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1.
Biochem J ; 475(1): 137-150, 2018 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-29187521

RESUMO

Dihydrodipicolinate reductase (DHDPR) catalyses the second reaction in the diaminopimelate pathway of lysine biosynthesis in bacteria and plants. In contrast with the tetrameric bacterial DHDPR enzymes, we show that DHDPR from Vitis vinifera (grape) and Selaginella moellendorffii are dimeric in solution. In the present study, we have also determined the crystal structures of DHDPR enzymes from the plants Arabidopsis thaliana and S. moellendorffii, which are the first dimeric DHDPR structures. The analysis of these models demonstrates that the dimer forms through the intra-strand interface, and that unique secondary features in the plant enzymes block tetramer assembly. In addition, we have also solved the structure of tetrameric DHDPR from the pathogenic bacteria Neisseria meningitidis Measuring the activity of plant DHDPR enzymes showed that they are much more prone to substrate inhibition than the bacterial enzymes, which appears to be a consequence of increased flexibility of the substrate-binding loop and higher affinity for the nucleotide substrate. This higher propensity to substrate inhibition may have consequences for ongoing efforts to increase lysine biosynthesis in plants.


Assuntos
Proteínas de Bactérias/química , Di-Hidrodipicolinato Redutase/química , Ácidos Picolínicos/química , Proteínas de Plantas/química , Vitis/enzimologia , Motivos de Aminoácidos , Arabidopsis/química , Arabidopsis/enzimologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Coenzimas/química , Coenzimas/metabolismo , Cristalografia por Raios X , Di-Hidrodipicolinato Redutase/genética , Di-Hidrodipicolinato Redutase/metabolismo , Expressão Gênica , Cinética , Lisina/biossíntese , Modelos Moleculares , NAD/química , NAD/metabolismo , NADP/química , NADP/metabolismo , Neisseria meningitidis/química , Neisseria meningitidis/enzimologia , Ácidos Picolínicos/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Multimerização Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Selaginellaceae/química , Selaginellaceae/enzimologia , Especificidade da Espécie , Especificidade por Substrato , Vitis/química
2.
Biotechnol Bioeng ; 115(7): 1764-1777, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29574741

RESUMO

l-lysine is an important amino acid in animals and humans and NADPH is a vital cofactor for maximizing the efficiency of l-lysine fermentation. Dihydrodipicolinate reductase (DHDPR), an NAD(P)H-dependent enzyme, shows a variance in nucleotide-cofactor affinity in bacteria. In this study, we rationally engineered Corynebacterium glutamicum DHDPR (CgDHDPR) to switch its nucleotide-cofactor specificity resulting in an increase in final titer (from 82.6 to 117.3 g L-1 ), carbon yield (from 0.35 to 0.44 g [g glucose]-1 ) and productivity (from 2.07 to 2.93 g L-1 hr-1 ) of l-lysine in JL-6 ΔdapB::Ec-dapBC115G,G116C in fed-batch fermentation. To do this, we comparatively analyzed the characteristics of CgDHDPR and Escherichia coli DHDPR (EcDHDPR), indicating that hetero-expression of NADH-dependent EcDHDPR increased l-lysine production. Subsequently, we rationally modified the conserved structure of cofactor-binding motif, and results indicated that introducing the mutation K11A or R13A in CgDHDPR and introducing the mutation R16A or R39A in EcDHDPR modifies the nucleotide-cofactor affinity of DHDPR. Lastly, the effects of these mutated DHDPRs on l-lysine production were investigated. The highest increase (26.2%) in l-lysine production was observed for JL-6 ΔdapB::Ec-dapBC115G,G116C , followed by JL-6 Cg-dapBC37G,G38C (21.4%) and JL-6 ΔdapB::Ec-dapBC46G,G47C (15.2%). This is the first report of a rational modification of DHDPR that enhances the l-lysine production and yield through the modulation of nucleotide-cofactor specificity.


