570, on average) have a conservation over 90 %, and that the most conserved regions in the protein are observed around the TPP and FAD binding sites. We systematized the presence of conserved features involved in Mg2+, TPP and FAD binding, as well as residues directly linked to the catalytic mechanism. We also established the presence of a new motif named "HEH lock", possibly involved in the dimerization process. The results here obtained for the PQO protein family contribute to a better understanding of the biochemistry of these respiratory enzymes.


Subject(s)
Pyruvic Acid , Quinone Reductases , Amino Acid Sequence , Flavin-Adenine Dinucleotide/metabolism , Proteins , Quinone Reductases/metabolism , Amino Acids , NAD(P)H Dehydrogenase (Quinone)/metabolism , Quinones
4.
Biochim Biophys Acta Bioenerg ; 1864(2): 148948, 2023 04 01.
Article in English | MEDLINE | ID: mdl-36481274

ABSTRACT

Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.


Subject(s)
Quinones , Staphylococcus aureus , Atovaquone , Electron Transport , Quinones/metabolism , Staphylococcus aureus/genetics , Staphylococcus aureus/metabolism , Quinone Reductases/metabolism
5.
Biochem Soc Trans ; 49(6): 2669-2685, 2021 12 17.
Article in English | MEDLINE | ID: mdl-34854900

ABSTRACT

Energy transduction is the conversion of one form of energy into another; this makes life possible as we know it. Organisms have developed different systems for acquiring energy and storing it in useable forms: the so-called energy currencies. A universal energy currency is the transmembrane difference of electrochemical potential (Δµ~). This results from the translocation of charges across a membrane, powered by exergonic reactions. Different reactions may be coupled to charge-translocation and, in the majority of cases, these reactions are catalyzed by modular enzymes that always include a transmembrane subunit. The modular arrangement of these enzymes allows for different catalytic and charge-translocating modules to be combined. Thus, a transmembrane charge-translocating module can be associated with different catalytic subunits to form an energy-transducing complex. Likewise, the same catalytic subunit may be combined with a different membrane charge-translocating module. In this work, we analyze the modular arrangement of energy-transducing membrane complexes and discuss their different combinations, focusing on the charge-translocating module.


Subject(s)
Cell Membrane/chemistry , Membrane Proteins/chemistry , Catalytic Domain
6.
Front Chem ; 9: 663706, 2021.
Article in English | MEDLINE | ID: mdl-33928068

ABSTRACT

Several energy-transducing microbial enzymes have their peripheral subunits connected to the membrane through an integral membrane protein, that interacts with quinones but does not have redox cofactors, the so-called NrfD-like subunit. The periplasmic nitrite reductase (NrfABCD) was the first complex recognized to have a membrane subunit with these characteristics and consequently provided the family's name: NrfD. Sequence analyses indicate that NrfD homologs are present in many diverse enzymes, such as polysulfide reductase (PsrABC), respiratory alternative complex III (ACIII), dimethyl sulfoxide (DMSO) reductase (DmsABC), tetrathionate reductase (TtrABC), sulfur reductase complex (SreABC), sulfite dehydrogenase (SoeABC), quinone reductase complex (QrcABCD), nine-heme cytochrome complex (NhcABCD), group-2 [NiFe] hydrogenase (Hyd-2), dissimilatory sulfite-reductase complex (DsrMKJOP), arsenate reductase (ArrC) and multiheme cytochrome c sulfite reductase (MccACD). The molecular structure of ACIII subunit C (ActC) and Psr subunit C (PsrC), NrfD-like subunits, revealed the existence of ion-conducting pathways. We performed thorough primary structural analyses and built structural models of the NrfD-like subunits. We observed that all these subunits are constituted by two structural repeats composed of four-helix bundles, possibly harboring ion-conducting pathways and containing a quinone/quinol binding site. NrfD-like subunits may be the ion-pumping module of several enzymes. Our data impact on the discussion of functional implications of the NrfD-like subunit-containing complexes, namely in their ability to transduce energy.

