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1.
Eur J Neurosci ; 59(7): 1621-1637, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38369911

RESUMEN

Deficits in cost/benefit decision making is a critical risk factor for gambling disorder. Reward-paired cues may play an important role, as these stimuli can enhance risk preference in rats. Despite extensive research implicating the dorsal striatum in the compulsive aspects of addiction, the role of nigrostriatal dopaminergic activity in cue-induced risk preference remains unclear, particularly in females. Accordingly, we examined the effects of manipulating the dopaminergic nigrostriatal pathway on cue-induced risky choice in female rats. TH:Cre rats were trained on the cued version of the rat Gambling Task. This task was designed such that maximal reward is attained by avoiding the high-risk, high-reward options and instead favouring the options associated with lower per-trial gains, as they feature less frequent and shorter time-out penalties. Adding reward-paired audiovisual cues to the task leads to greater risky choice on average. To assess the role of the nigrostriatal pathway, a viral vector carrying either Cre-dependent inhibitory or excitatory DREADD was infused into the substantia nigra. Rats then received clozapine-N-oxide either during task acquisition or after a stable performance baseline was reached. Inhibition of this pathway accelerated the development of risk preference in early sessions and increased risky choice during performance, but long-term inhibition actually improved decision making. Activation of this pathway had minimal effects. These results provide evidence for the involvement of the dopaminergic nigrostriatal pathway in cue-induced risk preference in females, therefore shedding light on its role in cost/benefit decision-making deficits and expanding our knowledge of the female dopaminergic system.


Asunto(s)
Dopamina , Juego de Azar , Ratas , Femenino , Animales , Dopamina/metabolismo , Conducta de Elección/fisiología , Señales (Psicología) , Ratas Long-Evans , Recompensa , Toma de Decisiones/fisiología
2.
Nucleic Acids Res ; 51(6): 2778-2789, 2023 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-36762473

RESUMEN

Transcriptional pause is essential for all types of termination. In this single-molecule study on bacterial Rho factor-dependent terminators, we confirm that the three Rho-dependent termination routes operate compatibly together in a single terminator, and discover that their termination efficiencies depend on the terminational pauses in unexpected ways. Evidently, the most abundant route is that Rho binds nascent RNA first and catches up with paused RNA polymerase (RNAP) and this catch-up Rho mediates simultaneous releases of transcript RNA and template DNA from RNAP. The fastest route is that the catch-up Rho effects RNA-only release and leads to 1D recycling of RNAP on DNA. The slowest route is that the RNAP-prebound stand-by Rho facilitates only the simultaneous rather than sequential releases. Among the three routes, only the stand-by Rho's termination efficiency positively correlates with pause duration, contrary to a long-standing speculation, invariably in the absence or presence of NusA/NusG factors, competitor RNAs or a crowding agent. Accordingly, the essential terminational pause does not need to be long for the catch-up Rho's terminations, and long pauses benefit only the stand-by Rho's terminations. Furthermore, the Rho-dependent termination of mgtA and ribB riboswitches is controlled mainly by modulation of the stand-by rather than catch-up termination.


Asunto(s)
Proteínas de Escherichia coli , Factor Rho , Terminación de la Transcripción Genética , ARN Polimerasas Dirigidas por ADN/metabolismo , Proteínas de Escherichia coli/genética , Factor Rho/genética , Factor Rho/metabolismo , Riboswitch , Transcripción Genética
3.
Nat Commun ; 13(1): 1663, 2022 03 29.
Artículo en Inglés | MEDLINE | ID: mdl-35351884

RESUMEN

Rho is a general transcription termination factor in bacteria, but many aspects of its mechanism of action are unclear. Diverse models have been proposed for the initial interaction between the RNA polymerase (RNAP) and Rho (catch-up and stand-by pre-terminational models); for the terminational release of the RNA transcript (RNA shearing, RNAP hyper-translocation or displacing, and allosteric models); and for the post-terminational outcome (whether the RNAP dissociates or remains bound to the DNA). Here, we use single-molecule fluorescence assays to study those three steps in transcription termination mediated by E. coli Rho. We find that different mechanisms previously proposed for each step co-exist, but apparently occur on various timescales and tend to lead to specific outcomes. Our results indicate that three kinetically distinct routes take place: (1) the catch-up mode leads first to RNA shearing for RNAP recycling on DNA, and (2) later to RNAP displacement for decomposition of the transcriptional complex; (3) the last termination usually follows the stand-by mode with displacing for decomposing. This three-route model would help reconcile current controversies on the mechanisms.


