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1.
Biochemistry ; 57(50): 6816-6821, 2018 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-30431267

RESUMO

The mild acetylating agent, methyl acetyl phosphate, is used to estimate the p Ka values of some of the amine groups in peptides with sequences corresponding to a segment of the N-terminal tail of histone H4. When Ser-1 is not phosphorylated, the Lys ε amines have p Ka values in the range of 7.8-8.3, which are much lower than the currently assumed values. When Ser-1 is phosphorylated, the p Ka values of these Lys amines are elevated to the range of 8.8-10.3, thus providing the rationale for reports that they are then better substrates for acetyltransferases. Thus, reversal of suppressed p Ka values of Lys ε amines by Ser phosphorylation represents the basis for signaling in histone N-terminal tails to promote hyperacetylation, which is a hallmark of transcriptionally active euchromatin. In contrast, a state of hypoacetylation is present in the absence of phosphorylation as in transcriptionally inactive heterochromatin. A novel approach for estimating p Ka values based on a linkage between the Henderson-Hasselbalch and Michaelis-Menten equations indicates that the p Ka values of the Lys ε amines in H3 and H4 N-terminal tails have a highly variable charge gradient dependent on the location and proximity to the phosphorylation site.


Assuntos
Histonas/química , Histonas/metabolismo , Acetilação , Sequência de Aminoácidos , Animais , Sítios de Ligação , Código das Histonas , Histonas/genética , Humanos , Cinética , Lisina/química , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/genética , Fragmentos de Peptídeos/metabolismo , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/química , Ácido Fosfonoacéticos/metabolismo , Serina/química , Transdução de Sinais , Transcrição Gênica
2.
Sci Rep ; 8(1): 11079, 2018 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-30038211

RESUMO

Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently developed method, bond-to-bond propensity analysis, has proven capable of predicting allosteric sites in a wide range of proteins using an energy-weighted atomistic graph obtained from the protein structure and given knowledge only of the location of the active site. Bond-to-bond propensity establishes if energy fluctuations at given bonds have significant effects on any other bond in the protein, by considering their propagation through the protein graph. In this work, we use bond-to-bond propensity analysis to study different aspects of ATCase activity using three different protein structures and sources of fluctuations. First, we predict key residues and bonds involved in the transition between inactive (T) and active (R) states of ATCase by analysing allosteric substrate binding as a source of energy perturbations in the protein graph. Our computational results also indicate that the effect of multiple allosteric binding is non linear: a switching effect is observed after a particular number and arrangement of substrates is bound suggesting a form of long range communication between the distantly arranged allosteric sites. Second, cooperativity is explored by considering a bisubstrate analogue as the source of energy fluctuations at the active site, also leading to the identification of highly significant residues to the T ↔ R transition that enhance cooperativity across active sites. Finally, the inactive (T) structure is shown to exhibit a strong, non linear communication between the allosteric sites and the interface between catalytic subunits, rather than the active site. Bond-to-bond propensity thus offers an alternative route to explain allosteric and cooperative effects in terms of detailed atomistic changes to individual bonds within the protein, rather than through phenomenological, global thermodynamic arguments.


Assuntos
Aspartato Carbamoiltransferase/metabolismo , Multimerização Proteica , Trifosfato de Adenosina/metabolismo , Regulação Alostérica , Sítio Alostérico , Aspartato Carbamoiltransferase/química , Ácido Aspártico/análogos & derivados , Ácido Aspártico/metabolismo , Domínio Catalítico , Citidina Trifosfato/metabolismo , Estabilidade Enzimática , Modelos Moleculares , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/metabolismo , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , Especificidade por Substrato
3.
Proc Natl Acad Sci U S A ; 114(35): 9355-9360, 2017 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-28808005