7.
J Chem Inf Model ; 61(1): 335-346, 2021 01 25.
Article in English | MEDLINE | ID: mdl-33400529

ABSTRACT

Nucleotides are structural units relevant not only in nucleic acids but also as substrates or cofactors in key biochemical reactions. The size- and timescales of such nucleotide-protein interactions fall well within the scope of coarse-grained molecular dynamics, which holds promise of important mechanistic insight. However, the lack of specific parameters has prevented accurate coarse-grained simulations of protein interactions with most nucleotide compounds. In this work, we comprehensively develop coarse-grained parameters for key metabolites/cofactors (FAD, FMN, riboflavin, NAD, NADP, ATP, ADP, AMP, and thiamine pyrophosphate) in different oxidation and protonation states as well as for smaller molecules derived from them (among others, nicotinamide, adenosine, adenine, ribose, thiamine, and lumiflavin), summing up a total of 79 different molecules. In line with the Martini parameterization methodology, parameters were tuned to reproduce octanol-water partition coefficients. Given the lack of existing data, we set out to experimentally determine these partition coefficients, developing two methodological approaches, based on 31P-NMR and fluorescence spectroscopy, specifically tailored to the strong hydrophilicity of most of the parameterized compounds. To distinguish the partition of each relevant protonation species, we further potentiometrically characterized the protonation constants of key molecules. This work successfully builds a comprehensive and relevant set of computational models that will boost the biochemical application of coarse-grained simulations. It does so based on the measurement of partition and acid-base physicochemical data that, in turn, covers important gaps in nucleotide characterization.


Subject(s)
Molecular Dynamics Simulation , Nucleotides , Hydrophobic and Hydrophilic Interactions , Octanols , Water
8.
Chem Rev ; 121(3): 1804-1844, 2021 02 10.
Article in English | MEDLINE | ID: mdl-33398986

ABSTRACT

Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (ΔµÌƒ). Membrane proteins contribute to the establishment of ΔµÌƒ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.


Subject(s)
Membrane Proteins/metabolism , Thermodynamics , Electrochemical Techniques , Electron Transport , Membrane Proteins/chemistry
9.
Biochim Biophys Acta Bioenerg ; 1862(1): 148321, 2021 01 01.
Article in English | MEDLINE | ID: mdl-32991846

ABSTRACT

Dihydroorotate:quinone oxidoreductases (DHOQOs) are membrane bound enzymes responsible for oxidizing dihydroorotate (DHO) to orotate with concomitant reduction of quinone to quinol. They have FMN as prosthetic group and are part of the monotopic quinone reductase superfamily. These enzymes are also members of the dihydroorotate dehydrogenases (DHODHs) family, which besides membrane bound DHOQOs, class 2, includes soluble enzymes which reduce either NAD+ or fumarate, class 1. As key enzymes in both the de novo pyrimidine biosynthetic pathway as well as in the energetic metabolism, inhibitors of DHOQOs have been investigated as leads for therapeutics in cancer, immunological disorders and bacterial/viral infections. This work is a thorough bioinformatic approach on the structural conservation and taxonomic distribution of DHOQOs. We explored previously established structural/functional hallmarks of these enzymes, while searching for uncharacterized common elements. We also discuss the cellular role of DHOQOs and organize the identified protein sequences within six sub-classes 2A to 2F, according to their taxonomic origin and sequence traits. We concluded that DHOQOs are present in Archaea, Eukarya and Bacteria, including the first recognition in Gram-positive organisms. DHOQOs can be the single dihydroorotate dehydrogenase encoded in the genome of a species, or they can coexist with other DHODHs, as the NAD+ or fumarate reducing enzymes. Furthermore, we show that the type of catalytic base present in the active site is not an absolute criterium to distinguish between class 1 and class 2 enzymes. We propose the existence of a quinone binding motif ("ExAH") adjacent to a hydrophobic cavity present in the membrane interacting N-terminal domain.


