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1.
Biochemistry ; 61(17): 1824-1835, 2022 09 06.
Article in English | MEDLINE | ID: mdl-35943735

ABSTRACT

Biotin-dependent enzymes employ a carrier domain to efficiently transport reaction intermediates between distant active sites. The translocation of this carrier domain is critical to the interpretation of kinetic and structural studies, but there have been few direct attempts to investigate the dynamic interplay between ligand binding and carrier domain positioning in biotin-dependent enzymes. Pyruvate carboxylase (PC) catalyzes the MgATP-dependent carboxylation of pyruvate where the biotinylated carrier domain must translocate ∼70 Šfrom the biotin carboxylase domain to the carboxyltransferase domain. Many prior studies have assumed that carrier domain movement is governed by ligand-induced conformational changes, but the mechanism underlying this movement has not been confirmed. Here, we have developed a system to directly observe PC carrier domain positioning in both the presence and absence of ligands, independent of catalytic turnover. We have incorporated a cross-linking trap that reports on the interdomain conformation of the carrier domain when it is positioned in proximity to a neighboring carboxyltransferase domain. Cross-linking was monitored by gel electrophoresis, inactivation kinetics, and intrinsic tryptophan fluorescence. We demonstrate that the carrier domain positioning equilibrium is sensitive to substrate analogues and the allosteric activator acetyl-CoA. Notably, saturating concentrations of biotin carboxylase ligands do not prevent carrier domain trapping proximal to the neighboring carboxyltransferase domain, demonstrating that carrier domain positioning is governed by conformational selection. This model of carrier domain translocation in PC can be applied to other multi-domain enzymes that employ large-scale domain motions to transfer intermediates during catalysis.


Subject(s)
Carboxyl and Carbamoyl Transferases , Pyruvate Carboxylase , Acetyl-CoA Carboxylase/metabolism , Biotin/chemistry , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Catalytic Domain , Ligands , Pyruvate Carboxylase/chemistry , Staphylococcus aureus
2.
Anal Chem ; 92(17): 11505-11510, 2020 09 01.
Article in English | MEDLINE | ID: mdl-32794704

ABSTRACT

We developed a simple and rapid method for analyzing nonproteinogenic amino acids that does not require conventional chromatographic equipment. In this technique, nonproteinogenic amino acids were first converted to a proteinogenic amino acid through in vitro metabolism in a cell extract. The proteinogenic amino acid generated from the nonproteinogenic precursors were then incorporated into a reporter protein using a cell-free protein synthesis system. The titers of the nonproteinogenic amino acids could be readily quantified by measuring the activity of reporter proteins. This method, which combines the enzymatic conversion of target amino acids with translational analysis, makes amino acid analysis more accessible while minimizing the cost and time requirements. We anticipate that the same strategy could be extended to the detection of diverse biochemical molecules with clinical and industrial implications.


Subject(s)
Cell Extracts/chemistry , Citrulline/chemistry , Ornithine/chemistry , Proteins/chemistry , Amino Acid Sequence , Arginine/chemistry , Argininosuccinate Lyase/genetics , Argininosuccinate Lyase/metabolism , Argininosuccinate Synthase/genetics , Argininosuccinate Synthase/metabolism , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Citrulline/metabolism , Escherichia coli/enzymology , Escherichia coli/genetics , Ornithine/metabolism , Protein Processing, Post-Translational , Proteomics , Stereoisomerism , Substrate Specificity
3.
Fitoterapia ; 130: 17-25, 2018 Oct.
Article in English | MEDLINE | ID: mdl-30076887

ABSTRACT

In previous work, a series of bioactive natural products had been isolated from the plant endophytic Streptomyces sp. CS, which was isolated from Maytenus hookeri. To mine new active metabolites, we describe introducing an alien carbamoyltransferase (asm21) gene into the strain CS by conjugal transfer. As a result, three recombinatorial mutants named CS/asm21-1, CS/asm21-2 and CS/asm21-4 were successfully constructed. Three mutants and wild type CS were cultured on solid medium, and the extracts were detected and analyzed by liquid chromatography-mass spectrometry (LC-MS). The LC-MS profiles showed several unknown peaks that were present in the spectra of extracts of the CS/asm21-4 cultured on oatmeal solid medium. Then, three new naphthomycins O-Q (1-3), a new macrolide hookerolide (4) as well as nine known compounds were obtained from the solid cultured medium. Their structures were identified by spectra data. These new compounds showed moderate antimicrobial activities.