Assuntos
Coenzimas/metabolismo , Corynebacterium glutamicum/enzimologia , Di-Hidrodipicolinato Redutase/genética , Di-Hidrodipicolinato Redutase/metabolismo , Lisina/metabolismo , Nucleotídeos/metabolismo , Substituição de Aminoácidos , Escherichia coli/genética , Escherichia coli/metabolismo , Fermentação , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
3.
World J Microbiol Biotechnol ; 34(2): 22, 2018 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-29302824

RESUMO

Brucellae are intracellular bacterial pathogens that cause Brucellosis, bringing great economic burdens to developing countries. The pathogenic mechanisms of Brucella are still poorly understood. Earlier immune response plays an important role in the Brucella infection. Phosphoglyceromutase (PGM) and dihydrodipicolinate reductase (DapB) were cloned, expressed, purified, and their immunocompetence was analyzed. Cytokines were detected by murine macrophages (RAW 264.7) and splenocytes that stimulated with the two recombinant proteins. The immune responses were analyzed by ELISA from mice with the two recombinant proteins immunized. TNF-α, IL-6 and IL-8 were produced in stimulated RAW 264.7 cells and splenocytes. Th1-type cytokines, IFN-γ and IL-2, induced in RAW 264.7 cells and splenocytes were higher then Th2-type cytokines, IL-4 and IL-5. Th2-related immune response was induced in splenocytes obtained 35 days after mice immunized with the two proteins. The production of IgG1 was higher than IgG2a in immunized mice. Taken together, our results demonstrated that the two proteins could induce Th1 and Th2-type immune responses in vivo and in vitro.


Assuntos
Brucella abortus/enzimologia , Brucella abortus/imunologia , Brucelose/imunologia , Di-Hidrodipicolinato Redutase/farmacologia , Fosfoglicerato Mutase/farmacologia , Células Th1/efeitos dos fármacos , Células Th2/efeitos dos fármacos , Animais , Brucella abortus/genética , Brucelose/microbiologia , China , Clonagem Molecular , Citocinas/imunologia , Citocinas/metabolismo , Di-Hidrodipicolinato Redutase/genética , Feminino , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos , Imunização , Imunoglobulina G , Interferon gama/metabolismo , Interleucina-2/metabolismo , Interleucina-4/metabolismo , Interleucina-5/metabolismo , Interleucina-6/metabolismo , Interleucina-8/metabolismo , Macrófagos/efeitos dos fármacos , Macrófagos/imunologia , Camundongos , Camundongos Endogâmicos BALB C , Fosfoglicerato Mutase/genética , Células RAW 264.7/efeitos dos fármacos , Proteínas Recombinantes/imunologia , Células Th1/imunologia , Células Th2/imunologia , Fator de Necrose Tumoral alfa/imunologia , Fator de Necrose Tumoral alfa/metabolismo
4.
Artigo em Inglês | MEDLINE | ID: mdl-23722845

RESUMO

Acinetobacter baumannii is a virulent pathogenic bacterium that is resistant to most currently available antibiotics. Therefore, the design of drugs for the treatment of infections caused by A. baumannii is urgently required. Dihydrodipicolinate reductase (DHDPR) is an important enzyme which is involved in the biosynthetic pathway that leads to the production of L-lysine in bacteria. In order to design potent inhibitors against this enzyme, its detailed three-dimensional structure is required. DHDPR from A. baumannii (AbDHDPR) has been cloned, expressed, purified and crystallized. Here, the preliminary X-ray crystallographic data of AbDHDPR are reported. The crystals were grown using the hanging-drop vapour-diffusion method with PEG 3350 as the precipitating agent The crystals belonged to the orthorhombic space group P222, with unit-cell parameters a = 80.0, b = 100.8, c = 147.6 Å, and contained four molecules in the asymmetric unit. The complete structure determination of AbDHDPR is in progress.


Assuntos
Clonagem Molecular , Di-Hidrodipicolinato Redutase/química , Di-Hidrodipicolinato Redutase/genética , Regulação Enzimológica da Expressão Gênica , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Clonagem Molecular/métodos , Cristalização , Cristalografia por Raios X , Di-Hidrodipicolinato Redutase/isolamento & purificação , Dados de Sequência Molecular
5.
Microbiol Spectr ; 11(6): e0135923, 2023 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-37855602