Subject(s)
Escherichia coli Proteins , Escherichia coli/enzymology , Oxidoreductases Acting on CH-CH Group Donors , Dihydroorotate Dehydrogenase , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/classification , Oxidoreductases Acting on CH-CH Group Donors/chemistry , Oxidoreductases Acting on CH-CH Group Donors/classification , Structural Homology, Protein
10.
Adv Microb Physiol ; 74: 331-414, 2019.
Article in English | MEDLINE | ID: mdl-31126533

ABSTRACT

The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.


Subject(s)
Archaea/metabolism , Bacteria/metabolism , Cell Membrane/metabolism , Eukaryota/metabolism , Animals , Archaea/classification , Archaea/genetics , Bacteria/classification , Bacteria/genetics , Cell Membrane/enzymology , Cell Membrane/genetics , Electron Transport , Eukaryota/classification , Eukaryota/genetics , Membrane Proteins/genetics , Membrane Proteins/metabolism , Models, Biological , Oxidation-Reduction
11.
Nat Commun ; 9(1): 1728, 2018 04 30.
Article in English | MEDLINE | ID: mdl-29712914

ABSTRACT

Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may have alternative complexes performing the same catalytic reactions as the mitochondrial complexes. This is the case for the alternative complex III (ACIII), a quinol:cytochrome c/HiPIP oxidoreductase. In order to understand the catalytic mechanism of this respiratory enzyme, we determined the structure of ACIII from Rhodothermus marinus at 3.9 Å resolution by single-particle cryo-electron microscopy. ACIII presents a so-far unique structure, for which we establish the arrangement of the cofactors (four iron-sulfur clusters and six c-type hemes) and propose the location of the quinol-binding site and the presence of two putative proton pathways in the membrane. Altogether, this structure provides insights into a mechanism for energy transduction and introduces ACIII as a redox-driven proton pump.


Subject(s)
Bacterial Proteins/chemistry , Electron Transport Complex III/chemistry , Heme/chemistry , Hydroquinones/chemistry , Protein Subunits/chemistry , Protons , Rhodothermus/enzymology , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Cryoelectron Microscopy , Electron Transport/genetics , Electron Transport Complex III/genetics , Electron Transport Complex III/metabolism , Gene Expression , Heme/metabolism , Hydroquinones/metabolism , Kinetics , Models, Molecular , Oxidation-Reduction , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Subunits/genetics , Protein Subunits/metabolism , Rhodothermus/genetics , Thermodynamics
12.
Biochim Biophys Acta Bioenerg ; 1859(9): 742-753, 2018 09.
Article in English | MEDLINE | ID: mdl-29684324

ABSTRACT

Hydrogen sulfide (H2S) is a versatile molecule with different functions in living organisms: it can work as a metabolite of sulfur and energetic metabolism or as a signaling molecule in higher Eukaryotes. H2S is also highly toxic since it is able to inhibit heme cooper oxygen reductases, preventing oxidative phosphorylation. Due to the fact that it can both inhibit and feed the respiratory chain, the immediate role of H2S on energy metabolism crucially relies on its bioavailability, meaning that studying the central players involved in the H2S homeostasis is key for understanding sulfide metabolism. Two different enzymes with sulfide oxidation activity (sulfide dehydrogenases) are known: flavocytochrome c sulfide dehydrogenase (FCSD), a sulfide:cytochrome c oxidoreductase; and sulfide:quinone oxidoreductase (SQR). In this work we performed a thorough bioinformatic study of SQRs and FCSDs and integrated all published data. We systematized several properties of these proteins: (i) nature of flavin binding, (ii) capping loops and (iii) presence of key amino acid residues. We also propose an update to the SQR classification system and discuss the role of these proteins in sulfur metabolism.