Subject(s)
Macrolides/isolation & purification , Maytenus/microbiology , Streptomyces/chemistry , Carboxyl and Carbamoyl Transferases/genetics , Chromatography, Liquid , Conjugation, Genetic , Endophytes/chemistry , Mass Spectrometry , Microbial Sensitivity Tests , Microorganisms, Genetically-Modified , Molecular Structure , Plants, Medicinal/microbiology , Plasmids , Secondary Metabolism
4.
Mol Microbiol ; 108(4): 424-442, 2018 05.
Article in English | MEDLINE | ID: mdl-29488667

ABSTRACT

In starving Bacillus subtilis cells, the accDA operon encoding two subunits of the essential acetyl-CoA carboxylase (ACC) has been proposed to be tightly regulated by direct binding of the master regulator Spo0A to a cis element (0A box) in the promoter region. When the 0A box is mutated, biofilm formation and sporulation have been reported to be impaired. Here, we present evidence that two 0A boxes, one previously known (0A-1) and another newly discovered (0A-2) in the accDA promoter region are positively and negatively regulated by Spo0A∼P respectively. Cells with mutated 0A boxes experience slight delays in sporulation, but eventually sporulate with high efficiency. In contrast, cells harboring a single mutated 0A-2 box are deficient for biofilm formation, while cells harboring either a mutated 0A-1 box or both mutated 0A boxes form biofilms. We further show that the essential ACC enzyme localizes on or near the cell membrane by directly observing a functional GFP fusion to one of the enzyme's subunits. Collectively, we propose a revised model in which accDA is primarily transcribed by a major σA -RNA polymerase, while Spo0A∼P plays an additional role in the fine-tuning of accDA expression upon starvation to support proper biofilm formation and sporulation.


Subject(s)
Acetyl-CoA Carboxylase/genetics , Acetyl-CoA Carboxylase/metabolism , Bacillus subtilis/enzymology , Bacterial Proteins/metabolism , Fatty Acids/biosynthesis , Transcription Factors/metabolism , Acetyl-CoA Carboxylase/chemistry , Bacillus subtilis/genetics , Bacterial Proteins/genetics , Biofilms/growth & development , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Cell Membrane/enzymology , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , DNA-Directed RNA Polymerases/genetics , DNA-Directed RNA Polymerases/metabolism , Green Fluorescent Proteins/chemistry , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Operon/genetics , Promoter Regions, Genetic/genetics , Sigma Factor/genetics , Sigma Factor/metabolism , Spores, Bacterial/genetics , Spores, Bacterial/growth & development , Transcription Factors/genetics
5.
J Biol Chem ; 292(28): 11670-11681, 2017 07 14.
Article in English | MEDLINE | ID: mdl-28539366

ABSTRACT

Metalloenzymes catalyze complex and essential processes, such as photosynthesis, respiration, and nitrogen fixation. For example, bacteria and archaea use [NiFe]-hydrogenases to catalyze the uptake and release of molecular hydrogen (H2). [NiFe]-hydrogenases are redox enzymes composed of a large subunit that harbors a NiFe(CN)2CO metallo-center and a small subunit with three iron-sulfur clusters. The large subunit is synthesized with a C-terminal extension, cleaved off by a specific endopeptidase during maturation. The exact role of the C-terminal extension has remained elusive; however, cleavage takes place exclusively after assembly of the [NiFe]-cofactor and before large and small subunits form the catalytically active heterodimer. To unravel the functional role of the C-terminal extension, we used an enzymatic in vitro maturation assay that allows synthesizing functional [NiFe]-hydrogenase-2 of Escherichia coli from purified components. The maturation process included formation and insertion of the NiFe(CN)2CO cofactor into the large subunit, endoproteolytic cleavage of the C-terminal extension, and dimerization with the small subunit. Biochemical and spectroscopic analysis indicated that the C-terminal extension of the large subunit is essential for recognition by the maturation machinery. Only upon completion of cofactor insertion was removal of the C-terminal extension observed. Our results indicate that endoproteolytic cleavage is a central checkpoint in the maturation process. Here, cleavage temporally orchestrates cofactor insertion and protein assembly and ensures that only cofactor-containing protein can continue along the assembly line toward functional [NiFe]-hydrogenase.


