RESUMO
The synergistic regulation of the multi-functional sites on one receptor molecule with different cationic effectors for anion recognition is scarce to be well understood from the experiment and theory. In this work, a new anion receptor with three functional zones including ether hole, biurea and double bipyridine groups (EUPR) is designed expecting to enhance the chloride anion recognition together with a rational synthesis path being proposed based on four simple and mature organic reaction steps. The conformational structures of the designed receptor EUPR and the binding behaviors for three kinds of ions (Cl-, Na+, and Ag+) are deeply investigated by using density functional theoretical calculations. It is found that Cl- binding via the hydrogen bond interaction can be significantly enhanced and synergistically regulated by the two kinds of cations and the corresponding conformational changes of receptor EUPR. Especially, the conformational pre-organization of receptor caused by the encapsulation of sodium ion into ether hole is benefit to the binding for Cl- in both thermodynamics and kinetics. Na+ binding, in turn, can ever be enhanced by chloride anion, whereas it seems that Ag+ binding cannot always be enhanced by chloride anion, reflecting an electrical complementary matching and mutual enhancement effect for different counter ions. Moreover, solvent effect calculations indicate that EUPR may be an ideal candidate structure for Cl- recognition by strategy of counter ion enhancement in water. Additionally, a visual study of intermolecular noncovalent interaction (NCI) and molecular electrostatic potential (ESP) are used for the analysis on the nature of interactions between receptor and bound ions.
RESUMO
The mutual synergistic regulation of the multi-functional sites on a single receptor molecule for ion-binding/recognition is vital for the new receptor design and needs to be well explored from experiment and theory. In this work, a new macrocyclic ion receptor (BEBUR) with three functional zones, including two ether holes and one biurea groups, is designed expecting to mutually enhance the ion-binding performance. The binding behaviors of BEBUR mainly for Cl- and Cs+ are deeply investigated by using density functional theoretical calculations. It is found that Cl-/Cs+ binding can be mutually enhanced and synergistically regulated via corresponding conformational changes of the receptor, well reflecting an electrical complementary matching and mutual reinforcement effect. Moreover, solvent effect calculations indicate that BEBUR may be an excellent candidate structure for Cl--binding with the enhancement of counter ion (Cs+) in water and toluene. In addition, visualization of intermolecular noncovalent interaction is used for analysis on the nature of the binding interactions between receptor and ions.
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BACKGROUND: Osteoarthritis (OA) is a degenerative joint disease characterized by the progressive degeneration of articular cartilage, leading to pain, stiffness, and loss of joint function. The pathogenesis of OA involves multiple factors, including increased intracellular reactive oxygen species (ROS), enhanced chondrocyte apoptosis, and disturbances in cartilage matrix metabolism. These processes contribute to the breakdown of the extracellular matrix (ECM) and the loss of cartilage integrity, ultimately resulting in joint damage and dysfunction. RNA interference (RNAi) therapy has emerged as a promising approach for the treatment of various diseases, including hATTR and acute hepatic porphyria. By harnessing the natural cellular machinery for gene silencing, RNAi allows for the specific inhibition of target genes involved in disease pathogenesis. In the context of OA, targeting key molecules such as matrix metalloproteinase-13 (MMP13), which plays a critical role in cartilage degradation, holds great therapeutic potential. RESULTS: In this study, we developed an innovative therapeutic approach for OA using a combination of liposome-encapsulated siMMP13 and NG-Monomethyl-L-arginine Acetate (L-NMMA) to form an injectable hydrogel. The hydrogel served as a delivery vehicle for the siMMP13, allowing for sustained release and targeted delivery to the affected joint. Experiments conducted on destabilization of the medial meniscus (DMM) model mice demonstrated the therapeutic efficacy of this composite hydrogel. Treatment with the hydrogel significantly inhibited the degradation of cartilage matrix, as evidenced by histological analysis showing preserved cartilage structure and reduced loss of proteoglycans. Moreover, the hydrogel effectively suppressed intracellular ROS accumulation in chondrocytes, indicating its anti-oxidative properties. Furthermore, it attenuated chondrocyte apoptosis, as demonstrated by decreased levels of apoptotic markers. CONCLUSION: In summary, the injectable hydrogel containing siMMP13, endowed with anti-ROS and anti-apoptotic properties, may represent an effective therapeutic strategy for osteoarthritis in the future.