Subject(s)
Cytochrome c Group/chemistry , Cytochrome c Group/classification , Flavin-Adenine Dinucleotide/metabolism , Oxidoreductases/chemistry , Oxidoreductases/classification , Quinone Reductases/chemistry , Quinone Reductases/classification , Sulfides/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/classification , Bacterial Proteins/metabolism , Biocatalysis , Cytochrome c Group/metabolism , Kinetics , Models, Molecular , Oxidation-Reduction , Oxidoreductases/metabolism , Protein Conformation , Quinone Reductases/metabolism , Structure-Activity Relationship
13.
Langmuir ; 34(20): 5703-5711, 2018 05 22.
Article in English | MEDLINE | ID: mdl-29553272

ABSTRACT

Respiratory complex I (CpI) is a key player in the way organisms obtain energy, being an energy transducer, which couples nicotinamide adenine dinucleotide (NADH)/quinone oxidoreduction with proton translocation by a mechanism that remains elusive so far. In this work, we monitored the function of CpI in a biomimetic, supported lipid membrane system assembled on a 4-aminothiophenol (4-ATP) self-assembled monolayer by surface-enhanced infrared absorption spectroscopy. 4-ATP serves not only as a linker molecule to a nanostructured gold surface but also as pH sensor, as indicated by concomitant density functional theory calculations. In this way, we were able to monitor NADH/quinone oxidoreduction-induced transmembrane proton translocation via the protonation state of 4-ATP, depending on the net orientation of CpI molecules induced by two complementary approaches. An associated change of the amide I/amide II band intensity ratio indicates conformational modifications upon catalysis which may involve movements of transmembrane helices or other secondary structural elements, as suggested in the literature [ Di Luca , Proc. Natl. Acad. Sci. U.S.A. , 2017 , 114 , E6314 - E6321 ].


Subject(s)
Electron Transport Complex I/metabolism , Protons , Spectrophotometry, Infrared , Catalysis , Electron Transport Complex I/chemistry , NAD/chemistry , Oxidation-Reduction
14.
Redox Biol ; 16: 209-214, 2018 06.
Article in English | MEDLINE | ID: mdl-29524843

ABSTRACT

Type-II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and the only enzymes with NADH:quinone oxidoreductase activity expressed in Staphylococcus aureus (S. aureus), one of the most common causes of clinical infections. NDH-2s are members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, having a flavin adenine dinucleotide, FAD, as prosthetic group and NAD(P)H as substrate. The establishment of a Charge-Transfer Complex (CTC) between the isoalloxazine ring of the reduced flavin and the nicotinamide ring of NAD+ in NDH-2 was described, and in this work we explored its role in the kinetic mechanism using different electron donors and electron acceptors. We observed that CTC slows down the rate of the second half reaction (quinone reduction) and determines the effect of HQNO, an inhibitor. Also, protonation equilibrium simulations clearly indicate that the protonation probability of an important residue for proton transfer to the active site (D302) is influenced by the presence of the CTC. We propose that CTC is critical for the overall mechanism of NDH-2 and possibly relevant to keep a low quinol/quinone ratio and avoid excessive ROS production in vivo.


Subject(s)
Electron Transport , NAD(P)H Dehydrogenase (Quinone)/chemistry , Reactive Oxygen Species/metabolism , Staphylococcus aureus/enzymology , Binding Sites , Catalytic Domain , Flavin-Adenine Dinucleotide/chemistry , Flavin-Adenine Dinucleotide/metabolism , Kinetics , NAD(P)H Dehydrogenase (Quinone)/metabolism , Quinones/chemistry , Quinones/metabolism , Reactive Oxygen Species/chemistry , Staphylococcus aureus/pathogenicity , Substrate Specificity
15.
Molecules ; 23(4)2018 Mar 27.
Article in English | MEDLINE | ID: mdl-29584709

ABSTRACT

There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from Leishmania infantum (LiNDH2) is an enzyme of the parasite's respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from Saccharomyces cerevisiae, two ubiquinone-binding sites (UQI and UQII) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of LiNDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the LiNDH2 ubiquinone-binding site 1-UQI. Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally similar recombinant NDH-2 from S. aureus and leishmanicidal activity was determined in the wild-type axenic amastigotes and promastigotes of L. infantum. The identified compound, a substituted 6-methoxy-quinalidine, showed promising nanomolar leishmanicidal activity on wild-type axenic promastigotes and amastigotes of L. infantum and the potential for further development.