Subject(s)
Coenzymes/metabolism , Enzyme Precursors/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Hydrogenase/metabolism , Models, Molecular , Protein Processing, Post-Translational , Carboxyl and Carbamoyl Transferases/chemistry , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Carrier Proteins/chemistry , Carrier Proteins/genetics , Carrier Proteins/metabolism , Dimerization , Endopeptidases/chemistry , Endopeptidases/genetics , Endopeptidases/metabolism , Enzyme Precursors/chemistry , Enzyme Precursors/genetics , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , GTP-Binding Proteins/chemistry , GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Hydrogenase/chemistry , Hydrogenase/genetics , Intracellular Signaling Peptides and Proteins , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Molecular Chaperones/chemistry , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Mutagenesis, Site-Directed , Mutation , Protein Folding , Protein Multimerization , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Proteolysis , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism
6.
Sci Rep ; 7: 42692, 2017 02 16.
Article in English | MEDLINE | ID: mdl-28205597

ABSTRACT

Malonyl-coenzyme A (CoA) is a crucial extender unit for the synthesis of mycolic and other fatty acids in mycobacteria, generated in a reaction catalyzed by acetyl-CoA carboxylase. We previously reported on the essentiality of accD6Mtb encoding the functional acetyl-CoA carboxylase subunit in Mycobacterium tuberculosis. Strikingly, the homologous gene in the fast-growing, non-pathogenic Mycobacterium smegmatis - (accD6Msm) appeared to be dispensable, and its deletion did not influence the cell lipid content. Herein, we demonstrate that, despite the difference in essentiality, accD6Msm and accD6Mtb encode proteins of convergent catalytic activity in vivo. To identify an alternative, AccD6-independent, malonyl-CoA synthesis pathway in M. smegmatis, a complex genetic approach combined with lipid analysis was applied to screen all five remaining carboxyltransferase genes (accD1-accD5) with respect to their involvement in mycolic acid biosynthesis and ability to utilize acetyl-CoA as the substrate for carboxylation. This approach revealed that AccD1Msm, AccD2Msm and AccD3Msm are not essential for mycolic acid biosynthesis. Furthermore, we confirmed in vivo the function of AccD4Msm as an essential, long-chain acyl-CoA carboxyltransferase, unable to carboxylate short-chain substrate. Finally, our comparative studies unambiguously demonstrated between-species difference in in vivo ability of AccD5 carboxyltransferase to utilize acetyl-CoA that influences AccD6 essentiality in pathogenic and non-pathogenic mycobacteria.


Subject(s)
Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Mycobacterium/enzymology , Mycobacterium/genetics , Biosynthetic Pathways , Enzyme Activation , Fatty Acids/metabolism , Microbial Viability/genetics , Mutation , Mycobacterium smegmatis/genetics , Mycobacterium smegmatis/metabolism , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/metabolism , Mycolic Acids/metabolism , Phenotype , Substrate Specificity , Virulence
7.
Structure ; 24(8): 1227-1236, 2016 08 02.
Article in English | MEDLINE | ID: mdl-27396827

ABSTRACT

Biotin-dependent acyl-coenzyme A (CoA) carboxylases (aCCs) are involved in key steps of anabolic pathways and comprise three distinct functional units: biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and carboxyl transferase (CT). YCC multienzymes are a poorly characterized family of prokaryotic aCCs of unidentified substrate specificity, which integrate all functional units into a single polypeptide chain. We employed a hybrid approach to study the dynamic structure of Deinococcus radiodurans (Dra) YCC: crystal structures of isolated domains reveal a hexameric CT core with extended substrate binding pocket and a dimeric BC domain. Negative-stain electron microscopy provides an approximation of the variable positioning of the BC dimers relative to the CT core. Small-angle X-ray scattering yields quantitative information on the ensemble of Dra YCC structures in solution. Comparison with other carrier protein-dependent multienzymes highlights a characteristic range of large-scale interdomain flexibility in this important class of biosynthetic enzymes.


Subject(s)
Acetyl-CoA Carboxylase/chemistry , Bacterial Proteins/chemistry , Biotin/chemistry , Carbon-Nitrogen Ligases/chemistry , Carboxyl and Carbamoyl Transferases/chemistry , Deinococcus/chemistry , Acetyl-CoA Carboxylase/genetics , Acetyl-CoA Carboxylase/metabolism , Amino Acid Motifs , Animals , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Baculoviridae/genetics , Baculoviridae/metabolism , Binding Sites , Biotin/metabolism , Carbon-Nitrogen Ligases/genetics , Carbon-Nitrogen Ligases/metabolism , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Cloning, Molecular , Crystallography, X-Ray , Deinococcus/enzymology , Escherichia coli/chemistry , Escherichia coli/enzymology , Fatty Acid Synthase, Type II/chemistry , Fatty Acid Synthase, Type II/genetics , Fatty Acid Synthase, Type II/metabolism , Gene Expression , Models, Molecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Scattering, Small Angle , Sf9 Cells , Spodoptera , Substrate Specificity , X-Ray Diffraction
8.
Biochim Biophys Acta ; 1861(9 Pt B): 1207-1213, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27091637

ABSTRACT

The enzyme acetyl-CoA carboxylase (ACCase) catalyzes the committed step of the de novo fatty acid biosynthesis (FAS) pathway by converting acetyl-CoA to malonyl-CoA. Two forms of ACCase exist in nature, a homomeric and heteromic form. The heteromeric form of this enzyme requires four different subunits for activity: biotin carboxylase; biotin carboxyl carrier protein; and α- and ß-carboxyltransferases. Heteromeric ACCases (htACCase) can be found in prokaryotes and the plastids of most plants. The plant htACCase is regulated by diverse mechanisms reflected by the biochemical and genetic complexity of this multienzyme complex and the plastid stroma where it resides. In this review we summarize the regulation of the plant htACCase and also describe the structural characteristics of this complex from both prokaryotes and plants. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.