Assuntos
Apoptose , Condrócitos , Hidrogéis , Metaloproteinase 13 da Matriz , Osteoartrite , Espécies Reativas de Oxigênio , Animais , Osteoartrite/tratamento farmacológico , Osteoartrite/metabolismo , Osteoartrite/patologia , Espécies Reativas de Oxigênio/metabolismo , Apoptose/efeitos dos fármacos , Hidrogéis/química , Metaloproteinase 13 da Matriz/metabolismo , Camundongos , Condrócitos/metabolismo , Condrócitos/efeitos dos fármacos , Camundongos Endogâmicos C57BL , Masculino , Cartilagem Articular/metabolismo , Cartilagem Articular/efeitos dos fármacos , Cartilagem Articular/patologia , Lipossomos/química , HumanosRESUMO
Plant growth exhibits rhythmic characteristics, and gibberellins (GAs) are involved in regulating cell growth, but it is still unclear how GAs crosstalk with circadian rhythm to regulate cell elongation. The study analyzed growth characteristics of wild-type (WT), zmga3ox and zmga3ox with GA3 seedlings. We integrated metabolomes and transcriptomes to study the interaction between GAs and circadian rhythm in mediating leaf elongation. The rates of leaf growth were higher in WT than zmga3ox, and zmga3ox cell length was shorter when proliferated in darkness than light, and GA3 restored zmga3ox leaf growth. The differentially expressed genes (DEGs) between WT and zmga3ox were mainly enriched in hormone signaling and cell wall synthesis, while DEGs in zmga3ox were restored to WT by GA3. Moreover, the number of circadian DEGs that reached the peak expression in darkness was more than light, and the upregulated circadian DEGs were mainly enriched in cell wall synthesis. The differentially accumulated metabolites (DAMs) were mainly attributed to flavonoids and phenolic acid. Twenty-two DAMs showed rhythmic accumulation, especially enriched in lignin synthesis. The circadian DEGs ZmMYBr41/87 and ZmHB34/70 were identified as regulators of ZmHCT8 and ZmBM1, which were enzymes in lignin synthesis. Furthermore, GAs regulated ZmMYBr41/87 and ZmHB34/70 to modulate lignin biosynthesis for mediating leaf rhythmic growth.
Assuntos
Giberelinas , Zea mays , Giberelinas/metabolismo , Zea mays/genética , Lignina/metabolismo , Perfilação da Expressão Gênica , Transcriptoma , Folhas de Planta/metabolismo , Ritmo Circadiano , Regulação da Expressão Gênica de PlantasRESUMO
BACKGROUND: Auxin plays a crucial role in nitrate (NO3-)-mediated root architecture, and it is still unclear that if NO3- supply modulates auxin reallocation for regulating root formation in maize (Zea mays L.). This study was conducted to investigate the role of auxin efflux carrier ZmPIN1a in the root formation in response to NO3- supply. RESULTS: Low NO3- (LN) promoted primary root (PR) elongation, while repressed the development of lateral root primordia (LRP) and total root length. LN modulated auxin levels and polar transport and regulated the expression of auxin-responsive and -signaling genes in roots. Moreover, LN up-regulated the expression level of ZmPIN1a, and overexpression of ZmPIN1a enhanced IAA efflux and accumulation in PR tip, while repressed IAA accumulation in LRP initiation zone, which consequently induced LN-mediated PR elongation and LR inhibition. The inhibition rate of PR length, LRP density and number of ZmPIN1a-OE plants was higher than that of wild-type plants after auxin transport inhibitor NPA treatment under NN and LN conditions, and the degree of inhibition of root growth in ZmPIN1a-OE plants was more obvious under LN condition. CONCLUSION: These findings suggest that ZmPIN1a was involved in modulating auxin levels and transport to alter NO3--mediated root formation in maize.
