RESUMO
PII proteins are signal transduction proteins that belong to a widely distributed family of proteins involved in the modulation of different metabolisms in bacteria. These proteins are homotrimers carrying a flexible loop, named T-loop, which changes its conformation due to the recognition of diverse key metabolites, ADP, ATP, and 2-oxoglutarate. PII proteins interact with different partners to primarily regulate a set of nitrogen pathways. In some organisms, PII proteins can also control carbon metabolism by interacting with the biotin carboxyl carrier protein (BCCP), a key component of the acetyl-CoA carboxylase (ACC) enzyme complex, inhibiting its activity with the consequent reduction of fatty acid biosynthesis. Most bacteria contain at least two PII proteins, named GlnB and GlnK, with different regulatory roles. In mycobacteria, only one PII protein was identified, and the three-dimensional structure was solved, however, its physiological role is unknown. In this study we purified the Mycobacterium tuberculosis (M. tb) PII protein, named GlnB, and showed that it weakly interacts with the AccA3 protein, the α subunit shared by the three different, and essential, Acyl-CoA carboxylase complexes (ACCase 4, 5, and 6) present in M. tb. A M. smegmatis deletion mutant, ∆MsPII, exhibited a growth deficiency on nitrate and nitrite as unique nitrogen sources, and accumulated nitrite in the culture supernatant. In addition, M. tb PII protein was able to interact with the C-terminal domain of the ammonium transporter Amt establishing the ancestral role for this PII protein as a GlnK functioning protein.
RESUMO
The PII family comprises a group of widely distributed signal transduction proteins ubiquitous in prokaryotes and in the chloroplasts of plants. PII proteins sense the levels of key metabolites ATP, ADP, and 2-oxoglutarate, which affect the PII protein structure and thereby the ability of PII to interact with a range of target proteins. Here, we performed multiple ligand fishing assays with the PII protein orthologue GlnZ from the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense to identify 37 proteins that are likely to be part of the PII protein-protein interaction network. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, coenzyme synthesis, RNA catabolism, and transcription. Direct binary PII-target complex was confirmed for 15 protein complexes using pulldown assays with recombinant proteins. Untargeted metabolome analysis showed that PII is required for proper homeostasis of important metabolites. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII-deficient strain showed reduced c-di-GMP levels and altered aerotaxis and flocculation behavior. These data support that PII acts as a major metabolic hub controlling important enzymes and the homeostasis of key metabolites such as c-di-GMP in response to the prevailing nutritional status.IMPORTANCE The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors.
RESUMO
Herbaspirillum seropedicae is a plant growth promoting bacterium that is able to fix nitrogen and to colonize the surface and internal tissues of important crops. Nitrogen fixation in H. seropedicae is regulated at the transcriptional level by the prokaryotic enhancer binding protein NifA. The activity of NifA is negatively affected by oxygen and positively stimulated by interaction with GlnK, a PII signaling protein that monitors intracellular levels of the key metabolite 2-oxoglutarate (2-OG) and functions as an indirect sensor of the intracellular nitrogen status. GlnK is also subjected to a cycle of reversible uridylylation in response to intracellular levels of glutamine. Previous studies have established the role of the N-terminal GAF domain of NifA in intramolecular repression of NifA activity and the role of GlnK in relieving this inhibition under nitrogen-limiting conditions. However, the mechanism of this control of NifA activity is not fully understood. Here, we constructed a series of GlnK variants to elucidate the role of uridylylation and effector binding during the process of NifA activation. Our data support a model whereby GlnK uridylylation is not necessary to activate NifA. On the other hand, binding of 2-OG and MgATP to GlnK are very important for NifA activation and constitute the most important signal of cellular nitrogen status to NifA.
Assuntos
Proteínas de Bactérias/metabolismo , Herbaspirillum , Proteínas PII Reguladoras de Nitrogênio/metabolismo , Fatores de Transcrição/metabolismo , Trifosfato de Adenosina/metabolismo , Sítio Alostérico , Escherichia coli/metabolismo , Ácidos Cetoglutáricos/metabolismo , Mutagênese , Proteínas PII Reguladoras de Nitrogênio/química , Proteínas PII Reguladoras de Nitrogênio/genética , Ligação ProteicaRESUMO
The committed and rate-limiting step in fatty acid biosynthesis is catalyzed by acetyl-CoA carboxylase (ACC). In previous studies we showed that ACC activity is inhibited through interactions with the PII signaling proteins in vitro. Here we provide in vivo support for that model; we noted that PII proteins are able to reduce malonyl-CoA levels in vivo in Escherichia coli. Furthermore, we show that fatty acid biosynthesis is strongly enhanced in E. coli strains carrying deletions in PII coding genes. Given that PII proteins act as conserved negative regulators of ACC in Bacteria, our findings may be explored to engineer other prokaryotes to improve fatty acid yields, thereby turning microbial biofuel production economically competitive in the future.