Subject(s)
Acetyl-CoA Carboxylase/genetics , Carbon-Nitrogen Ligases/genetics , Fatty Acids/biosynthesis , Acetyl Coenzyme A/metabolism , Acetyl-CoA Carboxylase/chemistry , Amino Acid Sequence/genetics , Carbon-Nitrogen Ligases/chemistry , Carboxyl and Carbamoyl Transferases/chemistry , Carboxyl and Carbamoyl Transferases/genetics , Fatty Acid Synthase, Type II/chemistry , Fatty Acid Synthase, Type II/genetics , Fatty Acids/genetics , Plants/enzymology , Plastids/enzymology , Prokaryotic Cells/enzymology
9.
ACS Chem Biol ; 11(5): 1198-204, 2016 05 20.
Article in English | MEDLINE | ID: mdl-26886160

ABSTRACT

Albicidin is a potent antibiotic and phytotoxin produced by Xanthomonas albilineans which targets the plant and bacterial DNA gyrase. We now report on a new albicidin derivative which is carbamoylated at the N-terminal coumaric acid by the action of the ATP-dependent O-carbamoyltransferase Alb15, present in the albicidin (alb) gene cluster. Carbamoyl-albicidin was characterized by tandem mass spectrometry from cultures of a Xanthomonas overproducer strain and the gene function confirmed by gene inactivation of alb15 in X. albilineans. Expression of alb15 in Escherichia coli and in vitro reconstitution of the carbamoyltransferase activity confirmed albicidin as the substrate. The chemical synthesis of carbamoyl-albicidin finally enabled us to assess its bioactivity by means of in vitro gyrase inhibition and antibacterial assays. Compared to albicidin, carbamoyl-albicidin showed a significantly higher inhibitory efficiency against bacterial gyrase (∼8 vs 49 nM), which identifies the carbamoyl group as an important structural feature of albicidin maturation.


Subject(s)
Bacterial Proteins/metabolism , Carboxyl and Carbamoyl Transferases/metabolism , Xanthomonas/enzymology , Bacterial Proteins/genetics , Carboxyl and Carbamoyl Transferases/genetics , Genes, Bacterial , Multigene Family , Organic Chemicals/chemistry , Organic Chemicals/metabolism , Substrate Specificity , Xanthomonas/chemistry , Xanthomonas/genetics , Xanthomonas/metabolism
10.
Int J Mol Sci ; 16(8): 18836-64, 2015 Aug 12.
Article in English | MEDLINE | ID: mdl-26274952

ABSTRACT

Enzymes in the transcarbamylase family catalyze the transfer of a carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate. The two best-characterized members, aspartate transcarbamylase (ATCase) and ornithine transcarbamylase (OTCase), are present in most organisms from bacteria to humans. Recently, structures of four new transcarbamylase members, N-acetyl-L-ornithine transcarbamylase (AOTCase), N-succinyl-L-ornithine transcarbamylase (SOTCase), ygeW encoded transcarbamylase (YTCase) and putrescine transcarbamylase (PTCase) have also been determined. Crystal structures of these enzymes have shown that they have a common overall fold with a trimer as their basic biological unit. The monomer structures share a common CP binding site in their N-terminal domain, but have different second substrate binding sites in their C-terminal domain. The discovery of three new transcarbamylases, l-2,3-diaminopropionate transcarbamylase (DPTCase), l-2,4-diaminobutyrate transcarbamylase (DBTCase) and ureidoglycine transcarbamylase (UGTCase), demonstrates that our knowledge and understanding of the spectrum of the transcarbamylase family is still incomplete. In this review, we summarize studies on the structures and function of transcarbamylases demonstrating how structural information helps to define biological function and how small structural differences govern enzyme specificity. Such information is important for correctly annotating transcarbamylase sequences in the genome databases and for identifying new members of the transcarbamylase family.