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Ácidos Indolacéticos , Nitratos , Ácidos Indolacéticos/metabolismo , Nitratos/metabolismo , Raízes de Plantas/metabolismo , Regulação da Expressão Gênica de Plantas , Transporte Biológico/genética , Zea mays/metabolismoRESUMO
With increased diabetes incidence, diabetic wound healing is one of the most common diabetes complications and is characterized by easy infection, chronic inflammation, and reduced vascularization. To address these issues, biomaterials with multifunctional antibacterial, immunomodulatory, and angiogenic properties must be developed to improve overall diabetic wound healing for patients. In our study, we prepared porous poly (L-lactic acid) (PLA) nanofiber membranes using electrospinning and solvent evaporation methods. Then, sulfated chitosan (SCS) combined with polydopamine-gentamicin (PDA-GS) was stepwise modified onto porous PLA nanofiber membrane surfaces. Controlled GS release was facilitated via dopamine self-polymerization to prevent early stage infection. PDA was also applied to PLA nanofiber membranes to suppress inflammation. In vitro cell tests results showed that PLA/SCS/PDA-GS nanofiber membranes immuomodulated macrophage toward the M2 phenotype and increased endogenous vascular endothelial growth factor secretion to induce vascularization. Moreover, SCS-contained PLA nanofiber membranes also showed good potential in enhancing macrophage trans-differentiation to fibroblasts, thereby improving wound healing processes. Furthermore, our in vitro antibacterial studies against Staphylococcus aureus indicated the effective antibacterial properties of the PLA/SCS/PDA-GS nanofiber membranes. In summary, our novel porous PLA/SCS/PDA-GS nanofiber membranes possessing enhanced antibacterial, anti-inflammatory, and angiogenic properties demonstrate promising potential in diabetic wound healing processes.
Assuntos
Quitosana , Diabetes Mellitus , Nanofibras , Humanos , Porosidade , Fator A de Crescimento do Endotélio Vascular , Poliésteres/farmacologia , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Cicatrização , Anti-Inflamatórios , Ácido LácticoRESUMO
Allosteric ligands are promising drugs owing to their remote regulations of the orthosteric ligand signaling pathway. There are few allosteric ligands due to the lack of handy and efficacious method for the screening. Herein, we developed an affinity chromatographic method for allosteric ligand screening by immobilizing purified beta2 adrenoceptor (ß2-AR) onto macroporous silica gel by a two-point tethering method. The method relies on the occupation of the orthosteric site by an antagonist and the chelation of N-terminal His-tag of the receptor and Ni2+ coated on the gel. The immobilized ß2-AR demonstrated the greatest allosteric responsive feature when Cmpd-15 (0.25 µM) was included in the mobile phase. Under the same conditions, the association constants of three agonists (salbutamol, terbutaline, and tulobuterol) reduced to 47%, 19%, and 27% compared with the data without the inclusion of Cmpd-15 in the mobile phase. APF was screened as a potential allosteric modulator of ß2-AR by applying the immobilized receptor in a natural product-derived DNA-encoded chemical library (DEL). Relying on these results, we reasoned that the current method has potential in screening allosteric ligands of the receptor. We expect that it is applicable for the discovery of new allosteric binding sites of a target protein and screening allosteric modulators of the other receptors from complex samples.