Assuntos
Proteínas de Escherichia coli/genética , Escherichia coli/metabolismo , Ácidos Graxos/biossíntese , Acetil-CoA Carboxilase/metabolismo , Biocombustíveis , Escherichia coli/genética , Deleção de Genes , Transdução de SinaisRESUMO
The nitrogen metabolism of Proteobacteria is controlled by the general Ntr system in response to nitrogen quality and availability. The PII proteins play an important role in this system by modulating the cellular metabolism through physical interaction with protein partners. Herbaspirillum seropedicae, a nitrogen-fixing bacterium, has two PII proteins paralogues, GlnB and GlnK. The interaction of H. seropedicae PII proteins with its targets is regulated by allosteric ligands and by reversible post-translational uridylylation. Both uridylylation and deuridylylation reactions are catalyzed by the same bifunctional enzyme, GlnD. The mechanism of regulation of GlnD activity is still not fully understood. Here, we characterized the regulation of deuridylylation activity of H. seropedicae GlnD in vitro. To this purpose, fully modified PII proteins were submitted to kinetics analysis of its deuridylylation catalyzed by purified GlnD. The deuridylylation activity was strongly stimulated by glutamine and repressed by 2-oxoglutarate and this repression was strong enough to overcome the glutamine stimulus of enzymatic activity. We also constructed and analyzed a truncated version of GlnD, lacking the C-terminal regulatory ACT domains. The GlnDΔACT protein catalyzed the futile cycle of uridylylation and deuridylylation of PII, regardless of glutamine and 2-oxoglutarate levels. The results presented here suggest that GlnD can sense the glutamine:2-oxoglutarate ratio and confirm that the ACT domains of GlnD are the protein sensors of environment clues of nitrogen availability.
Assuntos
Proteínas de Bactérias/metabolismo , Glutamina/metabolismo , Herbaspirillum/enzimologia , Ácidos Cetoglutáricos/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Biocatálise , Glutamina/química , Ácidos Cetoglutáricos/química , Cinética , Ligação Proteica , Domínios Proteicos , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/isolamento & purificaçãoRESUMO
The carbohydrate-uptake phosphorelay PTS system plays a key role in metabolic regulation in Bacteria controlling the utilization of secondary carbon sources. Some bacteria, such as Escherichia coli, encode a paralogous system named PTSNtr (nitrogen related PTS). PTSNtr is composed of EINtr (ptsP), NPr (ptsO), and EIIANtr (ptsN). These proteins act as a phosphorelay system from phosphoenolpyruvate to EINtr, NPr and them to EIIANtr. PTSNtr is not involved in carbohydrate uptake and it may be dedicated to performing regulatory functions. The phosphorylation state of EINtr is regulated by allosteric binding of glutamine and 2-oxoglutarate, metabolites whose intracellular levels reflect the nitrogen status. Although PTSNtr is designated as having nitrogen-sensory properties, no major effect of this system on nitrogen regulation has been described in E. coli. Here we show that an E. coli ptsN deletion mutant has impaired growth in minimal medium. Proteome analysis of the ∆ptsN strain under different nitrogen regimes revealed no involvement in regulation of the canonical nitrogen regulatory (Ntr) system. The proteomic data support the conclusion that ptsN is required to balance the activities of the sigma factors RpoS and RpoD in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed. SIGNIFICANCE: The nitrogen related PTSNtr phosphorelay system has been hypothesized to participate in the control of nitrogen metabolism. Here we used a proteomics approach to show that an Escherichia coli ptsN null strain, which misses the final module of PTSNtr phosphorelay, has no significant effects on nitrogen metabolism under different nitrogen regimes. We noted that ptsN is required for fitness under minimal medium and for the proper balance between RpoS and sigma 70 activities in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed.