RESUMO

IMPORTANCE: Non-compliance to lengthy antituberculosis (TB) treatment regimen, associated side effects, and emergence of drug-resistant strains of Mycobacterium tuberculosis (M. tb) emphasize the need to develop more effective anti-TB drugs. Here, we have evaluated the role of M. tb dihydrodipicolinate reductase (DapB), a component of the diaminopimelate pathway, which is involved in the biosynthesis of both lysine and mycobacterial cell wall. We showed that DapB is essential for the in vitro as well as intracellular growth of M. tb. We further utilized M. tb DapB, as a target for identification of inhibitors by employing in silico virtual screening, and conducted various in vitro screening assays to identify inhibitors with potential to inhibit DapB activity and in vitro and intracellular growth of M. tb with no significant cytotoxicity against various mammalian cell lines. Altogether, M. tb DapB serves as an important drug target and a hit molecule, namely, 4-(3-Phenylazoquinoxalin-2-yl) butanoic acid methyl ester has been identified as an antimycobacterial molecule in our study.


Assuntos
Mycobacterium tuberculosis , Animais , Di-Hidrodipicolinato Redutase/farmacologia , Oxirredutases/metabolismo , Sistemas de Liberação de Medicamentos , Antituberculosos/farmacologia , Mamíferos
6.
Commun Biol ; 6(1): 550, 2023 05 22.
Artigo em Inglês | MEDLINE | ID: mdl-37217566

RESUMO

Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.


Assuntos
Arabidopsis , Herbicidas , Humanos , Herbicidas/farmacologia , Di-Hidrodipicolinato Redutase/farmacologia , Lisina , Plantas Daninhas , Bactérias
7.
Biochim Biophys Acta ; 1814(12): 1900-9, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21803176

RESUMO

To gain insights into the role of quaternary structure in the TIM-barrel family of enzymes, we introduced mutations to the DHDPS enzyme of Thermotoga maritima, which we have previously shown to be a stable tetramer in solution. These mutations were aimed at reducing the number of salt bridges at one of the two tetramerization interface of the enzyme, which contains many more interactions than the well characterized equivalent interface of the mesophilic Escherichia coli DHDPS enzyme. The resulting variants had altered quaternary structure, as shown by analytical ultracentrifugation, gel filtration liquid chromatography, and small angle X-ray scattering, and X-ray crystallographic studies confirmed that one variant existed as an independent monomer, but with few changes to the secondary and tertiary structure. Reduction of higher order assembly resulted in a loss of thermal stability, as measured by a variety of methods, and impaired catalytic function. Binding of pyruvate increased the oligomeric status of the variants, with a concomitant increase in thermal stability, suggesting a role for substrate binding in optimizing stable, higher order structures. The results of this work show that the salt bridges located at the tetramerization interface of DHDPS play a significant role in maintaining higher order structures, and demonstrate the importance of quaternary structure in determining protein stability and in the optimization of enzyme catalysis.


Assuntos
Di-Hidrodipicolinato Redutase/química , Di-Hidrodipicolinato Redutase/metabolismo , Multimerização Proteica/fisiologia , Calibragem , Clonagem Molecular , Di-Hidrodipicolinato Redutase/genética , Di-Hidrodipicolinato Redutase/isolamento & purificação , Variação Genética , Isoenzimas/química , Isoenzimas/genética , Isoenzimas/metabolismo , Modelos Moleculares , Mutagênese Sítio-Dirigida , Proteínas Mutantes/química , Proteínas Mutantes/isolamento & purificação , Proteínas Mutantes/metabolismo , Ligação Proteica/genética , Ligação Proteica/fisiologia , Domínios e Motivos de Interação entre Proteínas/genética , Domínios e Motivos de Interação entre Proteínas/fisiologia , Multimerização Proteica/genética , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Especificidade por Substrato/genética , Thermotoga maritima/química , Thermotoga maritima/enzimologia , Thermotoga maritima/genética , Thermotoga maritima/metabolismo
8.
Protein Expr Purif ; 85(1): 66-76, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-22776412

RESUMO

Given the rise of multi drug resistant bacterial strains, such as methicillin-resistant Staphylococcus aureus (MRSA), there is an urgent need to discover new antimicrobial agents. A validated but as yet unexplored target for new antibiotics is dihydrodipicolinate reductase (DHDPR), an enzyme that catalyzes the second step of the lysine biosynthesis pathway in bacteria. We report here the cloning, expression and purification of N-terminally his-tagged recombinant DHDPR from MRSA (6H-MRSA-DHDPR) and compare its secondary and quaternary structure with the wild type (MRSA-DHDPR) enzyme. Comparative analyses demonstrate that recombinant 6H-MRSA-DHDPR is folded and adopts the native tetrameric quaternary structure in solution. Furthermore, kinetic studies show 6H-MRSA-DHDPR is functional, displaying parameters for K(m)(NADH) of 6.0 µM, K(m)(DHDP) of 22 µM, and k(cat) of 21s(-1), which are similar to those reported for the native enzyme. The solution properties and stability of the 6H-MRSA-DHDPR enzyme are also reported in varying physicochemical conditions.