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Produtos Biológicos , Regulação Alostérica , Sítio Alostérico , DNA , Ligantes , Receptores Adrenérgicos , Transdução de Sinais , Bibliotecas de Moléculas Pequenas/químicaRESUMO
Early potential evaluation of lead compounds is critical to decrease downstream lead-optimization cycle times and clinical attrition rates for drug development. This increasingly necessitates the methodologies for accurately evaluating the potential compounds. This work immobilized ß2-adrenoceptor (ß2-AR) onto microspheres through Halo-tag mediated reaction. Characterizing the resulting microspheres by elemental and functional analysis, we utilized the immobilized receptor to determine the thermodynamics of terbutaline, tulobuterol, clorprenaline, salbutamol, and methoxyphenamine. The association constants correlated to their capacity factors on the column containing the immobilized ß2-AR, thus providing a possibility for early potential evaluation of lead compounds from complex matrices like a DNA-encoded library. By this model, the lead compound (XC267) was predicted to have an association constant higher than terbutaline, salbutamol, and methoxyphenamine, but lower than tulobuterol and clorprenaline. The binding interaction between XC267 and ß2-AR is a spontaneous endothermic process with an association constant of (6.62 ± 0.13) × 104 M-1 at 37 °C. The change of Gibbs free energy(ΔGθ), enthalpy change (ΔHθ), and entropy change (ΔSθ) was -28.49 kJ/mol, -10.58 kJ/mol, and 57.79 J/moL·K at 37 °C. By the semi-empirical rule of Ross, the driving force of the interaction between XC267 and ß2-AR was electrostatic interaction. Such binding force was also achieved by molecular docking. These results suggested that XC267 is a candidate to treat asthma by specific binding to ß2-AR. We reasoned that receptor chromatography is able to the early potential evaluation of lead compounds from complex matrices.
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Chumbo , Terbutalina , Albuterol/química , Cromatografia , DNA , Simulação de Acoplamento Molecular , Terbutalina/química , TermodinâmicaRESUMO
Bacterial toxin-antitoxin pairs play important roles in bacterial multidrug tolerance. Gcn5-related N-acetyltransferase (GNAT) toxins inhibit translation by acetylation of aminoacyl-tRNAs and are counteracted by direct contacts with cognate ribbon-helix-helix (RHH) antitoxins. Our previous analysis showed that the GNAT toxin KacT and RHH antitoxin KacA of Klebsiella pneumoniae form a heterohexamer in solution and that the complex interacts with the cognate promoter DNA, resulting in negative autoregulation of kacAT transcription. Here, we present the crystal structure of DNA-bound KacAT complex at 2.2 Å resolution. The crystal structure revealed the formation of a unique heterohexamer, KacT-KacA2-KacA2-KacT. The direct interaction of KacA and KacT involves a unique W-shaped structure with the two KacT molecules at opposite ends. Inhibition of KacT is achieved by the binding of four KacA proteins that preclude the formation of an active KacT dimer. The kacAT operon is auto-regulated and we present an experimentally supported molecular model proposing that the KacT:KacA ratio controls kacAT transcription by conditional cooperativity. These results yield a profound understanding of how transcription GNAT-RHH pairs are regulated.
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Antitoxinas/genética , Proteínas de Bactérias/genética , Toxinas Bacterianas/genética , Klebsiella pneumoniae/genética , Complexos Multiproteicos/genética , Óperon , Antitoxinas/química , Antitoxinas/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Toxinas Bacterianas/química , Toxinas Bacterianas/metabolismo , Cristalografia por Raios X , Regulação Bacteriana da Expressão Gênica , Klebsiella pneumoniae/metabolismo , Modelos Moleculares , Complexos Multiproteicos/química , Complexos Multiproteicos/metabolismo , Ligação Proteica , Conformação Proteica , Multimerização ProteicaRESUMO
Producing normal eggs for fertilization and species propagation requires completion of meiosis and protection of the genome from the ravages of retrotransposons. Mutation of Marf1 (meiosis regulator and mRNA stability factor 1) results in defects in both these key processes in mouse oocytes and thus in infertility. MARF1 was predicted to have ribonuclease activity, but the structural basis for the function of MARF1 and the contribution of its putative ribonuclease domain to the mutant oocyte phenotype was unknown. Therefore, we resolved the crystal structures of key domains of MARF1 and demonstrated by biochemical and mutagenic analyses that the ribonuclease activity of MARF1 controls oocyte meiotic progression and retrotransposon surveillance. The N-terminal NYN domain of MARF1 resembles the nuclease domains of Vpa0982, T4 RNase H, and MCPIP1 and contains four conserved aspartate residues, D178, D215, D246, and D272. The C-terminal LOTUS domain of MARF1 adopts a winged helix-turn-helix fold and binds ssRNA and dsRNA. Purified MARF1 cleaved ssRNAs in vitro, but this cleavage activity was abolished by mutations of conserved aspartates in its NYN domain and truncation of the LOTUS domain. Furthermore, a point mutation in the D272 residue in vivo caused a female-only infertile phenotype in mice, with failure of meiotic resumption and elevation of Line1 and Iap retrotransposon transcripts and DNA double-strand breaks in oocytes. Therefore, the ribonuclease activity of MARF1 controls oocyte meiosis and genome integrity. This activity depends upon conserved aspartic residues in the catalytic NYN domain and the RNA-binding activity of the LOTUS domain.