Assuntos
Proteínas de Bactérias/genética , Proteínas de Escherichia coli/genética , Escherichia coli/química , Nitrogênio/metabolismo , Sistema Fosfotransferase de Açúcar do Fosfoenolpiruvato/genética , Proteoma/análise , Fator sigma/genética , RNA Polimerases Dirigidas por DNA/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica , Técnicas de Inativação de Genes , Sistema Fosfotransferase de Açúcar do Fosfoenolpiruvato/metabolismo , Fosforilação , ProteômicaRESUMO
The PII protein family constitutes one of the most conserved and well distributed family of signal transduction proteins in nature. These proteins play key roles in nitrogen and carbon metabolism. PII function has been well documented in Gram-negative bacteria. However, there are very few reports describing the in vitro properties and function of PII derived from Gram-positive bacteria. Here we present the heterologous expression and efficient purification protocols for untagged PII from three Actinobacteria of medical and biotechnological interest namely: Mycobacterium tuberculosis, Rhodococcus jostii and Streptomyces coelicolor. Circular dichroism and gel filtration analysis supported that the purified proteins are correctly folded. The purification protocol described here will facilitate biochemical studies and help to uncover the biochemical functions of PII proteins in Actinobacteria.
RESUMO
Nitrogen is needed for the biosynthesis of biomolecules including proteins and nucleic acids. In the absence of fixed nitrogen prokaryotes such as E. coli immediately ceases growth. Ammonium is the preferred nitrogen source for E. coli supporting the fastest growth rates. Under conditions of ammonium limitation, E. coli can use alternative nitrogen sources to supply ammonium ions and this reprogramming is led by the induction of the NtrC regulon. Here we used label free proteomics to determine the dynamics of E. coli proteins expression in response to ammonium starvation in both the short (30min) and the longer (60min) starvation. Protein abundances and post-translational modifications confirmed that activation of the NtrC regulon acts as the first line of defense against nitrogen starvation. The ribosome inactivating protein Rmf was induced shortly after ammonium exhaustion and this was preceded by induction of other ribosome inactivating proteins such as Hpf and RaiA supporting the hypothesis that ribosome shut-down is a key process during nitrogen limitation stress. The proteomic data revealed that growth arrest due to nitrogen starvation correlates with the accumulation of proteins involved in DNA condensation, RNA and protein catabolism and ribosome hibernation. Collectively, these proteome adaptations will result in metabolic inactive cells which are likely to exhibit multidrug tolerance.
Assuntos
Escherichia coli/metabolismo , Nitrogênio/metabolismo , Proteoma/metabolismo , Compostos de Amônio/metabolismo , Proteínas de Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica/fisiologia , Processamento de Proteína Pós-Traducional/fisiologia , Proteômica/métodos , Proteínas Ribossômicas/metabolismo , Ribossomos/metabolismoRESUMO
Snake venom metalloproteinases (SVMPs) play key biological roles in prey immobilization and digestion. The majority of these activities depend on the hydrolysis of relevant protein substrates in the tissues. Hereby, we describe several isoforms and a cDNA clone sequence, corresponding to PII SVMP homologues from the venom of the Central American pit viper Bothriechis lateralis, which have modifications in the residues of the canonical sequence of the zinc-binding motif HEXXHXXGXXH. As a consequence, the proteolytic activity of the isolated proteins was undetectable when tested on azocasein and gelatin. These PII isoforms comprise metalloproteinase and disintegrin domains in the mature protein, thus belonging to the subclass PIIb of SVMPs. PII SVMP homologues were devoid of hemorrhagic and in vitro coagulant activities, effects attributed to the enzymatic activity of SVMPs, but induced a mild edema. One of the isoforms presents the characteristic RGD sequence in the disintegrin domain and inhibits ADP- and collagen-induced platelet aggregation. Catalytically-inactive SVMP homologues may have been hitherto missed in the characterization of snake venoms. The presence of such enzymatically-inactive homologues in snake venoms and their possible toxic and adaptive roles deserve further investigation.