Assuntos
Di-Hidrodipicolinato Redutase/química , Di-Hidrodipicolinato Redutase/metabolismo , Staphylococcus aureus Resistente à Meticilina/enzimologia , Clonagem Molecular , Di-Hidrodipicolinato Redutase/genética , Di-Hidrodipicolinato Redutase/isolamento & purificação , Estabilidade Enzimática , Histidina/química , Histidina/genética , Histidina/isolamento & purificação , Histidina/metabolismo , Cinética , Staphylococcus aureus Resistente à Meticilina/química , Staphylococcus aureus Resistente à Meticilina/genética , Concentração Osmolar , Conformação Proteica , Dobramento de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo
9.
Arch Biochem Biophys ; 512(2): 167-74, 2011 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-21704017

RESUMO

Given the rapid rise in antibiotic resistance, including methicillin resistance in Staphylococcus aureus (MRSA), there is an urgent need to characterize novel drug targets. Enzymes of the lysine biosynthesis pathway in bacteria are examples of such targets, including dihydrodipicolinate reductase (DHDPR, E.C. 1.3.1.26), which is the product of an essential bacterial gene. DHDPR catalyzes the NAD(P)H-dependent reduction of dihydrodipicolinate (DHDP) to tetrahydrodipicolinate (THDP) in the lysine biosynthesis pathway. We show that MRSA-DHDPR exhibits a unique nucleotide specificity utilizing NADPH (K(m)=12µM) as a cofactor more effectively than NADH (K(m)=26µM). However, the enzyme is inhibited by high concentrations of DHDP when using NADPH as a cofactor, but not with NADH. Isothermal titration calorimetry (ITC) studies reveal that MRSA-DHDPR has ∼20-fold greater binding affinity for NADPH (K(d)=1.5µM) relative to NADH (K(d)=29µM). Kinetic investigations in tandem with ITC studies show that the enzyme follows a compulsory-order ternary complex mechanism; with inhibition by DHDP through the formation of a nonproductive ternary complex with NADP(+). This work describes, for the first time, the catalytic mechanism and cofactor preference of MRSA-DHDPR, and provides insight into rational approaches to inhibiting this valid antimicrobial target.


Assuntos
Di-Hidrodipicolinato Redutase/metabolismo , Staphylococcus aureus Resistente à Meticilina/enzimologia , Sequência de Aminoácidos , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Calorimetria , Catálise , Di-Hidrodipicolinato Redutase/antagonistas & inibidores , Di-Hidrodipicolinato Redutase/química , Di-Hidrodipicolinato Redutase/genética , Escherichia coli/enzimologia , Escherichia coli/genética , Cinética , Staphylococcus aureus Resistente à Meticilina/genética , Dados de Sequência Molecular , NAD/metabolismo , NADP/metabolismo , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Termodinâmica
10.
Acta Crystallogr D Biol Crystallogr ; 66(Pt 1): 61-72, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-20057050

RESUMO

Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the alpha,beta-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.


Assuntos
Proteínas de Bactérias/química , Di-Hidrodipicolinato Redutase/química , Mycobacterium tuberculosis/enzimologia , NAD/química , Regulação Alostérica , Proteínas de Bactérias/metabolismo , Cristalização , Cristalografia por Raios X , Di-Hidrodipicolinato Redutase/metabolismo , Hidroliases/metabolismo , NAD/metabolismo , Ligação Proteica , Conformação Proteica , Piridinas/metabolismo
11.
Metab Eng ; 12(4): 341-51, 2010 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-20381632