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Proteínas de Ciclo Celular/metabolismo , Genoma/genética , Homeostase/genética , Oócitos/metabolismo , RNA/genética , Ribonuclease H/metabolismo , Animais , Ácido Aspártico/genética , Domínio Catalítico/genética , Quebras de DNA de Cadeia Dupla , Feminino , Infertilidade Feminina/genética , Infertilidade Feminina/metabolismo , Meiose/genética , Camundongos , Mutação/genética , Fenótipo , Retroelementos/genéticaRESUMO
The 3' end methylation catalyzed by HUA Enhancer 1 (HEN1) is a crucial step of small RNA stabilization in plants, yet how unmethylated small RNAs undergo degradation remains largely unknown. Using a reverse genetic approach, we here show that Atrimmer 2 (ATRM2), a DEDDy-type 3' to 5' exoribonuclease, acts in the degradation of unmethylated miRNAs and miRNA*s in Arabidopsis Loss-of-function mutations in ATRM2 partially suppress the morphological defects caused by HEN1 malfunction, with restored levels of a subset of miRNAs and receded expression of corresponding miRNA targets. Dysfunction of ATRM2 has negligible effect on miRNA trimming, and further increase the fertility of hen1 heso1 urt1, a mutant with an almost complete abolishment of miRNA uridylation, indicating that ATRM2 may neither be involved in 3' to 5' trimming nor be the enzyme that specifically degrades uridylated miRNAs. Notably, the fold changes of miRNAs and their corresponding miRNA*s were significantly correlated in hen1 atrm2 versus hen1 Unexpectedly, we observed a marked increase of 3' to 5' trimming of several miRNA*s but not miRNAs in ATRM2 compromised backgrounds. These data suggest an action of ATRM2 on miRNA/miRNA* duplexes, and the existence of an unknown exoribonuclease for specific trimming of miRNA*. This asymmetric effect on miRNA/miRNA* is likely related to Argonaute (AGO) proteins, which can distinguish miRNAs from miRNA*s. Finally, we show that ATRM2 colocalizes and physically interacts with Argonaute 1 (AGO1). Taken together, our results suggest that ATRM2 may be involved in the surveillance of unmethylated miRNA/miRNA* duplexes during the initiation step of RNA-induced silencing complex assembly.