Subject(s)
Carboxyl and Carbamoyl Transferases/chemistry , Carboxyl and Carbamoyl Transferases/genetics , Amino Acid Sequence , Carboxyl and Carbamoyl Transferases/metabolism , Catalysis , Catalytic Domain , Databases, Genetic , Humans , Models, Molecular , Molecular Sequence Data , Protein Conformation , Protein Interaction Domains and Motifs , Protein Multimerization , Sequence Alignment , Substrate Specificity
11.
ACS Chem Biol ; 9(10): 2309-17, 2014 Oct 17.
Article in English | MEDLINE | ID: mdl-25079908

ABSTRACT

The misfolding and aberrant assembly of peptides and proteins into fibrillar aggregates is the hallmark of many pathologies. Fibril formation is accompanied by oligomeric species thought to be the primary pathogenic agents in many of these diseases. With the aim of identifying the structural determinants responsible for the toxicity of misfolded oligomers, we created 12 oligomeric variants from the N-terminal domain of the E. coli HypF protein (HypF-N) by replacing one or more charged amino acid residues with neutral apolar residues and allowing the mutated proteins to aggregate under two sets of conditions. The resulting oligomeric species have different degrees of cytotoxicity when added to the extracellular medium of the cells, as assessed by the extent of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction, apoptosis, and influx of Ca2+ into the cells. The structural properties of the oligomeric variants were characterized by evaluating their surface hydrophobicity with 8-anilinonaphthalene-1-sulfonate (ANS) binding and by measuring their size by means of turbidimetry as well as light scattering. We find that increases in the surface hydrophobicity of the oligomers following mutation can promote the formation of larger assemblies and that the overall toxicity correlates with a combination of both surface hydrophobicity and size, with the most toxic oligomers having high hydrophobicity and small size. These results have allowed the relationships between these three parameters to be studied simultaneously and quantitatively, and have enabled the generation of an equation that is able to rationalize and even predict toxicity of the oligomers resulting from their surface hydrophobicity and size.


Subject(s)
Carboxyl and Carbamoyl Transferases/chemistry , Carboxyl and Carbamoyl Transferases/metabolism , Cell Proliferation/drug effects , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Hydrophobic and Hydrophilic Interactions/drug effects , Protein Multimerization , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/toxicity , Circular Dichroism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/toxicity , Hydrogen-Ion Concentration , Mutation/genetics
12.
J Biol Chem ; 288(27): 19915-25, 2013 Jul 05.
Article in English | MEDLINE | ID: mdl-23698000

ABSTRACT

Biotin-dependent enzymes catalyze carboxyl transfer reactions by efficiently coordinating multiple reactions between spatially distinct active sites. Pyruvate carboxylase (PC), a multifunctional biotin-dependent enzyme, catalyzes the bicarbonate- and MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To complete the overall reaction, the tethered biotin prosthetic group must first gain access to the biotin carboxylase domain and become carboxylated and then translocate to the carboxyltransferase domain, where the carboxyl group is transferred from biotin to pyruvate. Here, we report structural and kinetic evidence for the formation of a substrate-induced biotin binding pocket in the carboxyltransferase domain of PC from Rhizobium etli. Structures of the carboxyltransferase domain reveal that R. etli PC occupies a symmetrical conformation in the absence of the biotin carboxylase domain and that the carboxyltransferase domain active site is conformationally rearranged upon pyruvate binding. This conformational change is stabilized by the interaction of the conserved residues Asp(590) and Tyr(628) and results in the formation of the biotin binding pocket. Site-directed mutations at these residues reduce the rate of biotin-dependent reactions but have no effect on the rate of biotin-independent oxaloacetate decarboxylation. Given the conservation with carboxyltransferase domains in oxaloacetate decarboxylase and transcarboxylase, the structure-based mechanism described for PC may be applicable to the larger family of biotin-dependent enzymes.


Subject(s)
Bacterial Proteins/chemistry , Biotin/chemistry , Carboxyl and Carbamoyl Transferases/chemistry , Pyruvate Carboxylase/chemistry , Pyruvic Acid/chemistry , Rhizobium etli/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Biotin/genetics , Biotin/metabolism , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Mutagenesis, Site-Directed , Protein Structure, Tertiary , Pyruvate Carboxylase/genetics , Pyruvate Carboxylase/metabolism , Pyruvic Acid/metabolism , Rhizobium etli/chemistry
13.
Biochemistry ; 52(19): 3346-57, 2013 May 14.
Article in English | MEDLINE | ID: mdl-23594205