RESUMO

In the present work the Gram-positive bacterium Corynebacterium glutamicum was engineered into an efficient, tailor-made production strain for diaminopentane (cadaverine), a highly attractive building block for bio-based polyamides. The engineering comprised expression of lysine decarboxylase (ldcC) from Escherichia coli, catalyzing the conversion of lysine into diaminopentane, and systems-wide metabolic engineering of central supporting pathways. Substantially re-designing the metabolism yielded superior strains with desirable properties such as (i) the release from unwanted feedback regulation at the level of aspartokinase and pyruvate carboxylase by introducing the point mutations lysC311 and pycA458, (ii) an optimized supply of the key precursor oxaloacetate by amplifying the anaplerotic enzyme, pyruvate carboxylase, and deleting phosphoenolpyruvate carboxykinase which otherwise removes oxaloacetate, (iii) enhanced biosynthetic flux via combined amplification of aspartokinase, dihydrodipicolinate reductase, diaminopimelate dehydrogenase and diaminopimelate decarboxylase, and (iv) attenuated flux into the threonine pathway competing with production by the leaky mutation hom59 in the homoserine dehydrogenase gene. Lysine decarboxylase proved to be a bottleneck for efficient production, since its in vitro activity and in vivo flux were closely correlated. To achieve an optimal strain having only stable genomic modifications, the combination of the strong constitutive C. glutamicum tuf promoter and optimized codon usage allowed efficient genome-based ldcC expression and resulted in a high diaminopentane yield of 200 mmol mol(-1). By supplementing the medium with 1 mgL(-1) pyridoxal, the cofactor of lysine decarboxylase, the yield was increased to 300 mmol mol(-1). In the production strain obtained, lysine secretion was almost completely abolished. Metabolic analysis, however, revealed substantial formation of an as yet unknown by-product. It was identified as an acetylated variant, N-acetyl-diaminopentane, which reached levels of more than 25% of that of the desired product.


Assuntos
Cadaverina/biossíntese , Corynebacterium glutamicum/genética , Corynebacterium glutamicum/metabolismo , Redes e Vias Metabólicas/genética , Aminoácido Oxirredutases/metabolismo , Aspartato Quinase/genética , Aspartato Quinase/metabolismo , Carboxiliases/genética , Carboxiliases/metabolismo , Di-Hidrodipicolinato Redutase/metabolismo , Retroalimentação Fisiológica , Regulação Bacteriana da Expressão Gênica , Engenharia Genética , Homosserina Desidrogenase/genética , Homosserina Desidrogenase/metabolismo , Lisina/metabolismo , Ácido Oxaloacético/metabolismo , Fosfoenolpiruvato Carboxiquinase (ATP)/metabolismo , Mutação Puntual , Piridoxal/metabolismo , Piruvato Carboxilase/genética , Piruvato Carboxilase/metabolismo , Biologia de Sistemas , Treonina/metabolismo
12.
Artigo em Inglês | MEDLINE | ID: mdl-20057072

RESUMO

Dihydrodipicolinate reductase (DHDPR; EC 1.3.1.26) catalyzes the nucleotide (NADH/NADPH) dependent second step of the lysine-biosynthesis pathway in bacteria and plants. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPR from methicillin-resistant Staphylococcus aureus (MRSA-DHDPR) are presented. The enzyme was crystallized in a number of forms, predominantly with ammonium sulfate as a precipitant, with the best crystal form diffracting to beyond 3.65 A resolution. Crystal structures of the apo form as well as of cofactor (NADPH) bound and inhibitor (2,6-pyridinedicarboxylate) bound forms of MRSA-DHDPR will provide insight into the structure and function of this essential enzyme and valid drug target.


Assuntos
Di-Hidrodipicolinato Redutase/química , Staphylococcus aureus Resistente à Meticilina/enzimologia , Clonagem Molecular , Cristalização , Cristalografia por Raios X
13.
Biochim Biophys Acta Mol Cell Res ; 1867(11): 118822, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32800924