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Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Exorribonucleases/metabolismo , MicroRNAs/metabolismo , Mutação , RNA de Plantas/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Exorribonucleases/genética , Metilação , MicroRNAs/genética , RNA de Plantas/genéticaRESUMO
African swine fever virus (ASFV) can cause highly lethal disease in pigs and is becoming a global threat. ASFV DNA Polymerase X (AsfvPolX) is the most distinctive DNA polymerase identified to date; it lacks two DNA-binding domains (the thumb domain and 8-KD domain) conserved in the homologous proteins. AsfvPolX catalyzes the gap-filling reaction during the DNA repair process of the ASFV virus genome; it is highly error prone and plays an important role during the strategic mutagenesis of the viral genome. The structural basis underlying the natural substrate binding and the most frequent dG:dGTP misincorporation of AsfvPolX remain poorly understood. Here, we report eight AsfvPolX complex structures; our structures demonstrate that AsfvPolX has one unique 5'-phosphate (5'-P) binding pocket, which can favor the productive catalytic complex assembly and enhance the dGTP misincorporation efficiency. In combination with mutagenesis and in vitro catalytic assays, our study also reveals the functional roles of the platform His115-Arg127 and the hydrophobic residues Val120 and Leu123 in dG:dGTP misincorporation and can provide information for rational drug design to help combat ASFV in the future.
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Vírus da Febre Suína Africana/enzimologia , DNA Polimerase Dirigida por DNA/metabolismo , Nucleotídeos de Desoxiguanina/metabolismo , Aminoácidos/metabolismo , Sequência de Bases , Sítios de Ligação , Cristalografia por Raios X , DNA Viral/química , DNA Viral/metabolismo , Cinética , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Ligação Proteica , Estrutura Secundária de Proteína , Homologia Estrutural de ProteínaRESUMO
DNA can form diverse structures, which predefine their physiological functions. Besides duplexes that carry the genetic information, quadruplexes are the most well-studied DNA structures. In addition to their important roles in recombination, replication, transcription and translation, DNA quadruplexes have also been applied as diagnostic aptamers and antidisease therapeutics. Herein we further expand the sequence and structure complexity of DNA quadruplex by presenting a high-resolution crystal structure of DNA1 (5'-AGAGAGATGGGTGCGTT-3'). This is the first quadruplex structure that contains all the internal A-, G-, C-, T-tetrads, A:T:A:T tetrads and bulged nucleotides in one single structure; as revealed by site-specific mutagenesis and biophysical studies, the central ATGGG motif plays important role in the quadruplex formation. Interestingly, our structure also provides great new insights into cation recognition, including the first-time reported Pb2+, by tetrad structures.
Assuntos
Quadruplex G , Dicroísmo Circular , Cristalografia por Raios X , Metais/química , Modelos Moleculares , Mutagênese Sítio-Dirigida , Ressonância Magnética Nuclear Biomolecular , Conformação de Ácido Nucleico , Motivos de NucleotídeosRESUMO
OBJECTIVE: Identification and characterization of a novel bacterial carbohydrate esterase (PaCes7) with application potential for lignocellulose and pesticide degradation. RESULTS: PaCes7 was identified from the lignocellulolytic bacterium, Pantoea ananatis Sd-1 as a new carbohydrate esterase. Recombinant PaCes7 heterologously expressed in Escherichia coli showed a clear preference for esters with short-chain fatty acids and exhibited maximum activity towards α-naphthol acetate at 37 °C and pH 7.5. Purified PaCes7 exhibited its catalytic activity under mesophilic conditions and retained more than 40% activity below 30 °C. It displayed a relatively wide pH stability from pH 6-11. Furthermore, the enzyme was strongly resistant to Mg2+, Pb2+, and Co2+ and activated by K+ and Ca2+. Both P. ananatis Sd-1 and PaCes7 could degrade the pesticide carbaryl. Additionally, PaCes7 was shown to work in combination with cellulase and/or xylanase in rice straw degradation. CONCLUSIONS: The data suggest that PaCes7 possesses promising biotechnological potential.