Subject(s)
Antiprotozoal Agents/chemistry , Leishmania infantum/enzymology , NADH Dehydrogenase/metabolism , Quinaldines/chemistry , Antiprotozoal Agents/pharmacology , Catalytic Domain/drug effects , Computer Simulation , Drug Evaluation, Preclinical , Leishmania infantum/drug effects , Models, Molecular , NADH Dehydrogenase/chemistry , Protozoan Proteins/chemistry , Protozoan Proteins/metabolism , Quinaldines/pharmacology , Structural Homology, Protein , Structure-Activity Relationship
16.
Biochim Biophys Acta Bioenerg ; 1858(10): 823-832, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28801048

ABSTRACT

Type II NADH:quinone oxidoreductases (NDH-2s) are membrane bound enzymes that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones. In this way, these enzymes also contribute to the regeneration of NAD+, allowing several metabolic pathways to proceed. As for the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, the enzymatic mechanism of NDH-2s is still little explored and elusive. In this work we addressed the role of the conserved glutamate 172 (E172) residue in the enzymatic mechanism of NDH-2 from Staphylococcus aureus. We aimed to test our earlier hypothesis that E172 plays a key role in proton transfer to allow the protonation of the quinone. For this we performed a complete biochemical characterization of the enzyme's variants E172A, E172Q and E172S. Our steady state kinetic measurements show a clear decrease in the overall reaction rate, and our substrate interaction studies indicate the binding of the two substrates is also affected by these mutations. Interestingly our fast kinetic results show quinone reduction is more affected than NADH oxidation. We have also determined the X-ray crystal structure of the E172S mutant (2.55Ǻ) and compared it with the structure of the wild type (2.32Ǻ). Together these results support our hypothesis for E172 being of central importance in the catalytic mechanism of NDH-2, which may be extended to other members of the tDBDF superfamily.


Subject(s)
Bacterial Proteins/metabolism , Benzoquinones/metabolism , Glutamic Acid/metabolism , NADH Dehydrogenase/metabolism , NAD/metabolism , Quinone Reductases/metabolism , Staphylococcus aureus/metabolism , Oxidation-Reduction , Protein Binding/physiology
17.
Biol Chem ; 398(9): 1037-1044, 2017 08 28.
Article in English | MEDLINE | ID: mdl-28141544

ABSTRACT

Alternative Complex III (ACIII) is an example of the robustness and flexibility of prokaryotic respiratory chains. It performs quinol:cytochrome c oxidoreductase activity, being functionally equivalent to the bc1 complex but structurally unrelated. In this work we further explored ACIII investigating the role of its monoheme cytochrome c subunit (ActE). We expressed and characterized the individually isolated ActE, which allowed us to suggest that ActE is a lipoprotein and to show its function as a direct electron donor to the caa3 oxygen reductase.