Asunto(s)
Proteínas de Escherichia coli , Escherichia coli , ADN/metabolismo , ARN Polimerasas Dirigidas por ADN/genética , ARN Polimerasas Dirigidas por ADN/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , ARN/metabolismo , Transcripción Genética
4.
Biophys J ; 121(7): 1276-1288, 2022 04 05.
Artículo en Inglés | MEDLINE | ID: mdl-35183522

RESUMEN

Polymerase chain reaction (PCR) is a powerful tool to diagnose infectious diseases. Uracil DNA glycosylase (UDG) is broadly used to remove carryover contamination in PCR. However, UDG can contribute to false negative results when not inactivated completely, leading to DNA degradation during the amplification step. In this study, we designed novel thermolabile UDG derivatives by supercomputing molecular dynamic simulations and residual network analysis. Based on enzyme activity analysis, thermolability, thermal stability, and biochemical experiments of Escherichia coli-derived UDG and 22 derivatives, we uncovered that the UDG D43A mutant eliminated the false negative problem, demonstrated high efficiency, and offered great benefit for use in PCR diagnosis. We further obtained structural and thermodynamic insights into the role of the D43A mutation, including perturbed protein structure near D43; weakened pairwise interactions of D43 with K42, N46, and R80; and decreased melting temperature and native fraction of the UDG D43A mutant compared with wild-type UDG.


Asunto(s)
Escherichia coli , Uracil-ADN Glicosidasa , Escherichia coli/metabolismo , Mutación , Uracil-ADN Glicosidasa/química , Uracil-ADN Glicosidasa/genética , Uracil-ADN Glicosidasa/metabolismo
5.
FEBS J ; 288(4): 1224-1242, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-32638513

RESUMEN

Dna2 can efficiently process 5' flaps containing DNA secondary structure using coordinated action of the three biochemical activities: the N-terminally encoded DNA-binding activity and the C-terminally encoded endonuclease and helicase activities. In this study, we investigated the cross talk among the three functional domains using a variety of dna2 mutant alleles and enzymes derived thereof. We found that disruption of the catalytic activities of Dna2 activated Dna2-dependent checkpoint, residing in the N-terminal domain. This checkpoint activity contributed to growth defects of dna2 catalytic mutants, revealing the presence of an intramolecular functional cross talk in Dna2. The N-terminal domain of Dna2 bound specifically to substrates that mimic DNA replication fork intermediates, including Holliday junctions. Using site-directed mutagenesis of the N-terminal domain of Dna2, we discovered that five consecutive basic amino acid residues were essential for the ability of Dna2 to bind hairpin DNA in vitro. Mutant cells expressing the dna2 allele containing all five basic residues substituted with alanine displayed three distinct phenotypes: (i) temperature-sensitive growth defects, (ii) bypass of S-phase arrest, and (iii) increased sensitivity to DNA-damaging agents. Taken together, our results indicate that the interplay between the N-terminal regulatory and C-terminal catalytic domains of Dna2 plays an important role in vivo, especially when cells are placed under replication stress.


Asunto(s)
ADN Helicasas/genética , Replicación del ADN/genética , ADN de Hongos/genética , Endonucleasas/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Biocatálisis , Ciclo Celular/genética , ADN Helicasas/química , ADN Helicasas/metabolismo , ADN de Hongos/química , ADN de Hongos/metabolismo , Endonucleasas/química , Endonucleasas/metabolismo , Péptidos y Proteínas de Señalización Intracelular/genética , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Modelos Moleculares , Mutación , Conformación de Ácido Nucleico , Oligonucleótidos/genética , Oligonucleótidos/metabolismo , Unión Proteica , Dominios Proteicos , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/crecimiento & desarrollo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Especificidad por Sustrato
6.
FEBS Lett ; 594(11): 1726-1737, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32239506