ABSTRACT

Acetyl-CoA carboxylase is a biotin-dependent enzyme that catalyzes the regulated step in fatty acid synthesis. The bacterial form has three separate components: biotin carboxylase, biotin carboxyl carrier protein (BCCP), and carboxyltransferase. Catalysis by acetyl-CoA carboxylase proceeds via two half-reactions. In the first half-reaction, biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin, which is covalently attached to BCCP, to form carboxybiotin. In the second half-reaction, carboxyltransferase transfers the carboxyl group from carboxybiotin to acetyl-CoA to form malonyl-CoA. All biotin-dependent carboxylases are proposed to have a two-site ping-pong mechanism in which the carboxylase and transferase activities are separate and do not interact. This posits two hypotheses: either biotin carboxylase and BCCP undergo the first half-reaction, BCCP dissociates, and then BCCP binds to carboxyltransferase, or all three constituents form an enzyme complex. To determine which hypothesis is correct, a steady-state enzyme kinetic analysis of Escherichia coli acetyl-CoA carboxylase was conducted. The results indicated the two active sites of acetyl-CoA carboxylase interact. Both in vitro and in vivo pull-down assays demonstrated that the three components of E. coli acetyl-CoA carboxylase form a multimeric complex and that complex formation is unaffected by acetyl-CoA, AMPPNP, and mRNA encoding carboxyltransferase. The implications of these findings for the regulation of acetyl-CoA carboxylase and fatty acid biosynthesis are discussed.


Subject(s)
Acetyl-CoA Carboxylase/chemistry , Acetyl-CoA Carboxylase/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Acetyl-CoA Carboxylase/genetics , Carbon-Nitrogen Ligases/chemistry , Carbon-Nitrogen Ligases/genetics , Carbon-Nitrogen Ligases/metabolism , Carboxyl and Carbamoyl Transferases/chemistry , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Catalytic Domain , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Fatty Acid Synthase, Type II/chemistry , Fatty Acid Synthase, Type II/genetics , Fatty Acid Synthase, Type II/metabolism , Kinetics , Models, Biological , Substrate Specificity
14.
J Bioenerg Biomembr ; 45(3): 253-60, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23271421

ABSTRACT

Proton motive force (Δp) generation by Escherichia coli wild type cells during glycerol fermentation was first studied. Its two components, electrical-the membrane potential (∆φ) and chemical-the pH transmembrane gradient (ΔpH), were established and the effects of external pH (pHex) were determined. Intracellular pH was 7.0 and 6.0 and lower than pHex at pH 7.5 and 6.5, respectively; and it was higher than pHex at pH 5.5. At high pHex, the increase of ∆φ (-130 mV) was only partially compensated by a reversed ΔpH, resulting in a low Δp. At low pHex ∆φ and consequently Δp were decreased. The generation of Δp during glycerol fermentation was compared with glucose fermentation, and the difference in Δp might be due to distinguished mechanisms for H(+) transport through the membrane, especially to hydrogenase (Hyd) enzymes besides the F0F1-ATPase. H(+) efflux was determined to depend on pHex; overall and N,N'-dicyclohexylcarbodiimide (DCCD)-inhibitory H(+) efflux was maximal at pH 6.5. Moreover, ΔpH was changed at pH 6.5 and Δp was different at pH 6.5 and 5.5 with the hypF mutant lacking all Hyd enzymes. DCCD-inhibited ATPase activity of membrane vesicles was maximal at pH 7.5 and decreased with the hypF mutant. Thus, Δp generation by E. coli during glycerol fermentation is different than that during glucose fermentation. Δp is dependent on pHex, and a role of Hyd enzymes in its generation is suggested.


Subject(s)
Escherichia coli/enzymology , Glycerol/metabolism , Hydrogenase/metabolism , Proton-Motive Force/physiology , Carboxyl and Carbamoyl Transferases/genetics , Carboxyl and Carbamoyl Transferases/metabolism , Cryoprotective Agents/metabolism , Cryoprotective Agents/pharmacology , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Glucose/genetics , Glucose/metabolism , Glycerol/pharmacology , Hydrogen-Ion Concentration , Hydrogenase/genetics , Mutation , Proton-Motive Force/drug effects , Proton-Translocating ATPases/genetics , Proton-Translocating ATPases/metabolism
15.
Biochem Biophys Res Commun ; 424(1): 158-63, 2012 Jul 20.
Article in English | MEDLINE | ID: mdl-22735263

ABSTRACT

Endoprotease-specific C-terminal processing is required to complete the maturation of the large subunit of [NiFe]-hydrogenases. This happens only after synthesis and insertion of the NiFe(CN)(2)CO cofactor by the Hyp maturases has occurred. It is assumed that in the absence of maturation the unprocessed species of the large subunit lacks cofactors. In this study we isolated a variant of the hydrogenase 2 large subunit, HybC, containing a fused C-terminal pentapeptide. The polypeptide could not be processed and was unable to associate with the small subunit to deliver an active enzyme. The His(6)-HybC variant protein isolated was brown and had sub-stoichiometric amounts of an oxygen-sensitive Iron-sulfur cluster, which could be chemically reconstituted to a [4Fe-4S] cluster. This cluster was coordinated by the conserved cysteinyl residues that normally ligate the NiFe(CN)(2)CO cofactor. Our findings provide evidence for temporary promiscuity of cofactor-binding sites.