Assuntos
Metaloproteases/isolamento & purificação , Peptídeos/isolamento & purificação , Venenos de Serpentes/química , Viperidae , Adulto , Sequência de Aminoácidos , Animais , Coagulação Sanguínea/efeitos dos fármacos , Caseínas/metabolismo , Clonagem Molecular , DNA Complementar/genética , Edema , Gelatina/metabolismo , Hemorragia , Humanos , Metaloproteases/química , Metaloproteases/genética , Metaloproteases/farmacologia , Camundongos , Modelos Moleculares , Peptídeos/química , Peptídeos/genética , Peptídeos/farmacologia , Agregação Plaquetária/efeitos dos fármacos , Domínios Proteicos , Proteólise , Zinco/metabolismoRESUMO
Nitrogen metabolism in Proteobacteria is controlled by the Ntr system, in which PII proteins play a pivotal role, controlling the activity of target proteins in response to the metabolic state of the cell. Characterization of the binding of molecular effectors to these proteins can provide information about their regulation. Here, the binding of ATP, ADP and 2-oxoglutarate (2-OG) to the Herbaspirillum seropedicae PII proteins, GlnB and GlnK, was characterized using isothermal titration calorimetry. Results show that these proteins can bind three molecules of ATP, ADP and 2-OG with homotropic negative cooperativity, and 2-OG binding stabilizes the binding of ATP. Results also show that the affinity of uridylylated forms of GlnB and GlnK for nucleotides is significantly lower than that of the nonuridylylated proteins. Furthermore, fluctuations in the intracellular concentration of 2-OG in response to nitrogen availability are shown. Results suggest that under nitrogen-limiting conditions, PII proteins tend to bind ATP and 2-OG. By contrast, after an ammonium shock, a decrease in the 2-OG concentration is observed causing a decrease in the affinity of PII proteins for ATP. This phenomenon may facilitate the exchange of ATP for ADP on the ligand-binding pocket of PII proteins, thus it is likely that under low ammonium, low 2-OG levels would favor the ADP-bound state.
Assuntos
Difosfato de Adenosina/metabolismo , Trifosfato de Adenosina/metabolismo , Proteínas de Bactérias/metabolismo , Herbaspirillum/enzimologia , Ácidos Cetoglutáricos/metabolismo , Nucleotidiltransferases/metabolismo , Proteínas PII Reguladoras de Nitrogênio/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Calorimetria , Glutamato-Amônia Ligase/química , Glutamato-Amônia Ligase/genética , Glutamato-Amônia Ligase/metabolismo , Herbaspirillum/fisiologia , Cinética , Ligantes , Fixação de Nitrogênio , Nucleotidiltransferases/química , Nucleotidiltransferases/genética , Proteínas PII Reguladoras de Nitrogênio/química , Proteínas PII Reguladoras de Nitrogênio/genética , Proteínas Quinases/química , Proteínas Quinases/genética , Proteínas Quinases/metabolismo , Processamento de Proteína Pós-Traducional , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Estresse Fisiológico , TitulometriaRESUMO
The trimeric PII signal transduction proteins regulate the function of a variety of target proteins predominantly involved in nitrogen metabolism. ATP, ADP and 2-oxoglutarate (2-OG) are key effector molecules influencing PII binding to targets. Studies of PII proteins have established that the 20-residue T-loop plays a central role in effector sensing and target binding. However, the specific effects of effector binding on T-loop conformation have remained poorly documented. We present eight crystal structures of the Azospirillum brasilense PII protein GlnZ, six of which are cocrystallized and liganded with ADP or ATP. We find that interaction with the diphosphate moiety of bound ADP constrains the N-terminal part of the T-loop in a characteristic way that is maintained in ADP-promoted complexes with target proteins. In contrast, the interactions with the triphosphate moiety in ATP complexes are much more variable and no single predominant interaction mode is apparent except for the ternary MgATP/2-OG complex. These conclusions can be extended to most investigated PII proteins of the GlnB/GlnK subfamily. Unlike reported for other PII proteins, microcalorimetry reveals no cooperativity between the three binding sites of GlnZ trimers for any of the three effectors under carefully controlled experimental conditions.
Assuntos
Azospirillum brasilense/metabolismo , Proteínas de Bactérias/química , Nitrogênio/metabolismo , Termodinâmica , Difosfato de Adenosina/metabolismo , Trifosfato de Adenosina/metabolismo , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Calorimetria , Cristalografia por Raios X , Ácidos Cetoglutáricos/metabolismo , Modelos Moleculares , Ligação Proteica , Conformação ProteicaRESUMO
A new homodimeric PII metalloproteinase, named BlatH1, was purified from the venom of the Central American arboreal viperid snake Bothriechis lateralis by a combination of anion-exchange chromatography, hydrophobic interaction chromatography, and gel filtration. BlatH1 is a glycoprotein of 84 kDa. The mature protein contains a metalloproteinase domain, with the characteristic zinc-binding motif (HEXXHXXGXXH) followed by the sequence CIM at the Met-turn. In the disintegrin domain, the tripeptide sequence TDN substitutes the characteristic RGD motif found in many disintegrins. BlatH1 hydrolyzed azocasein, gelatin and fibrinogen, and exerts a potent local and systemic hemorrhagic activity in mice. The hemorrhagic activity of BlatH1 is not inhibited by the plasma proteinase inhibitor α2-macroglobulin, although the SVMP is able to cleave this plasma inhibitor, generating a 90 kDa product. BlatH1 inhibits ADP- and collagen-induced human platelet aggregation (IC50 = 0.3 µM and 0.7 µM for ADP and collagen, respectively). This activity is abrogated when the enzyme is preincubated with the metalloproteinase inhibitor Batimastat, implying that it depends on proteolysis. In agreement, a synthetic peptide containing the sequence TDN of the disintegrin domain is unable to inhibit platelet aggregation. BlatH1 is a valuable tool to understand the structural determinants of toxicity in PII SVMPs.