RESUMEN

Polymerase η (Polη) is one of the Y-family polymerases that is recruited by monoubiquitinated proliferating cell nuclear antigen (Ub-PCNA) to DNA damage sites during translesion synthesis (TLS). This interaction is mediated by an ubiquitin-binding zinc-finger (UBZ) domain and a PCNA-interacting protein (PIP) box in Polη, which binds to ubiquitin and PCNA, respectively. Here, we show that without the UBZ domain, the PIP box of yeast Polη has a novel binding function with ubiquitin. Furthermore, the UBZ domain and the PIP box share the same binding surfaces for ubiquitin. The interaction with ubiquitin via the PIP box stabilizes the Ub-PCNA/Polη complex. Moreover, the PIP residues I624 and L625 contribute to Polη function in TLS in vivo.


Asunto(s)
ADN Polimerasa Dirigida por ADN/química , ADN Polimerasa Dirigida por ADN/metabolismo , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/metabolismo , Ubiquitina/química , Ubiquitina/metabolismo , Secuencia de Aminoácidos , ADN/biosíntesis , Daño del ADN , Replicación del ADN , Isoleucina/metabolismo , Leucina/metabolismo , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Antígeno Nuclear de Célula en Proliferación/metabolismo , Unión Proteica , Dominios Proteicos , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/genética , Dedos de Zinc
7.
Front Mol Biosci ; 5: 26, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29651420

RESUMEN

DNA helicases unwind or rearrange duplex DNA during replication, recombination and repair. Helicases of many pathogenic organisms such as viruses, bacteria, and protozoa have been studied as potential therapeutic targets to treat infectious diseases, and human DNA helicases as potential targets for anti-cancer therapy. DNA replication machineries perform essential tasks duplicating genome in every cell cycle, and one of the important functions of these machineries are played by DNA helicases. Replicative helicases are usually multi-subunit protein complexes, and the minimal complex active as eukaryotic replicative helicase is composed of 11 subunits, requiring a functional assembly of two subcomplexes and one protein. The hetero-hexameric MCM2-7 helicase is activated by forming a complex with Cdc45 and the hetero-tetrameric GINS complex; the Cdc45-Mcm2-7-GINS (CMG) complex. The CMG complex can be a potential target for a treatment of cancer and the feasibility of this replicative helicase as a therapeutic target has been tested recently. Several different strategies have been implemented and are under active investigations to interfere with helicase activity of the CMG complex. This review focuses on the molecular function of the CMG helicase during DNA replication and its relevance to cancers based on data published in the literature. In addition, current efforts made to identify small molecules inhibiting the CMG helicase to develop anti-cancer therapeutic strategies were summarized, with new perspectives to advance the discovery of the CMG-targeting drugs.

8.
J Biol Chem ; 292(28): 11804-11814, 2017 07 14.
Artículo en Inglés | MEDLINE | ID: mdl-28559278

RESUMEN

MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally regulate gene expression. For example, miRNAs repress gene expression by recruiting the miRNA-induced silencing complex (miRISC), a ribonucleoprotein complex that contains miRNA-engaged Argonaute (Ago) and the scaffold protein GW182. Recently, ubiquitin-protein ligase E3 component N-recognin 5 (UBR5) has been identified as a component of miRISC. UBR5 directly interacts with GW182 proteins and participates in miRNA silencing by recruiting downstream effectors, such as the translation regulator DEAD-box helicase 6 (DDX6) and transducer of ERBB2,1/2,2 (Tob1/2), to the Ago-GW182 complex. However, the regulation of miRISC-associated UBR5 remains largely elusive. In the present study, we showed that UBR5 down-regulates the levels of TNF receptor-associated factor 3 (TRAF3), a key component of Toll-like receptor signaling, via the miRNA pathway. We further demonstrated that p90 ribosomal S6 kinase (p90RSK) is an upstream regulator of UBR5. p90RSK phosphorylates UBR5 at Thr637, Ser1227, and Ser2483, and this phosphorylation is required for the translational repression of TRAF3 mRNA. Phosphorylated UBR5 co-localized with GW182 and Ago2 in cytoplasmic speckles, which implies that miRISC is affected by phospho-UBR5. Collectively, these results indicated that the p90RSK-UBR5 pathway stimulates miRNA-mediated translational repression of TRAF3. Our work has added another layer to the regulation of miRISC.