RESUMO

The enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) is a key enzyme in the methylerythritol 4-phosphate pathway and is a target for the development of antibiotics, herbicides, and antimalarial drugs. DXPS catalyzes the formation of 1-deoxy-d-xylulose 5-phosphate (DXP), a branch point metabolite in isoprenoid biosynthesis, and is also used in the biosynthesis of thiamin (vitamin B1) and pyridoxal (vitamin B6). Previously, we found that DXPS is unique among the superfamily of thiamin diphosphate (ThDP)-dependent enzymes in stabilizing the predecarboxylation intermediate, C2-alpha-lactyl-thiamin diphosphate (LThDP), which has subsequent decarboxylation that is triggered by d-glyceraldehyde 3-phosphate (GAP). Herein, we applied hydrogen-deuterium (H/D) exchange MS (HDX-MS) of full-length Escherichia coli DXPS to provide a snapshot of the conformational dynamics of this enzyme, leading to the following conclusions. (i) The high sequence coverage of DXPS allowed us to monitor structural changes throughout the entire enzyme, including two segments (spanning residues 183-238 and 292-317) not observed by X-ray crystallography. (ii) Three regions of DXPS (spanning residues 42-58, 183-199, and 278-298) near the active center displayed both EX1 (monomolecular) and EX2 (bimolecuar) H/D exchange (HDX) kinetic behavior in both ligand-free and ligand-bound states. All other peptides behaved according to the common EX2 kinetic mechanism. (iii) The observation of conformational changes on DXPS provides support for the role of conformational dynamics in the DXPS mechanism: The closed conformation of DXPS is critical for stabilization of LThDP, whereas addition of GAP converts DXPS to the open conformation that coincides with decarboxylation of LThDP and DXP release.


Assuntos
Espectrometria de Massas/métodos , Transferases/metabolismo , Gliceraldeído 3-Fosfato/química , Gliceraldeído 3-Fosfato/metabolismo , Modelos Moleculares , Pentosefosfatos/química , Pentosefosfatos/metabolismo , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/química , Ácido Fosfonoacéticos/metabolismo , Ligação Proteica , Conformação Proteica
4.
Artigo em Inglês | MEDLINE | ID: mdl-28361036

RESUMO

Many microorganisms produce phosphonates, molecules characterized by stable carbon-phosphorus bonds that store phosphorus or act as antimicrobials. The role of phosphonates in the marine biosphere is well characterized but the role of these molecules in the intestine is poorly understood. Salmonella enterica uses its virulence factors to influence the host immune response to compete with the host and normal microflora for nutrients. Salmonella cannot produce phosphonates but encodes the enzymes to use them suggesting that it is exposed to phosphonates during its life cycle. The role of phosphonates during enteric salmonellosis is unexplored. We have previously shown that STM3602, encoding a putative regulator of phosphonate metabolism, is needed for colonization in calves. Here, we report that the necessity of STM3602 in colonization of the murine intestine results from multiple factors. STM3602 is needed for full activation of the type-3 secretion system-1 and for optimal invasion of epithelial cells. The ΔSTM3602 mutant grows poorly in phosphonoacetic acid (PA) as the sole phosphorus source, but can use 2-aminoethylphosphonate. PhnA, an enzyme required for PA breakdown, is not controlled by STM3602 suggesting an additional mechanism for utilization of PA in S. Typhimurium. Finally, the requirement of STM3602 for intestinal colonization differs depending on the composition of the microflora. Our data suggest that STM3602 has multiple regulatory targets that are necessary for survival within the microbial community in the intestine. Determination of the members of the STM3602 regulon may illuminate new pathways needed for colonization of the host.


Assuntos
Regulação Bacteriana da Expressão Gênica , Intestinos/microbiologia , Ácido Fosfonoacéticos/metabolismo , Salmonelose Animal/microbiologia , Salmonella enterica/fisiologia , Animais , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos CBA , Salmonella enterica/genética , Salmonella enterica/metabolismo
5.
ACS Synth Biol ; 6(2): 217-223, 2017 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-28103011

RESUMO

The activation of silent natural product gene clusters is a synthetic biology problem of great interest. As the rate at which gene clusters are identified outpaces the discovery rate of new molecules, this unknown chemical space is rapidly growing, as too are the rewards for developing technologies to exploit it. One class of natural products that has been underrepresented is phosphonic acids, which have important medical and agricultural uses. Hundreds of phosphonic acid biosynthetic gene clusters have been identified encoding for unknown molecules. Although methods exist to elicit secondary metabolite gene clusters in native hosts, they require the strain to be amenable to genetic manipulation. One method to circumvent this is pathway refactoring, which we implemented in an effort to discover new phosphonic acids from a gene cluster from Streptomyces sp. strain NRRL F-525. By reengineering this cluster for expression in the production host Streptomyces lividans, utility of refactoring is demonstrated with the isolation of a novel phosphonic acid, O-phosphonoacetic acid serine, and the characterization of its biosynthesis. In addition, a new biosynthetic branch point is identified with a phosphonoacetaldehyde dehydrogenase, which was used to identify additional phosphonic acid gene clusters that share phosphonoacetic acid as an intermediate.