Assuntos
Venenos de Crotalídeos/enzimologia , Metaloproteases/química , Proteínas de Répteis/química , Viperidae , Sequência de Aminoácidos , Animais , Sequência de Bases , Clonagem Molecular , Venenos de Crotalídeos/toxicidade , Hemorragia/induzido quimicamente , Humanos , Dose Letal Mediana , Pulmão/efeitos dos fármacos , Pulmão/patologia , Metaloproteases/fisiologia , Metaloproteases/toxicidade , Camundongos , Dados de Sequência Molecular , Agregação Plaquetária/efeitos dos fármacos , Estrutura Quaternária de Proteína , Proteólise , Proteínas de Répteis/fisiologia , Proteínas de Répteis/toxicidade , Análise de Sequência de Proteína , alfa-Macroglobulinas/químicaRESUMO
The control of nitrogen metabolism in pathogenic Gram-positive bacteria has been studied in a variety of species and is involved with the expression of virulence factors. To date, no data have been reported regarding nitrogen metabolism in the odontopathogenic species Streptococcus mutans. GlnR, which controls nitrogen assimilation in the related bacterial species, Bacillus subtilis, was assessed in S. mutans for its DNA and protein binding activity. Electrophoretic mobility shift assay of the S. mutans GlnR protein indicated that GlnR binds to promoter regions of the glnRA and amtB-glnK operons. Cross-linking and pull-down assays demonstrated that GlnR interacts with GlnK, a signal transduction protein that coordinates the regulation of nitrogen metabolism. Upon formation of this stable complex, GlnK enhances the affinity of GlnR for the glnRA operon promoter. These results support an involvement of GlnR in transcriptional regulation of nitrogen metabolism-related genes and indicate that GlnK relays information regarding ammonium availability to GlnR.
Assuntos
Animais , Ratos , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica/genética , Nitrogênio/metabolismo , Óperon/genética , Regiões Promotoras Genéticas/genética , Streptococcus mutans/metabolismo , Sequência de Bases , Proteínas de Bactérias/genética , DNA Bacteriano/genética , Dados de Sequência Molecular , Ratos Wistar , Streptococcus mutans/genéticaRESUMO
Azospirillum brasilense is a diazotroph found in association with important agricultural crops. In this organism, the regulation of nitrogen fixation by ammonium ions involves several proteins including the uridylyltransferase/uridylyl-removing enzyme, GlnD, which reversibly uridylylates the two PII proteins, GlnB and GlnZ, in response to the concentration of ammonium ions. In the present study, the uridylylation/deuridylylation cycle of A. brasilense GlnB and GlnZ proteins by GlnD was reconstituted in vitro using the purified proteins. The uridylylation assay was analyzed using non-denaturing polyacrylamide gel electrophoresis and fluorescent protein detection. Our results show that the purified A. brasilense GlnB and GlnZ proteins were uridylylated by the purified A. brasilense GlnD protein in a process dependent on ATP and 2-oxoglutarate. The dependence on ATP for uridylylation was similar for both proteins. On the other hand, at micromolar concentration of 2-oxoglutarate (up to 100 µM), GlnB uridylylation was almost twice that of GlnZ, an effect that was not observed at higher concentrations of 2-oxoglutarate (up to 10 mM). Glutamine inhibited uridylylation and stimulated deuridylylation of both GlnB and GlnZ. However, glutamine seemed to inhibit GlnZ uridylylation more efficiently. Our results suggest that the differences in the uridylylation pattern of GlnB and GlnZ might be important for fine-tuning of the signaling pathway of cellular nitrogen status in A. brasilense.