Assuntos
Proteínas de Bactérias , Esterases , Lignina/metabolismo , Pantoea/enzimologia , Praguicidas/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Carbaril/metabolismo , Estabilidade Enzimática , Esterases/química , Esterases/genética , Esterases/metabolismo , Pantoea/genéticaRESUMO
Modified gibberellin (GA) signaling leads to semi-dwarfism with low nitrogen (N) use efficiency (NUE) in crops. An understanding of GA-mediated N uptake is essential for the development of crops with improved NUE. The function of GA in modulating N uptake capacity and nitrate (NO3-) transporters (NRTs) was analyzed in the GA synthesis-deficient mutant zmga3ox grown under low (LN) and sufficient (SN) N conditions. LN significantly suppressed the production of GA1, GA3, and GA4, and the zmga3ox plants showed more sensitivity in shoots as well as LN stress. Moreover, the higher anthocyanin accumulation and the decrease of chlorophyll content were also recorded. The net NO3- fluxes and 15N content were decreased in zmga3ox plants under both LN and SN conditions. Exogenous GA3 could restore the NO3- uptake in zmga3ox plants, but uniconazole repressed NO3- uptake. Moreover, the transcript levels of ZmNRT2.1/2.2 were downregulated in zmga3ox plants, while the GA3 application enhanced the expression level. Furthermore, the RNA-seq analyses identified several transcription factors that are involved in the GA-mediated transcriptional operation of NRTs related genes. These findings revealed that GAs influenced N uptake involved in the transcriptional regulation of NRTs and physiological responses in maize responding to nitrogen supply.
Assuntos
Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Giberelinas/farmacologia , Nitrogênio/metabolismo , Proteínas de Plantas/metabolismo , Raízes de Plantas/fisiologia , Zea mays/fisiologia , Transporte Biológico , Fenótipo , Reguladores de Crescimento de Plantas/farmacologia , Proteínas de Plantas/genética , Raízes de Plantas/efeitos dos fármacos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Zea mays/efeitos dos fármacos , Zea mays/metabolismoRESUMO
A type II toxin-antitoxin (TA) system, in which the toxin contains a Gcn5-related N-acetyltransferase (GNAT) domain, has been characterized recently. GNAT toxin acetylates aminoacyl-tRNA and blocks protein translation. It is abolished by the cognate antitoxin that contains the ribbon-helix-helix (RHH) domain. Here, we present an experimental demonstration of the interaction of the GNAT-RHH complex with TA promoter DNA. First, the GNAT-RHH TA locus kacAT was found in Klebsiella pneumoniae HS11286, a strain resistant to multiple antibiotics. Overexpression of KacT halted cell growth and resulted in persister cell formation. The crystal structure also indicated that KacT is a typical acetyltransferase toxin. Co-expression of KacA neutralized KacT toxicity. Expression of the bicistronic kacAT locus was up-regulated during antibiotic stress. Finally, KacT and KacA formed a heterohexamer that interacted with promoter DNA, resulting in negative autoregulation of kacAT transcription. The N-terminus region of KacA accounted for specific binding to the palindromic sequence on the operator DNA, whereas its C-terminus region was essential for the inactivation of the GNAT toxin. These results provide an important insight into the regulation of the GNAT-RHH family TA system.
Assuntos
Acetiltransferases/química , Acetiltransferases/metabolismo , Toxinas Bacterianas/química , Toxinas Bacterianas/metabolismo , Klebsiella pneumoniae/patogenicidade , Acetiltransferases/genética , Antibacterianos/farmacologia , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Toxinas Bacterianas/genética , Simulação por Computador , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Loci Gênicos/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Meropeném/farmacologia , Regiões Promotoras Genéticas/genética , Conformação Proteica , Tigeciclina/farmacologia , Difração de Raios XRESUMO
SLC47A2 encodes MATE 2-K in the kidney, which mediates the secretion of certain endogenous and exogenous compounds. SLC47A2 was dramatically repressed in patients with renal cell carcinoma (RCC), and a lower level of SLC47A2 might act as a negative prognostic marker, although the mechanism is not well understood. In this study, we aimed to investigate the mechanism via which SLC47A2 is downregulated in RCC. Based on the annotation information of the SLC47A2 locus available in the UCSC genome browser database, we identified a novel lncRNA, which is transcribed from the SLC47A2 locus and named it SANT1. Overexpression and knock-down assays were performed to investigate the effects of SANT1 on cis-regulation of SLC47A2. We verified the direct binding between SANT1 and SFPQ/E2F1/HDAC1 using the cross-linking and immunoprecipitation (CLIP) assay. Chromatin immunoprecipitation was performed to confirm the molecular mechanism via which SANT1 activates the transcription of the SLC47A2 coding region. We observed that SANT1 can cis-regulate its own genetic locus. In tumour-adjacent tissues, the SLC47A2 locus highly expresses SANT1, which can remove the regulatory SFPQ/E2F1/HDAC1 suppressor complex from the promoter region, thereby significantly increasing the levels of the H3K27ac modification and RNAPII binding. Owing to a low SANT1 level, the binding of this inhibitory complex in the promoter region is upregulated in RCC, which results in silencing of the SLC47A2 coding region. In conclusion, we identified a novel lncRNA and elucidated the mechanism via which it regulates SLC47A2 expression in RCC.