Assuntos
Produtos Biológicos/metabolismo , Ácido Fosfonoacéticos/metabolismo , Hidrolases/metabolismo , Família Multigênica/genética , Ácidos Fosforosos/metabolismo , Streptomyces/crescimento & desenvolvimento , Biologia Sintética
6.
Folia Microbiol (Praha) ; 59(5): 375-80, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24570323

RESUMO

A psychrophilic fungal strain of Geomyces pannorum P15 was screened for its ability to utilize a range of synthetic and natural organophosphonate compounds as the sole source of phosphorus, nitrogen, or carbon. Only phosphonoacetic acid served as a phosphorus source for microbial growth in phosphate-independent manner. Substrate metabolism did not lead to extracellular release of inorganic phosphate. No phosphonate metabolizing enzyme activity was detectable in cell-free extracts prepared from Geomyces biomass pregrown on 2 mmol/L phosphonoacetic acid.


Assuntos
Ascomicetos/metabolismo , Ácido Fosfonoacéticos/metabolismo , Fósforo/metabolismo , Ascomicetos/crescimento & desenvolvimento , Carbono/metabolismo , Nitrogênio/metabolismo , Fosfatos/metabolismo
7.
Chem Biol ; 21(1): 125-35, 2014 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-24361046

RESUMO

Phosphonates (C-PO3²â») have applications as antibiotics, herbicides, and detergents. In some environments, these molecules represent the predominant source of phosphorus, and several microbes have evolved dedicated enzymatic machineries for phosphonate degradation. For example, most common naturally occurring phosphonates can be catabolized to either phosphonoacetaldehyde or phosphonoacetate, which can then be hydrolyzed to generate inorganic phosphate and acetaldehyde or acetate, respectively. The phosphonoacetaldehyde oxidase gene (phnY) links these two hydrolytic processes and provides a previously unknown catabolic mechanism for phosphonoacetate production in the microbial metabolome. Here, we present biochemical characterization of PhnY and high-resolution crystal structures of the apo state, as well as complexes with substrate, cofactor, and product. Kinetic analysis of active site mutants demonstrates how a highly conserved aldehyde dehydrogenase active site has been modified in nature to generate activity with a phosphonate substrate.


Assuntos
Acetaldeído/análogos & derivados , Oxirredutases/química , Oxirredutases/metabolismo , Ácido Fosfonoacéticos/metabolismo , Acetaldeído/química , Acetaldeído/metabolismo , Apoproteínas/química , Apoproteínas/metabolismo , Domínio Catalítico/genética , Cristalografia por Raios X , Cinética , Modelos Moleculares , Estrutura Molecular , NAD/química , NAD/metabolismo , Oxirredutases/genética , Ácido Fosfonoacéticos/química , Sinorhizobium meliloti/enzimologia
8.
Artigo em Inglês | MEDLINE | ID: mdl-24316846

RESUMO

Aspartate transcarbamoylase (ATCase) catalyzes the synthesis of N-carbamoyl-L-aspartate from carbamoyl phosphate and aspartate in the second step of the de novo biosynthesis of pyrimidines. In prokaryotes, the first three activities of the pathway, namely carbamoyl phosphate synthetase (CPSase), ATCase and dihydroorotase (DHOase), are encoded as distinct proteins that function independently or in noncovalent association. In animals, CPSase, ATCase and DHOase are part of a 243 kDa multifunctional polypeptide named CAD. Up-regulation of CAD is essential for normal and tumour cell proliferation. Although the structures of numerous prokaryotic ATCases have been determined, there is no structural information about any eukaryotic ATCase. In fact, the only detailed structural information about CAD is that it self-assembles into hexamers and trimers through interactions of the ATCase domains. Here, the expression, purification and crystallization of the ATCase domain of human CAD is reported. The recombinant protein, which was expressed in bacteria and purified with good yield, formed homotrimers in solution. Crystallization experiments both in the absence and in the presence of the inhibitor PALA yielded small crystals that diffracted X-rays to 2.1 Å resolution using synchrotron radiation. The crystals appeared to belong to the hexagonal space group P6(3)22, and Matthews coefficient calculation indicated the presence of one ATCase subunit per asymmetric unit, with a solvent content of 48%. However, analysis of the intensity statistics suggests a special case of the P21 lattice with pseudo-symmetry and possibly twinning.