RESUMO

Plastocyanin and cytochrome c6, abundant proteins in photosynthesis, are readouts for cellular copper status in Chlamydomonas and other algae. Their accumulation is controlled by a transcription factor copper response regulator (CRR1). The replacement of copper-containing plastocyanin with heme-containing cytochrome c6 spares copper and permits preferential copper (re)-allocation to cytochrome oxidase. Under copper-replete situations, the quota depends on abundance of various cuproproteins and is tightly regulated, except under zinc-deficiency where acidocalcisomes over-accumulate Cu(I). CRR1 has a transcriptional activation domain, a Zn-dependent DNA binding SBP-domain with a nuclear localization signal, and a C-terminal Cys-rich region that represses the zinc regulon. CRR1 activates >60 genes in Chlamydomonas through GTAC-containing CuREs; transcriptome differences are recapitulated in the proteome. The differentially-expressed genes encode assimilatory copper transporters of the CTR/SLC31 family including a novel soluble molecule, redox enzymes in the tetrapyrrole pathway that promote chlorophyll biosynthesis and photosystem 1 accumulation, and other oxygen-dependent enzymes, which may influence thylakoid membrane lipids, specifically polyunsaturated galactolipids and γ-tocopherol. CRR1 also down-regulates 2 proteins in Chlamydomonas: for plastocyanin, by activation of proteolysis, while for the di­iron subunit of the cyclase in chlorophyll biosynthesis, through activation of an upstream promoter that generates a poorly-translated 5' extended transcript containing multiple short ORFs that inhibit translation. The functions of many CRR1-target genes are unknown, and the copper protein inventory in Chlamydomonas includes several whose functions are unexplored. The comprehensive picture of cuproproteins and copper homeostasis in this system is well-suited for reverse genetic analyses of these under-investigated components in copper biology.


Assuntos
Chlamydomonas/genética , Cobre/metabolismo , Fotossíntese/genética , Transcriptoma/genética , Chlamydomonas/metabolismo , Citocromos c6/genética , Di-Hidrodipicolinato Redutase/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Regulação da Expressão Gênica de Plantas/genética , Homeostase/genética , Plastocianina/genética
14.
J Bacteriol ; 190(15): 5224-9, 2008 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-18502871

RESUMO

The Escherichia coli dapB gene encodes one of the enzymes of the biosynthetic pathway leading to lysine and its immediate precursor, diaminopimelate. Expression of dapB is repressed by lysine, but no trans-acting regulator has been identified so far. Our analysis of the dapB regulatory region shows that sequences located in the -81/-118 interval upstream of the transcription start site are essential for full expression of dapB, as well as for lysine repression. Screening a genomic library for a gene that could alleviate lysine repression when present in multicopy led to the recovery of argP, a gene encoding an activating protein of the LysR-type family, known to use lysine as an effector. An argP null mutation strongly decreases dapB transcription that becomes insensitive to lysine. Purified His(6)-tagged ArgP protein binds with an apparent K(d) of 35 nM to the dapB promoter in a gel retardation assay, provided that sequences up to -103 are present. In the presence of L-lysine and L-arginine, the binding of ArgP to dapB is partly relieved. These results fit with a model in which ArgP contributes to enhanced transcription of dapB when lysine becomes limiting.


Assuntos
Proteínas de Ligação a DNA/metabolismo , Di-Hidrodipicolinato Redutase/biossíntese , Proteínas de Escherichia coli/biossíntese , Escherichia coli/fisiologia , Regulação Bacteriana da Expressão Gênica , Lisina/metabolismo , Arginina/metabolismo , Fusão Gênica Artificial , Sequência de Bases , DNA Bacteriano/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/isolamento & purificação , Ensaio de Desvio de Mobilidade Eletroforética , Escherichia coli/enzimologia , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/isolamento & purificação , Proteínas de Escherichia coli/metabolismo , Deleção de Genes , Genes Reporter , Dados de Sequência Molecular , Regiões Promotoras Genéticas , Ligação Proteica , Sequências Reguladoras de Ácido Nucleico , Transcrição Gênica , beta-Galactosidase/biossíntese , beta-Galactosidase/genética
15.
Biochemistry ; 47(38): 9966-80, 2008 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-18710263