Asunto(s)
Autoantígenos/metabolismo , MicroARNs/metabolismo , Proteínas de Unión al ARN/metabolismo , Proteínas Quinasas S6 Ribosómicas 90-kDa/metabolismo , Transducción de Señal , Factor 3 Asociado a Receptor de TNF/metabolismo , Receptores Toll-Like/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo , Regiones no Traducidas 3' , Sustitución de Aminoácidos , Animales , Autoantígenos/genética , Células COS , Chlorocebus aethiops , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Células HEK293 , Células HeLa , Humanos , Mutación , Fosforilación , Procesamiento Proteico-Postraduccional , Interferencia de ARN , ARN Mensajero/antagonistas & inhibidores , ARN Mensajero/metabolismo , Proteínas de Unión al ARN/antagonistas & inhibidores , Proteínas de Unión al ARN/genética , Proteínas Recombinantes de Fusión/metabolismo , Proteínas Quinasas S6 Ribosómicas 90-kDa/genética , Factor 3 Asociado a Receptor de TNF/antagonistas & inhibidores , Factor 3 Asociado a Receptor de TNF/genética , Ubiquitina-Proteína Ligasas/antagonistas & inhibidores , Ubiquitina-Proteína Ligasas/genética
9.
Genetics ; 206(2): 829-842, 2017 06.
Artículo en Inglés | MEDLINE | ID: mdl-28468907

RESUMEN

Lagging strand synthesis is mechanistically far more complicated than leading strand synthesis because it involves multistep processes and requires considerably more enzymes and protein factors. Due to this complexity, multiple fail-safe factors are required to ensure successful replication of the lagging strand DNA. We attempted to identify novel factors that are required in the absence of the helicase activity of Dna2, an essential enzyme in Okazaki-fragment maturation. In this article, we identified Rim11, a GSK-3ß-kinase homolog, as a multicopy suppressor of dna2 helicase-dead mutant (dna2-K1080E). Subsequent epistasis analysis revealed that Ume6 (a DNA binding protein, a downstream substrate of Rim11) also acted as a multicopy suppressor of the dna2 allele. We found that the interaction of Ume6 with the conserved histone deacetylase complex Sin3-Rpd3 and the catalytic activity of Rpd3 were indispensable for the observed suppression of the dna2 mutant. Moreover, multicopy suppression by Rim11/Ume6 requires the presence of sister-chromatid recombination mediated by Rad52/Rad59 proteins, but not vice versa. Interestingly, the overexpression of Rim11 or Ume6 also suppressed the MMS sensitivity of rad59Δ. We also showed that the lethality of dna2 helicase-dead mutant was attributed to checkpoint activation and that decreased levels of deoxynucleotide triphosphates (dNTPs) by overexpressing Sml1 (an inhibitor of ribonucleotide reductase) rescued the dna2 mutant. We also present evidence that indicates Rim11/Ume6 works independently but in parallel with that of checkpoint inhibition, dNTP regulation, and sister-chromatid recombination. In conclusion, our results establish Rim11, Ume6, the histone deacetylase complex Sin3-Rpd3 and Sml1 as new factors important in the events of faulty lagging strand synthesis.


Asunto(s)
ADN Helicasas/genética , Histona Desacetilasas/genética , Péptidos y Proteínas de Señalización Intracelular/genética , Proteínas Serina-Treonina Quinasas/genética , Proteínas Represoras/genética , Proteínas de Saccharomyces cerevisiae/genética , ADN/genética , Replicación del ADN/genética , Glucógeno Sintasa Quinasa 3 beta/genética , Proteínas Mutantes/genética , Saccharomyces cerevisiae/genética , Complejo Correpresor Histona Desacetilasa y Sin3/genética
10.
ACS Appl Mater Interfaces ; 9(9): 7908-7917, 2017 Mar 08.
Artículo en Inglés | MEDLINE | ID: mdl-28198615