Assuntos
Aspartato Carbamoiltransferase/química , Ácido Aspártico/análogos & derivados , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/química , Di-Hidro-Orotase/química , Inibidores Enzimáticos/química , Ácido Fosfonoacéticos/análogos & derivados , Aspartato Carbamoiltransferase/genética , Aspartato Carbamoiltransferase/metabolismo , Ácido Aspártico/química , Ácido Aspártico/metabolismo , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/genética , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/metabolismo , Cristalização , Cristalografia por Raios X , Di-Hidro-Orotase/genética , Di-Hidro-Orotase/metabolismo , Inibidores Enzimáticos/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Modelos Moleculares , Ácido Fosfonoacéticos/química , Ácido Fosfonoacéticos/metabolismo , Multimerização Proteica , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Síncrotrons
9.
Biochemistry ; 52(15): 2505-7, 2013 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-23544868

RESUMO

Thiamin diphosphate (ThDP)-dependent enzymes play vital roles in cellular metabolism in all kingdoms of life. In previous kinetic and structural studies, a communication between the active centers in terms of a negative cooperativity had been suggested for some but not all ThDP enzymes, which typically operate as functional dimers. To further underline this hypothesis and to test its universality, we investigated the binding of substrate analogue methyl acetylphosphonate (MAP) to three different ThDP-dependent enzymes acting on substrate pyruvate, namely, the Escherichia coli E1 component of the pyruvate dehydrogenase complex, E. coli acetohydroxyacid synthase isoenzyme I, and the Lactobacillus plantarum pyruvate oxidase using isothermal titration calorimetry. The results unambiguously show for all three enzymes studied that only one active center of the functional dimers accomplishes covalent binding of the substrate analogue, supporting the proposed alternating sites reactivity as a common feature of all ThDP enzymes and resolving the recent controversy in the field.


Assuntos
Enzimas/química , Enzimas/metabolismo , Tiamina Pirofosfato/metabolismo , Acetolactato Sintase/química , Acetolactato Sintase/metabolismo , Sítios de Ligação , Calorimetria/métodos , Domínio Catalítico , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Cinética , Ressonância Magnética Nuclear Biomolecular , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/química , Ácido Fosfonoacéticos/metabolismo , Ligação Proteica , Piruvato Desidrogenase (Lipoamida)/química , Piruvato Desidrogenase (Lipoamida)/metabolismo , Piruvato Oxidase/química , Piruvato Oxidase/metabolismo , Termodinâmica , Tiamina Pirofosfato/química
10.
Chem Biol ; 18(10): 1230-40, 2011 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-22035792

RESUMO

Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 Å resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformate inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.


Assuntos
Fosfatase Alcalina/química , Fosfatase Alcalina/metabolismo , Sinorhizobium meliloti/enzimologia , Acetatos/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Domínio Catalítico , Cristalografia por Raios X , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Hidrólise , Metais/metabolismo , Modelos Moleculares , Ácido Fosfonoacéticos/metabolismo , Conformação Proteica , Sinorhizobium meliloti/metabolismo , Especificidade por Substrato
11.
Biochemistry ; 50(45): 9708-23, 2011 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-21958016