RESUMO

Dihydrodipicolinate reductase (DHPR) is a homotetramer that catalyzes reduction of dihydrodipicolinate (DHP). We recently reported a biligand inhibitor ( K i = 100 nM) of DHPR, comprised of fragments that bind in the NADH (CRAA = catechol rhodanine acetic acid) and DHP (PDC = pyridine dicarboxylate) binding sites. Herein, we characterize binding synergy and cooperativity for ligand binding to Escherichia coli DHPR: NADH or CRAA and PDC (stable analog of DHP). While K d values indicate little synergy between NADH and PDC, (1)H- (15)N HSQC chemical shift perturbation and saturation transfer difference (STD) titrations indicate that PDC induces a more dramatic conformational change than NADH, consistent with a role in domain closure. PDC binds cooperatively (Hill coefficient = 2), while NADH does not, based on STD titrations that monitor only fast exchange processes. However, HSQC titrations monitoring Trp253 (located between monomers) indicate that NADH binds in two steps, with high affinity binding to only one of the monomers. Therefore, DHPR binds cofactor via a sequential model, with negative cooperativity. These results, interpreted in light of steady-state data, suggest that DHPR activity requires NADH binding at only one of the four monomers. Implications of our results for fragment assembly are discussed, using CRAA tethering to PDC as a model biligand: (a) if one fragment (ex. PDC) must induce a large structural change before the other fragment is brought proximal, this must be screened for upfront, and (b) cooperative or synergistic interactions between binding sites can lead to unexpected and misleading effects in NMR-based screening.


Assuntos
Di-Hidrodipicolinato Redutase/química , Di-Hidrodipicolinato Redutase/metabolismo , Inibidores Enzimáticos/síntese química , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Sítios de Ligação/fisiologia , Di-Hidrodipicolinato Redutase/antagonistas & inibidores , Inibidores Enzimáticos/metabolismo , Proteínas de Escherichia coli/antagonistas & inibidores , Ligantes , Especificidade por Substrato/fisiologia
16.
J Biochem ; 143(5): 617-23, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18250105

RESUMO

In lysine biosynthesis, dihydrodipicolinate reductase (DHDPR) catalyses the formation of tetrahydrodipicolinate. Unlike DHDPR enzymes from Escherichia coli and Mycobacterium tuberculosis, which have dual specificity for both NADH and NADPH as co-factors, the enzyme from Thermotoga maritima has a significantly greater affinity for NADPH. Despite low sequence identity with the E. coli and M. tuberculosis DHDPR enzymes, DHDPR from T. maritima has a similar catalytic site, with many conserved residues involved in interactions with substrates. This suggests that as the enzyme evolved, the co-factor specificity was relaxed. Kinetic studies show that the T. maritima DHDPR enzyme is inhibited by high concentrations of its substrate, DHDP, and that at high concentrations NADH also acts as an inhibitor of the enzyme, suggesting a novel method of regulation for the lysine biosynthetic pathway. Increased thermal stability of the T. maritima DHDPR enzyme may be associated with the lack of C-terminal and N-terminal loops that are present in the E. coli DHDPR enzyme.


Assuntos
Proteínas de Bactérias/química , Di-Hidrodipicolinato Redutase/química , Thermotoga maritima/enzimologia , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Evolução Biológica , Di-Hidrodipicolinato Redutase/metabolismo , Estabilidade Enzimática , Cinética , Modelos Moleculares , NAD/metabolismo , NADP/metabolismo , Ligação Proteica , Temperatura
17.
Sci Rep ; 8(1): 7936, 2018 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-29786696

RESUMO

Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-terminal long loop (residues 34-59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2'-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.


Assuntos
Di-Hidrodipicolinato Redutase/química , Di-Hidrodipicolinato Redutase/metabolismo , NADP/metabolismo , Planococáceas/enzimologia , Sequência de Aminoácidos , Cristalografia por Raios X , Cinética , Modelos Moleculares , NADP/química , Conformação Proteica , Homologia de Sequência , Especificidade por Substrato
18.
Biochim Biophys Acta ; 1721(1-3): 27-36, 2005 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-15652176

RESUMO

With the aim of elucidating how plants synthesize lysine, extracts prepared from corn, tobacco, Chlamydomonas and soybean were tested and found to lack detectable amounts of N-alpha-acyl-L,L-diaminopimelate deacylase or N-succinyl-alpha-amino-epsilon-ketopimelate-glutamate aminotransaminase, two key enzymes in the central part of the bacterial pathway for lysine biosynthesis. Corn extracts missing two key enzymes still carried out the overall synthesis of lysine when provided with dihydrodipicolinate. An analysis of available plant DNA sequences was performed to test the veracity of the negative biochemical findings. Orthologs of dihydrodipicolinate reductase and diaminopimelate epimerase (enzymes on each side of the central pathway) were readily found in the Arabidopsis thaliana genome. Orthologs of the known enzymes needed to convert tetrahydrodipicolinate to diaminopimelic acid (DAP) were not detected in Arabidopsis or in the plant DNA sequence databases. The biochemical and reinforcing bioinformatics results provide evidence that plants may use a novel variant of the bacterial pathways for lysine biosynthesis.