Assuntos
Carcinoma de Células Renais/genética , Fator de Transcrição E2F1/metabolismo , Regulação Neoplásica da Expressão Gênica , Histona Desacetilase 1/metabolismo , Proteínas de Transporte de Cátions Orgânicos/metabolismo , Fator de Processamento Associado a PTB/metabolismo , Regiões Promotoras Genéticas , RNA Longo não Codificante/metabolismo , Sequência de Bases , Linhagem Celular Tumoral , Células HEK293 , Humanos , Neoplasias Renais/genética , Modelos Biológicos , Conformação de Ácido Nucleico , Proteínas de Transporte de Cátions Orgânicos/genética , Ligação Proteica , RNA Longo não Codificante/química , RNA Longo não Codificante/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Regulação para Cima/genéticaRESUMO
Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-HgII-T containing duplex, three T-HgII-T containing duplexes and one native duplex containing T-T pair without HgII. Our structures suggest that both C-T and T-T pairs are flexible in interacting with the HgII ion with various binding modes including N3-HgII-N3, N4-HgII-N3, O2-HgII-N3 and N3-HgII-O4. Our studies also reveal that the overall conformations of the C-HgII-T and T-HgII-T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C-HgII-T or T-HgII-T containing DNA nanodevices in the future.
Assuntos
Citosina/química , DNA/química , Mercúrio/química , Timina/química , Pareamento de Bases , Modelos Moleculares , Solventes/química , Estrôncio/químicaRESUMO
Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced silencing complex, the effector complex of RNA interference (RNAi). Here, we report three crystal structures of Nanoarchaeum equitans (Ne) C3PO. The apo-NeC3PO structure adopts an open form and unravels a potential substrates entryway for the first time. The NeC3PO:ssRNA and NeC3PO:ssDNA complexes fold like closed football with the substrates captured at the inner cavities. The NeC3PO:ssRNA structure represents the only catalytic form C3PO complex available to date; with mutagenesis and in vitro cleavage assays, the structure provides critical insights into the substrate binding and the two-cation-assisted catalytic mechanisms that are shared by eukaryotic C3POs. The work presented here further advances our understanding on the RNAi pathway.
Assuntos
Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Modelos Moleculares , Conformação Molecular , Clivagem do RNA , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo , RNA/química , Sítios de Ligação , Cátions/química , Ligação Proteica , RNA/metabolismo , Ribonucleases/química , Ribonucleases/metabolismo , Relação Estrutura-Atividade , Especificidade por SubstratoRESUMO
Metal-mediated base pairs have been extensively utilized in many research fields, including genetic-code extension, novel therapeutics development, and nanodevice design. Compared to other cations, AgI is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-AgI -C pairs and the first reported G-AgI -G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these AgI -mediated base-pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy-metal ions, thus further contributing to the structural diversity of DNA. This unique complex structure is highly sequence-dependent, thus implying functional potentials as a new DNA aptamer that can bind and recognize silver ions. These results not only advance our understanding of the interactions between AgI and nucleobases, but also provide a unique structural component for the rational design of new DNA nanodevices.