RESUMO

Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To effect catalysis, the tethered biotin of PC must gain access to active sites in both the biotin carboxylase domain and the carboxyl transferase domain. Previous studies have demonstrated that a mutation of threonine 882 to alanine in PC from Rhizobium etli renders the carboxyl transferase domain inactive and favors the positioning of biotin in the biotin carboxylase domain. We report the 2.4 Å resolution X-ray crystal structure of the Rhizobium etli PC T882A mutant which reveals the first high-resolution description of the domain interaction between the biotin carboxyl carrier protein domain and the biotin carboxylase domain. The overall quaternary arrangement of Rhizobium etli PC remains highly asymmetrical and is independent of the presence of allosteric activator. While biotin is observed in the biotin carboxylase domain, its access to the active site is precluded by the interaction between Arg353 and Glu248, revealing a mechanism for regulating carboxybiotin access to the BC domain active site. The binding location for the biotin carboxyl carrier protein domain demonstrates that tethered biotin cannot bind in the biotin carboxylase domain active site in the same orientation as free biotin, helping to explain the difference in catalysis observed between tethered biotin and free biotin substrates in biotin carboxylase enzymes. Electron density located in the biotin carboxylase domain active site is assigned to phosphonoacetate, offering a probable location for the putative carboxyphosphate intermediate formed during biotin carboxylation. The insights gained from the T882A Rhizobium etli PC crystal structure provide a new series of catalytic snapshots in PC and offer a revised perspective on catalysis in the biotin-dependent enzyme family.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Piruvato Carboxilase/química , Piruvato Carboxilase/metabolismo , Rhizobium etli/enzimologia , Proteínas de Bactérias/genética , Sequência de Bases , Biotina/metabolismo , Carbono-Nitrogênio Ligases/química , Carbono-Nitrogênio Ligases/genética , Carbono-Nitrogênio Ligases/metabolismo , Domínio Catalítico , Cristalografia por Raios X , Primers do DNA/genética , Cinética , Modelos Moleculares , Mutagênese Sítio-Dirigida , Ácido Fosfonoacéticos/metabolismo , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Piruvato Carboxilase/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Rhizobium etli/genética , Especificidade da Espécie , Staphylococcus aureus/enzimologia
12.
Mikrobiologiia ; 80(3): 329-34, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21861368

RESUMO

A novel phosphonoacetaldehyde-oxidizing activity was detected in cell-extracts of the marine bacterium Roseovarius nubinhibens ISM grown on 2-aminoethylphosphonic acid (2-AEP; ciliatine). Extracts also contained 2-AEP transaminase and phosphonoacetate hydrolase activities. These findings indicate the existence of a biological route from 2-AEP via phosphonoacetaldehyde for the production of phosphonoacetate, which has not previously been shown to be a natural product. The three enzymes appear to constitute a previously-unreported pathway for the mineralization of 2-AEP which is a potentially important source of phosphorus in the nutrient-stressed marine environment.


Assuntos
Fosfatase Alcalina/metabolismo , Ácido Aminoetilfosfônico/metabolismo , Ácido Fosfonoacéticos/metabolismo , Rhodobacteraceae , Acetaldeído/análogos & derivados , Acetaldeído/metabolismo , Organismos Aquáticos/enzimologia , Organismos Aquáticos/crescimento & desenvolvimento , Proteínas de Bactérias/metabolismo , Concentração de Íons de Hidrogênio , NADP/metabolismo , Fósforo/metabolismo , Rhodobacteraceae/enzimologia , Rhodobacteraceae/crescimento & desenvolvimento , Rhodobacteraceae/isolamento & purificação , Especificidade por Substrato , Temperatura , Transaminases/metabolismo
13.
Proc Natl Acad Sci U S A ; 107(7): 2890-5, 2010 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-20133652

RESUMO

A novel concept in eukaryotic signal transduction is the use of nutrient transporters and closely related proteins as nutrient sensors. The action mechanism of these "transceptors" is unclear. The Pho84 phosphate transceptor in yeast transports phosphate and mediates rapid phosphate activation of the protein kinase A (PKA) pathway during growth induction. We have now identified several phosphate-containing compounds that act as nontransported signaling agonists of Pho84. This indicates that signaling does not require complete transport of the substrate. For the nontransported agonist glycerol-3-phosphate (Gly3P), we show that it is transported by two other carriers, Git1 and Pho91, without triggering signaling. Gly3P is a competitive inhibitor of transport through Pho84, indicating direct interaction with its phosphate-binding site. We also identified phosphonoacetic acid as a competitive inhibitor of transport without agonist function for signaling. This indicates that binding of a compound into the phosphate-binding site of Pho84 is not enough to trigger signaling. Apparently, signaling requires a specific conformational change that may be part of, but does not require, the complete transport cycle. Using Substituted Cysteine Accessibility Method (SCAM) we identified Phe(160) in TMD IV and Val(392) in TMD VIII as residues exposed with their side chain into the phosphate-binding site of Pho84. Inhibition of both transport and signaling by covalent modification of Pho84(F160C) or Pho84(V392C) showed that the same binding site is used for transport of phosphate and for signaling with both phosphate and Gly3P. Our results provide to the best of our knowledge the first insight into the molecular mechanism of a phosphate transceptor.