Assuntos
Bactérias/metabolismo , Lisina/biossíntese , Plantas/metabolismo , Carboxiliases/metabolismo , Ácido Diaminopimélico/metabolismo , Di-Hidrodipicolinato Redutase , Proteínas de Escherichia coli/metabolismo , Oxirredutases atuantes sobre Doadores de Grupo CH-CH/metabolismo , Filogenia
19.
J Biotechnol ; 124(2): 327-37, 2006 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-16483680

RESUMO

Previously, we showed that the enzymes aspartokinase (AK) and dihydrodipicolinate synthase (DDPS), which are involved in L-lysine biosynthesis in the Gram-negative obligate methylotroph Methylophilus methylotrophus AS1, were inhibited by allosteric effectors, including L-lysine. To elucidate further the regulation of L-lysine biosynthesis in M. methylotrophus, we cloned the genes encoding three other enzymes involved in this pathway, L-aspartate-beta-semialdehyde dehydrogenase, dihydrodipicolinate reductase (DDPR) and diaminopimelate decarboxylase, and examined their properties. DDPR was markedly inhibited by L-lysine. Based on this and our previous results, we constructed an L-lysine-producing strain of M. methylotrophus by introducing well-characterized genes encoding desensitized forms of AK and DDPS, as well as dapB (encoding DDPR) from Escherichia coli, using a broad host range plasmid. L-Lysine production was significantly increased by employing an S-(2-aminoethyl)-L-cysteine (L-lysine analog)-resistant mutant as the host. This derivative accumulated L-lysine at a concentration of 1 g l(-1) of medium using methanol as a carbon source.


Assuntos
Aspartato-Semialdeído Desidrogenase/genética , Carboxiliases/genética , Di-Hidrodipicolinato Redutase/genética , Lisina/biossíntese , Methylophilus methylotrophus/enzimologia , Regulação Enzimológica da Expressão Gênica/genética , Vetores Genéticos/genética , Metanol/metabolismo , Plasmídeos/biossíntese , Engenharia de Proteínas/métodos
20.
Sci Rep ; 6: 37111, 2016 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-27845445

RESUMO

Lysine biosynthesis in bacteria and plants commences with a condensation reaction catalysed by dihydrodipicolinate synthase (DHDPS) followed by a reduction reaction catalysed by dihydrodipicolinate reductase (DHDPR). Interestingly, both DHDPS and DHDPR exist as different oligomeric forms in bacteria and plants. DHDPS is primarily a homotetramer in all species, but the architecture of the tetramer differs across kingdoms. DHDPR also exists as a tetramer in bacteria, but has recently been reported to be dimeric in plants. This study aimed to characterise for the first time the structure and function of DHDPS and DHDPR from cyanobacteria, which is an evolutionary important phylum that evolved at the divergence point between bacteria and plants. We cloned, expressed and purified DHDPS and DHDPR from the cyanobacterium Anabaena variabilis. The recombinant enzymes were shown to be folded by circular dichroism spectroscopy, enzymatically active employing the quantitative DHDPS-DHDPR coupled assay, and form tetramers in solution using analytical ultracentrifugation. Crystal structures of DHDPS and DHDPR from A. variabilis were determined at 1.92 Å and 2.83 Å, respectively, and show that both enzymes adopt the canonical bacterial tetrameric architecture. These studies indicate that the quaternary structure of bacterial and plant DHDPS and DHDPR diverged after cyanobacteria evolved.


Assuntos
Anabaena variabilis/enzimologia , Proteínas de Bactérias/química , Di-Hidrodipicolinato Redutase/química , Hidroliases/química , Anabaena variabilis/genética , Proteínas de Bactérias/genética , Dicroísmo Circular , Cristalografia por Raios X , Di-Hidrodipicolinato Redutase/genética , Hidroliases/genética , Estrutura Quaternária de Proteína , Relação Estrutura-Atividade
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