Subject(s)
Escherichia coli/enzymology , Hydrogenase/chemistry , Iron-Sulfur Proteins/chemistry , Oxidoreductases/chemistry , Oxygen/chemistry , Carboxyl and Carbamoyl Transferases/genetics , Carrier Proteins/genetics , Escherichia coli Proteins/genetics , Hydrogenase/genetics , Iron-Sulfur Proteins/genetics , Mutation , Oligopeptides/chemistry , Oligopeptides/genetics , Oxidoreductases/genetics
16.
Parasitol Res ; 111(3): 1401-5, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22453500

ABSTRACT

Genome analysis of Entamoeba histolytica predicts the presence of acetyl-CoA carboxylase. Using Western blot, histochemistry, and confocal microscopy, we demonstrated the presence of a biotin-containing protein in the cytoplasm of E. histolytica, with a molecular weight of 136 kDa and biotin-carboxylase activity. This protein probably corresponds to a transcarboxylase that catalyzes the rate-limiting reaction leading to fatty acid elongation.


Subject(s)
Carboxyl and Carbamoyl Transferases/metabolism , Entamoeba histolytica/enzymology , Gene Expression Regulation, Enzymologic/physiology , Protozoan Proteins/metabolism , Animals , Carboxyl and Carbamoyl Transferases/genetics , Entamoeba histolytica/genetics , Entamoeba histolytica/metabolism , Genome, Protozoan , Protozoan Proteins/genetics
17.
Chem Biol ; 18(12): 1571-80, 2011 Dec 23.
Article in English | MEDLINE | ID: mdl-22195559

ABSTRACT

Carbamoylation is one of the post-PKS modifications in ansamitocin biosynthesis. A novel ansamitocinoside with carbamoyl substitution at the C-4 hydroxyl group of the N-ß-D-glucosyl moiety was identified from the ansamitocin producer, Actinosynnema pretiosum. Through biotransformation, the carbamoyltransferase gene asm21 was suggested to be responsible for the carbamoylation of the glucosyl moiety. Three new derivatives without the backbone carbamoyl group were isolated from an asm21 mutant and characterized by NMR spectroscopy. Among them, 18-O-methyl-19-chloroproansamitocin was the major product and the preferred substrate for macrolactam C-7 carbamoylation by Asm21. However, Asm21 exhibited higher catalytic efficiency toward the glucosyl moiety. Furthermore, the dual carbamoylations and N-glycosylation were precisely demonstrated in vivo. This work represents the first biochemical characterization of an O-carbamoyltransferase performing dual actions on both a polyketide backbone and a glycosyl moiety during ansamitocin biosynthesis.


Subject(s)
Carboxyl and Carbamoyl Transferases/metabolism , Maytansine/analogs & derivatives , Polyketides/chemistry , Actinomycetales/enzymology , Biocatalysis , Carboxyl and Carbamoyl Transferases/genetics , Magnetic Resonance Spectroscopy , Maytansine/biosynthesis , Maytansine/chemistry , Mutation
18.
Microbiology (Reading) ; 157(Pt 11): 3150-3161, 2011 Nov.
Article in English | MEDLINE | ID: mdl-21835877

ABSTRACT

Listeria monocytogenes is a foodborne pathogen causing listeriosis. Acid is one of the stresses that foodborne pathogens encounter most frequently. The ability to survive and proliferate in acidic environments is a prerequisite for infection. However, there is limited knowledge about the molecular basis of adaptation of L. monocytogenes to acid. Arginine deiminase (ADI) and agmatine deiminase (AgDI) systems are implicated in bacterial tolerance to acidic environments. Homologues of ADI and AgDI systems have been found in L. monocytogenes lineages I and II strains. Sequence analysis indicated that lmo0036 encodes a putative carbamoyltransferase containing conserved motifs and residues important for substrate binding. Lmo0036 acted as an ornithine carbamoyltransferase and putrescine carbamoyltransferase, representing the first example, to our knowledge, that catalyses reversible ornithine and putrescine carbamoyltransfer reactions. Catabolic ornithine and putrescine carbamoyltransfer reactions constitute the second step of ADI and AgDI pathways. However, the equilibrium of in vitro carbamoyltransfer reactions was overwhelmingly towards the anabolic direction, suggesting that catabolic carbamoyltransferase was probably the limiting step of the pathways. lmo0036 was induced at the transcriptional level when L. monocytogenes was subjected to low-pH stress. Its expression product in Escherichia coli exhibited higher catabolic carbamoyltransfer activities under acidic conditions. Consistently, absence of this enzyme impaired the growth of Listeria under mild acidic conditions (pH 4.8) and reduced its survival in synthetic human gastric fluid (pH 2.5), and corresponded to a loss in ammonia production, indicating that Lmo0036 was responsible for acid tolerance at both sublethal and lethal pH levels. Furthermore, Lmo0036 played a possible role in Listeria virulence.