Subject(s)
Cytochrome c Group/metabolism , Cytochromes a3/metabolism , Cytochromes a/metabolism , Electron Transport Complex III/chemistry , Electron Transport Complex III/metabolism , Oxidoreductases/metabolism , Protein Subunits/metabolism , Rhodothermus/enzymology , Electron Transport , Lipid Metabolism , Models, Molecular , Protein Conformation , Protein Subunits/chemistry
18.
Sci Rep ; 7: 42303, 2017 02 09.
Article in English | MEDLINE | ID: mdl-28181562

ABSTRACT

Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains. These proteins contribute indirectly to the establishment of the transmembrane difference of electrochemical potential by catalyzing the reduction of quinone by oxidation of NAD(P)H. NDH-2s are widespread enzymes being present in the three domains of life. In this work, we explored the catalytic mechanism of NDH-2 by investigating the common elements of all NDH-2s, based on the rationale that conservation of such elements reflects their structural/functional importance. We observed conserved sequence motifs and structural elements among 1762 NDH-2s. We identified two proton pathways possibly involved in the protonation of the quinone. Our results led us to propose the first catalytic mechanism for NDH-2 family, in which a conserved glutamate residue, E172 (in NDH-2 from Staphylococcus aureus) plays a key role in proton transfer to the quinone pocket. This catalytic mechanism may also be extended to the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, such as sulfide:quinone oxidoreductases.


Subject(s)
Biocatalysis , Quinone Reductases/chemistry , Quinone Reductases/metabolism , Amino Acids/chemistry , Conserved Sequence , Models, Molecular , Protein Domains , Protons , Saccharomyces cerevisiae/enzymology , Staphylococcus aureus/enzymology , Structure-Activity Relationship
19.
Biochim Biophys Acta ; 1857(8): 1039-1067, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27044012

ABSTRACT

Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.


Subject(s)
Archaea/metabolism , Archaeal Proteins/metabolism , Bacteria/metabolism , Bacterial Proteins/metabolism , Cell Membrane/metabolism , Electron Transport Chain Complex Proteins/metabolism , Archaea/genetics , Archaeal Proteins/genetics , Bacteria/genetics , Bacterial Proteins/genetics , Cell Membrane/chemistry , Electron Transport , Electron Transport Chain Complex Proteins/genetics , Mitochondrial Proton-Translocating ATPases/genetics , Mitochondrial Proton-Translocating ATPases/metabolism , Oxidation-Reduction , Oxidoreductases/genetics , Oxidoreductases/metabolism , Quinone Reductases/genetics , Quinone Reductases/metabolism , Quinones/metabolism
20.
Environ Microbiol ; 18(12): 4697-4709, 2016 12.
Article in English | MEDLINE | ID: mdl-27105286

ABSTRACT

Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins, crucial for the catabolic metabolism, because they contribute to the maintenance of the NADH/NAD+ balance. In several pathogenic bacteria and protists, NDH-2s are the only enzymes performing respiratory NADH:quinone oxidoreductase activity. For this reason and for being considered absent in mammals, NDH-2s were proposed as suitable targets for novel antimicrobial therapies. We selected all sequences of genes encoding NDH-2s from fully sequenced genomes present in the KEGG database. These genes were present in 61% of the 1805 species belonging to Eukarya (83%), Bacteria (60%) and Archaea (32%). Notably sequences from mammal species including humans were retrieved in our selection as NDH-2s. The data obtained and the already available information allowed systematizing several properties of NDH-2s: (i) the existence of additional sequence motifs with putative regulatory functions, (ii) specificity towards NADH or NADPH and (iii) the type of quinone binding motif. We observed that NDH-2 family distribution is not congruent with the taxonomic tree, suggesting different origins for the eukaryotic sequences and possible lateral gene transfer among prokaryotes. We note the absence of genes coding for NDH-2 in anaerobic phyla and the presence of multiple copies in several genomes, specifically in cyanobacteria. These observations inspired us to propose a metabolic hypothesis for the appearance of NDH-2s.


Subject(s)
Cyanobacteria/metabolism , Evolution, Molecular , NADH, NADPH Oxidoreductases/metabolism , Archaea/enzymology , Archaea/genetics , Archaea/metabolism , Base Sequence , Cyanobacteria/enzymology , Cyanobacteria/genetics , NADP/metabolism , Oxidation-Reduction , Phylogeny , Prokaryotic Cells/enzymology , Prokaryotic Cells/metabolism , Quinones/metabolism
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