Assuntos
Simportadores de Próton-Fosfato/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Transdução de Sinais/fisiologia , Sítios de Ligação/genética , Proteínas Quinases Dependentes de AMP Cíclico/metabolismo , Glicerofosfatos/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Mutagênese Sítio-Dirigida , Ácido Fosfonoacéticos/metabolismo , Simportadores de Próton-Fosfato/agonistas , Simportadores de Próton-Fosfato/genética , Reprodutibilidade dos Testes , Proteínas de Saccharomyces cerevisiae/agonistas , Proteínas de Saccharomyces cerevisiae/genética
14.
Environ Microbiol ; 11(1): 111-25, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-18783384

RESUMO

Phosphonates are organic compounds that contain a C-P bond and are a poorly characterized component of the marine phosphorus cycle. They may represent a potential source of bioavailable phosphorus, particularly in oligotrophic conditions. This study has investigated the distribution of the phnA gene which encodes phosphonoacetate hydrolase, the enzyme that mineralizes phosphonoacetate. Using newly designed degenerate primers targeting the phnA gene we analysed the potential for phosphonoacetate utilization in DNA and cDNA libraries constructed from a phytoplankton bloom in the Western English Channel during July 2006. Total RNA was isolated and reverse transcribed and phosphonoacetate hydrolase (phnA) transcripts were PCR amplified from the cDNA with the degenerate primers, cloned and sequenced. Phylogenetic analysis demonstrated considerable diversity with 14 sequence types yielding five unique phnA protein groups. We also identified 28 phnA homologues in a 454-pyrosequencing metagenomic and metatranscriptomic study from a coastal marine mesocosm, indicating that > 3% of marine bacteria in this study contained phnA. phnA homologues were also present in a metagenomic fosmid library from this experiment. Finally, cultures of four isolates of potential coral pathogens belonging to the Vibrionaceae contained the phnA gene. In the laboratory, these isolates were able to grow with phosphonoacetate as sole P and C source. The fact that the capacity to utilize phosphonoacetate was evident in each of the three coastal environments suggests the potential for widespread utilization of this bioavailable P source.


Assuntos
Bactérias/classificação , Bactérias/metabolismo , Ácido Fosfonoacéticos/metabolismo , Água do Mar/microbiologia , Fosfatase Alcalina , Bactérias/genética , Bactérias/isolamento & purificação , Proteínas de Bactérias/genética , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Dados de Sequência Molecular , Monoéster Fosfórico Hidrolases/genética , Filogenia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos
15.
Microb Biotechnol ; 2(2): 234-40, 2009 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-21261917

RESUMO

The phnA gene that encodes the carbon-phosphorus bond cleavage enzyme phosphonoacetate hydrolase is widely distributed in the environment, suggesting that its phosphonate substrate may play a significant role in biogeochemical phosphorus cycling. Surprisingly, however, no biogenic origin for phosphonoacetate has yet been established. To facilitate the search for its natural source we have constructed a whole-cell phosphonoacetate biosensor. The gene encoding the LysR-type transcriptional activator PhnR, which controls expression of the phosphonoacetate degradative operon in Pseudomonas fluorescens 23F, was inserted in the broad-host-range promoter probe vector pPROBE-NT, together with the promoter region of the structural genes. Cells of Escherichia coli DH5α that contained the resultant construct, pPANT3, exhibited phosphonoacetate-dependent green fluorescent protein fluorescence in response to threshold concentrations of as little as 0.5 µM phosphonoacetate, some 100 times lower than the detection limit of currently available non-biological analytical methods; the pPANT3 biosensor construct in Pseudomonas putida KT2440 was less sensitive, although with shorter response times. From a range of other phosphonates and phosphonoacetate analogues tested, only phosphonoacetaldehyde and arsonoacetate induced green fluorescent protein fluorescence in the E. coli DH5α (pPANT3) biosensor, although at much-reduced sensitivities (50 µM phosphonoacetaldehyde and 500 µM arsonoacetate).