RESUMEN

Two-dimensional (2D) nanomaterials, such as graphene-based materials and transition metal dichalcogenide (TMD) nanosheets, are promising materials for biomedical applications owing to their remarkable cytocompatibility and physicochemical properties. On the basis of their potent antibacterial properties, 2D materials have potential as antibacterial films, wherein the 2D nanosheets are immobilized on the surface and the bacteria may contact with the basal planes of 2D nanosheets dominantly rather than contact with the sharp edges of nanosheets. To address these points, in this study, we prepared an effective antibacterial surface consisting of representative 2D materials, i.e., graphene oxide (GO) and molybdenum disulfide (MoS2), formed into nanosheets on a transparent substrate for real device applications. The antimicrobial properties of the GO-MoS2 nanocomposite surface toward the Gram-negative bacteria Escherichia coli were investigated, and the GO-MoS2 nanocomposite exhibited enhanced antimicrobial effects with increased glutathione oxidation capacity and partial conductivity. Furthermore, direct imaging of continuous morphological destruction in the individual bacterial cells having contacts with the GO-MoS2 nanocomposite surface was characterized by holotomographic (HT) microscopy, which could be used to detect the refractive index (RI) distribution of each voxel in bacterial cell and reconstruct the three-dimensional (3D) mapping images of bacteria. In this regard, the decreases in both the volume (67.2%) and the dry mass (78.8%) of bacterial cells that came in contact with the surface for 80 min were quantitatively measured, and releasing of intracellular components mediated by membrane and oxidative stress was observed. Our findings provided new insights into the antibacterial properties of 2D nanocomposite film with label-free tracing of bacterial cell which improve our understanding of antimicrobial activities and opened a window for the 2D nanocomposite as a practical antibacterial film in biomedical applications.

11.
FEBS J ; 283(23): 4247-4262, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27759916

RESUMEN

Highly conserved eukaryotic histones are polybasic proteins that package DNA into nucleosomes, a building block of chromatin, allowing extremely long DNA molecules to form compact and discrete chromosomes. The histone N-terminal tails that extend from the nucleosome core act as docking sites for many proteins through diverse post-translational modifications, regulating various DNA transactions. In this report, we present evidence that the nucleosomes can positively regulate the enzymatic activity of Rad27 (yeast Fen1), a major processing enzyme important for Okazaki fragment in eukaryotes. We found that individual histones, histone octamers, and nucleosomes are able to stimulate Rad27 in a manner dependent on the N-terminal tails of histones. Kinetic analyses suggest that an increase in catalytic efficiency of Rad27 was mainly due to increased affinity between DNA substrates and Rad27. It appears that the physical interaction in vivo between histones and Rad27 results in the enrichment of Rad27 in the vicinity of chromatin, increasing the availability of Rad27 for various DNA metabolisms. These results indicate that nucleosomes are not a mere structural component of chromatin, but an active regulator of DNA metabolisms that serves to ensure the efficient and faithful processing of structural intermediates arising during DNA transactions.


Asunto(s)
ADN de Hongos/metabolismo , Endonucleasas de ADN Solapado/metabolismo , Nucleosomas/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Secuencia de Aminoácidos , Western Blotting , Cromatina/genética , Cromatina/metabolismo , ADN de Hongos/genética , Endonucleasas de ADN Solapado/genética , Histonas/genética , Histonas/metabolismo , Cinética , Mutación , Nucleosomas/genética , Unión Proteica , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Especificidad por Sustrato
12.
Biotechnol Bioeng ; 113(12): 2544-2552, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27241141

RESUMEN

A polymerase chain reaction (PCR) using a thermostable DNA polymerase is the most widely applied method in many areas of research, including life sciences, biotechnology, and medical sciences. However, a conventional PCR incurs an amplification of undesired genes mainly owing to non-specifically annealed primers and the formation of a primer-dimer complex. Herein, we present the development of a Taq DNA polymerase-specific repebody, which is a small-sized protein binder composed of leucine rich repeat (LRR) modules, as a thermolabile inhibitor for a precise and accurate gene amplification by PCR. We selected a repebody that specifically binds to the DNA polymerase through a phage display, and increased its affinity to up to 10 nM through a modular evolution approach. The repebody was shown to effectively inhibit DNA polymerase activity at low temperature and undergo thermal denaturation at high temperature, leading to a rapid and full recovery of the polymerase activity, during the initial denaturation step of the PCR. The performance and utility of the repebody was demonstrated through an accurate and efficient amplification of a target gene without nonspecific gene products in both conventional and real-time PCRs. The repebody is expected to be effectively utilized as a thermolabile inhibitor in a PCR. Biotechnol. Bioeng. 2016;113: 2544-2552. © 2016 Wiley Periodicals, Inc.