Subject(s)
Acids/metabolism , Carboxyl and Carbamoyl Transferases/metabolism , Hydrolases/metabolism , Listeria monocytogenes/enzymology , Amino Acid Sequence , Ammonia/analysis , Animals , Biogenic Amines/analysis , Carboxyl and Carbamoyl Transferases/genetics , DNA, Bacterial/genetics , Female , Gene Expression Regulation, Bacterial , Gene Knockout Techniques , Genetic Complementation Test , Hydrogen-Ion Concentration , Listeria monocytogenes/genetics , Listeria monocytogenes/pathogenicity , Mice , Mice, Inbred ICR , Molecular Sequence Data , Mutagenesis, Site-Directed , Sequence Analysis, Protein , Virulence
19.
IET Syst Biol ; 5(3): 220-8, 2011 May.
Article in English | MEDLINE | ID: mdl-21639594

ABSTRACT

Acetyl-CoA carboxylase catalyses the first committed step in fatty acid synthesis in all organisms. The chemistry is accomplished in two half-reactions: activation of biotin via carboxylation by biotin carboxylase, followed by the carboxyltransferase-catalysed transfer of the carboxyl moiety from carboxybiotin to acetyl-CoA to generate malonyl-CoA. The Escherichia coli form of the carboxyltransferase subunit was recently found to regulate its own activity and expression by binding its own mRNA. By binding acetyl-CoA or the mRNA encoding its own subunits, carboxyltransferase is able to sense the metabolic state of the cell and attenuate its own translation and enzymatic activity using a negative feedback mechanism. Here, the network of these interactions is modelled mathematically with a set of non-linear differential equations. Numerical simulations of the model show that it qualitatively and quantitatively agrees with the experimental results for both inhibition of carboxyltransferase by mRNA and attenuation of translation. The modelling of the autoregulatory function of carboxyltransferase confirms that it is more than isolated interactions, but functions as a single dynamic system.


Subject(s)
Carboxyl and Carbamoyl Transferases/metabolism , Models, Biological , Acetyl Coenzyme A/metabolism , Base Sequence , Carboxyl and Carbamoyl Transferases/antagonists & inhibitors , Carboxyl and Carbamoyl Transferases/genetics , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Feedback, Physiological , Kinetics , Mathematical Concepts , Protein Biosynthesis , RNA, Bacterial/genetics , RNA, Bacterial/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Systems Biology
20.
Protein Eng Des Sel ; 24(7): 553-63, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21518735

ABSTRACT

The conversion of proteins into structured fibrillar aggregates is a central problem in protein chemistry, biotechnology, biology and medicine. It is generally accepted that aggregation takes place from partially structured states of proteins. However, the role of the residual structure present in such conformational states is not yet understood. In particular, it is not yet clear as to whether the α-helical structure represents a productive or counteracting structural element for protein aggregation. We have addressed this issue by studying the aggregation of pH-unfolded HypF-N. It has previously been shown that the two native α-helices of HypF-N retain a partial α-helical structure in the pH-unfolded state and that these regions are also involved in the formation of the cross-ß structure of the aggregates. We have introduced mutations in such stretches of the sequence, with the aim of increasing the α-helical structure in the key regions of the pH-unfolded state, while minimizing the changes of other factors known to influence protein aggregation, such as hydrophobicity, ß-Sheet propensity, etc. The resulting HypF-N mutants have higher contents of α-helical structure at the site(s) of mutation in their pH-unfolded states, but such an increase does not correlate with a change of aggregation rate. The results suggest that stabilisation of α-helical structure in amyloidogenic regions of the sequence of highly dynamic states does not have remarkable effects on the rate of protein aggregation from such conformational states. Comparison with other protein systems indicate that the effect of increasing α-helical propensity can vary if the stabilised helices are in non-amyloidogenic stretches of initially unstructured peptides (accelerating effect), in amyloidogenic stretches of initially unstructured peptides (no effect) or in amyloidogenic stretches of initially stable helices (decelerating effect).


Subject(s)
Carboxyl and Carbamoyl Transferases/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/chemistry , Protein Unfolding , Carboxyl and Carbamoyl Transferases/genetics , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Hydrogen-Ion Concentration , Models, Molecular , Mutation , Protein Stability , Protein Structure, Secondary
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