Assuntos
Proteínas de Bactérias/metabolismo , Técnicas Biossensoriais/métodos , Escherichia coli/metabolismo , Ácido Fosfonoacéticos/metabolismo , Monoéster Fosfórico Hidrolases/metabolismo , Pseudomonas fluorescens/enzimologia , Fosfatase Alcalina , Proteínas de Bactérias/genética , Técnicas Biossensoriais/instrumentação , Escherichia coli/genética , Engenharia Genética , Óperon , Ácido Fosfonoacéticos/análise , Monoéster Fosfórico Hidrolases/genética , Pseudomonas fluorescens/genética
17.
J Appl Microbiol ; 103(1): 237-44, 2007 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-17584470

RESUMO

AIMS: Use of molecular techniques for the isolation of bacteria capable of phosphonoacetate mineralization as carbon, phosphorus and energy source. METHODS AND RESULTS: RNA extracts obtained at three different stages of an enrichment selecting for phosphonoacetate degrading bacteria were reverse transcribed using 16S rRNA-specific primers, amplified and analysed by temperature gradient gel electrophoresis (TGGE). This information was used to devise a strategy for the isolation of members of the enrichment that were otherwise difficult to obtain in pure culture. We were able to pull out, in total, four out of the six main microbial cultures that were detected by TGGE. Two of the isolates belonging to Mycobacterium and Agromyces genera were for the first time shown to grow in the presence of phosphonoacetate as sole carbon, phosphorus and energy source releasing almost equimolar levels of inorganic phosphate into the culture medium, and they were shown to exhibit phosphonoacetate hydrolase activity in vitro. CONCLUSIONS: The ubiquity of pseudomonad in degradation processes is more likely a consequence of our ignorance of bacterial requirements and physiology, rather than their possession of unique metabolic properties. SIGNIFICANCE AND IMPACT OF THE STUDY: RT-TGGE analysis can be used to guide the successful isolation of micro-organisms difficult to obtain by culture-dependent methods alone.


Assuntos
Bactérias/metabolismo , Ácido Fosfonoacéticos/metabolismo , Actinomycetales , Fosfatase Alcalina , Bactérias/genética , Bactérias/isolamento & purificação , Biodegradação Ambiental , Biodiversidade , Impressões Digitais de DNA , Eletroforese em Gel de Poliacrilamida/métodos , Mycobacterium smegmatis/enzimologia , Monoéster Fosfórico Hidrolases/metabolismo , Filogenia , Reação em Cadeia da Polimerase/métodos , RNA Bacteriano/genética , RNA Ribossômico 16S/genética
18.
Mycol Res ; 110(Pt 12): 1455-63, 2006 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-17123811

RESUMO

Among a collection of 18 fungal strains representing eight genera, only two strains (Penicillium oxalicum and P. minioluteum) were capable of growth on phosphonoacetic acid as sole phosphorous source. Enrichment liquid cultures in minimal medium with the compound as the only P-source selected four isolates, that were also identified as Penicillium spp. Phosphonoacetate metabolism did not lead to extracellular release of inorganic phosphate. In all cases phosphonoacetate hydrolase activity was detected in partially purified extracts, and a protein of the expected molecular mass reacted with polyclonal antibodies raised against the enzyme from P. oxalicum. There was no relation between phosphonoacetate hydrolase specific activity and growth rate or yield. Phosphonoacetic acid was the inducer of the hydrolase, independently of the concurrent availability of inorganic phosphate. Notwithstanding this, the utilization of the phosphonate was significantly inhibited in the presence of phosphate, suggesting an interference of the latter with phosphonoacetic acid uptake.