Asunto(s)
ADN/genética , Amplificación de Genes/genética , Inhibidores de la Síntesis del Ácido Nucleico/farmacología , Reacción en Cadena de la Polimerasa/métodos , Secuencias Repetitivas de Aminoácido/genética , Polimerasa Taq/genética , Polimerasa Taq/antagonistas & inhibidores
13.
Nucleic Acids Res ; 43(3): 1684-99, 2015 Feb 18.
Artículo en Inglés | MEDLINE | ID: mdl-25628354

RESUMEN

Fen1 and Mus81-Mms4 are endonucleases involved in the processing of various DNA structural intermediates, and they were shown to have genetic and functional interactions with each other. Here, we show the in vivo significance of the interactions between Mus81 and Rad27 (yeast Fen1). The N-terminal 120 amino-acid (aa) region of Mus81, although entirely dispensable for its catalytic activity, was essential for the abilities of Mus81 to bind to and be stimulated by Rad27. In the absence of SGS1, the mus81Δ120N mutation lacking the N-terminal 120 aa region exhibited synthetic lethality, and the lethality was rescued by deletion of RAD52, a key homologous recombination mediator. These findings, together with the fact that Sgs1 constitutes a redundant pathway with Mus81-Mms4, indicate that the N-terminus-mediated interaction of Mus81 with Rad27 is physiologically important in resolving toxic recombination intermediates. Mutagenic analyses of the N-terminal region identified two distinct motifs, named N21-26 (aa from 21-26) and N108-114 (aa from 108-114) important for the in vitro and in vivo functions of Mus81. Our findings indicate that the N-terminal region of Mus81 acts as a landing pad to interact with Rad27 and that Mus81 and Rad27 work conjointly for efficient removal of various aberrant DNA structures.


Asunto(s)
Proteínas de Unión al ADN/metabolismo , Endonucleasas/metabolismo , Reparación del ADN por Recombinación , Proteínas de Saccharomyces cerevisiae/metabolismo , Secuencia de Aminoácidos , Secuencia de Bases , Cartilla de ADN , Proteínas de Unión al ADN/química , Endonucleasas/química , Endonucleasas de ADN Solapado/química , Endonucleasas de ADN Solapado/metabolismo , Unión Proteica , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química
14.
BMB Rep ; 48(1): 25-9, 2015 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24667174

RESUMEN

Ubiquitination is a post translational modification which mostly links with proteasome dependent protein degradation. This process has been known to play pivotal roles in the number of biological events including apoptosis, cell signaling, transcription and translation. Although the process of ubiquitination has been studied extensively, the mechanism of polyubiquitination by multi protein E3 ubiquitin ligase, SCF complex remains elusive. In the present study, we identified UbcH5a as a novel stimulating factor for poly-ubiquitination catalyzed by SCF(hFBH1) using biochemical fractionations and MALDI-TOF. Moreover, we showed that recombinant UbcH5a and Cdc34 synergistically stimulate SCF(hFBH1) catalyzed polyubiquitination in vitro. These data may provide an important cue to understand the mechanism how the SCF complex efficiently polyubiquitinates target substrates.


Asunto(s)
Proteínas Ligasas SKP Cullina F-box/metabolismo , Enzimas Ubiquitina-Conjugadoras/metabolismo , Secuencia de Aminoácidos , Biocatálisis , Células HeLa , Humanos , Datos de Secuencia Molecular , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/genética , Alineación de Secuencia , Enzimas Ubiquitina-Conjugadoras/genética , Ubiquitinación
15.
J Lipid Res ; 56(2): 294-303, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25548260

RESUMEN

Nucleoredoxin (NRX) is a member of the thioredoxin family of proteins that controls redox homeostasis in cell. Redox homeostasis is a well-known regulator of cell differentiation into various tissue types. We found that NRX expression levels were higher in white adipose tissue of obese ob/ob mice and increased in the early adipogenic stage of 3T3-L1 preadipocyte differentiation. Knockdown of NRX decreased differentiation of 3T3-L1 cells, whereas overexpression increased differentiation. Adipose tissue-specific NRX transgenic mice showed increases in adipocyte size as well as number compared with WT mice. We further confirmed that the Wingless/int-1 class (Wnt)/ß-catenin pathway was also involved in NRX-promoted adipogenesis, consistent with a previous report showing NRX regulation of this pathway. Genes involved in lipid metabolism were downregulated, whereas inflammatory genes, including those encoding macrophage markers, were significantly upregulated, likely contributing to the obesity in Adipo-NRX mice. Our results therefore suggest that NRX acts as a novel proadipogenic factor and controls obesity in vivo.