Assuntos
Penicillium/enzimologia , Penicillium/crescimento & desenvolvimento , Ácido Fosfonoacéticos/metabolismo , Monoéster Fosfórico Hidrolases/metabolismo , Fosfatase Alcalina , Western Blotting , Cinética , Penicillium/metabolismo , Fosfatos/metabolismo , Monoéster Fosfórico Hidrolases/antagonistas & inibidores
19.
FEMS Microbiol Lett ; 261(1): 133-40, 2006 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-16842370

RESUMO

A strain of Agromyces fucosus, designated Vs2, metabolized a range of organophosphonate compounds as sole phosphorus sources for growth and metabolized phosphonoacetate as a sole carbon, energy and phosphorus source for growth. With phosphonoacetate as the sole phosphorus source and a pyruvate carbon source, transient phosphate release to the medium was observed, in contrast to cultures grown with glucose and phosphonoacetate, where no phosphate release to the medium was observed. Carbon catabolite repression, specifically by means of inducer exclusion of phosphonoacetate, was proposed as the mechanism responsible, and phosphonoacetate hydrolase enzyme assays carried out on cell extracts confirmed that induced phosphonoacetate hydrolase activities were indeed higher in cells grown on pyruvate with phosphonoacetate as sole phosphorus source. This phenomenon has not previously been demonstrated in vivo, and must represent a significant metabolic control of organophosphonate metabolism. The catabolite repression phenomenon was also evident when A. fucosus grew on 2-aminoethylphosphonate as sole phosphorus source, allowing demonstration of a third mode of control for biodegradation of this compound. Excision of stained zymogram gel pieces, followed by tryptic digestion and mass spectrometric analysis, allowed the identification of phosphonoacetate hydrolase-derived peptides.


Assuntos
Actinomycetales/enzimologia , Carbono/metabolismo , Ácido Fosfonoacéticos/metabolismo , Actinomycetales/crescimento & desenvolvimento , Fosfatase Alcalina/metabolismo , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/fisiologia , Glucose/fisiologia , Hidrólise , Espectrometria de Massas , Monoéster Fosfórico Hidrolases/metabolismo , Ácido Pirúvico/metabolismo
20.
Biochemistry ; 44(29): 9871-9, 2005 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-16026159

RESUMO

Highly concentrated human recombinant interleukin-1 receptor antagonist (IL-1ra) aggregates at elevated temperature without perturbation in its secondary structure. The protein aggregation can be suppressed depending on the buffer ionic strength and the type of anion present in the sample solution. Phosphate is an approximately 4-fold weaker suppressant than either citrate or pyrophosphate on the basis of the measured protein aggregation rates. This is in agreement with the strength of protein-anion interactions at the IL-1ra single anion-binding site as judged by the estimated dissociation constant values of 2.9 mM, 3.8 mM, and 13.7 mM for pyrophosphate, citrate, and phosphate, respectively. The strength of binding also correlates with the anion size and with the number of ionized groups available per molecule at a given pH. Affinity probing of IL-1ra with methyl acetyl phosphate (MAP) in combination with proteolytic digestion and mass spectral analysis show that an anion-binding site location on the IL-1ra surface is contributed by lysine-93 and lysine-96 of the loop 84-98 as well as by lysine-6 of the unstructured N-terminal region 1-7. The replacement of lysine-93 with alanine by site-directed mutagenesis results in dramatically suppressed IL-1ra aggregation. Furthermore, when the unstructured N-terminal region of IL-1ra is removed by limited proteolysis, a 2-fold increase in the time course of the aggregation lag phase is observed for the truncated protein. An anion-controlled mechanism of IL-1ra aggregation is proposed by which the anion competition for the protein cationic site prevents formation of intermolecular cation-pi interactions and, thus, interferes with the protein asymmetric self-association pathway.


Assuntos
Receptores de Interleucina-1/antagonistas & inibidores , Sialoglicoproteínas/metabolismo , Marcadores de Afinidade/metabolismo , Ânions/metabolismo , Sítios de Ligação/genética , Ligação Competitiva/genética , Cátions/metabolismo , Ácido Cítrico/metabolismo , Difosfatos/metabolismo , Temperatura Alta , Humanos , Proteína Antagonista do Receptor de Interleucina 1 , Lisina/genética , Mutagênese Sítio-Dirigida , Fosfatos/metabolismo , Ácido Fosfonoacéticos/análogos & derivados , Ácido Fosfonoacéticos/metabolismo , Desnaturação Proteica , Proteínas Recombinantes/antagonistas & inibidores , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Deleção de Sequência , Sialoglicoproteínas/antagonistas & inibidores , Sialoglicoproteínas/química , Sialoglicoproteínas/genética , Transdução de Sinais/genética , Relação Estrutura-Atividade
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