Asunto(s)
Diferenciación Celular/fisiología , Proteínas Nucleares/metabolismo , Oxidorreductasas/metabolismo , Transducción de Señal , beta Catenina/metabolismo , Células 3T3-L1 , Adipocitos/citología , Adipogénesis/genética , Adipogénesis/fisiología , Animales , Diferenciación Celular/genética , Células Cultivadas , Femenino , Masculino , Ratones , Ratones Transgénicos , Proteínas Nucleares/genética , Oxidorreductasas/genética , Vía de Señalización Wnt/genética , Vía de Señalización Wnt/fisiología
16.
Nucleic Acids Res ; 42(9): 5846-62, 2014 May.
Artículo en Inglés | MEDLINE | ID: mdl-24692662

RESUMEN

MUS81 shares a high-degree homology with the catalytic XPF subunit of the XPF-ERCC1 endonuclease complex. It is catalytically active only when complexed with the regulatory subunits Mms4 or Eme1 in budding and fission yeasts, respectively, and EME1 or EME2 in humans. Although Mus81 complexes are implicated in the resolution of recombination intermediates in vivo, recombinant yeast Mus81-Mms4 and human MUS81-EME1 isolated from Escherichia coli fail to cleave intact Holliday junctions (HJs) in vitro. In this study, we show that human recombinant MUS81-EME2 isolated from E. coli cleaves HJs relatively efficiently, compared to MUS81-EME1. Furthermore, MUS81-EME2 catalyzed cleavage of nicked and gapped duplex deoxyribonucleic acids (DNAs), generating double-strand breaks. The presence of a 5' phosphate terminus at nicks and gaps rendered DNA significantly less susceptible to the cleavage by MUS81-EME2 than its absence, raising the possibility that this activity could play a role in channeling damaged DNA duplexes that are not readily repaired into the recombinational repair pathways. Significant differences in substrate specificity observed with unmodified forms of MUS81-EME1 and MUS81-EME2 suggest that they play related but non-overlapping roles in DNA transactions.


Asunto(s)
ADN Cruciforme/química , Proteínas de Unión al ADN/química , Endodesoxirribonucleasas/química , Endonucleasas/química , Roturas del ADN de Doble Cadena , Roturas del ADN de Cadena Simple , División del ADN , Escherichia coli , Humanos , Cinética , Complejos Multiproteicos/química , Subunidades de Proteína/química , Especificidad por Sustrato
17.
J Biol Chem ; 289(21): 15064-79, 2014 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-24711454

RESUMEN

The correct removal of 5'-flap structures by Rad27 and Dna2 during Okazaki fragment maturation is crucial for the stable maintenance of genetic materials and cell viability. In this study, we identified RAD52, a key recombination protein, as a multicopy suppressor of dna2-K1080E, a lethal helicase-negative mutant allele of DNA2 in yeasts. In contrast, the overexpression of Rad51, which works conjointly with Rad52 in canonical homologous recombination, failed to suppress the growth defect of the dna2-K1080E mutation, indicating that Rad52 plays a unique and distinct role in Okazaki fragment metabolism. We found that the recombination-defective Rad52-QDDD/AAAA mutant did not rescue dna2-K1080E, suggesting that Rad52-mediated recombination is important for suppression. The Rad52-mediated enzymatic stimulation of Dna2 or Rad27 is not a direct cause of suppression observed in vivo, as both Rad52 and Rad52-QDDD/AAAA proteins stimulated the endonuclease activities of both Dna2 and Rad27 to a similar extent. The recombination mediator activity of Rad52 was dispensable for the suppression, whereas both the DNA annealing activity and its ability to interact with Rad59 were essential. In addition, we found that several cohesion establishment factors, including Rsc2 and Elg1, were required for the Rad52-dependent suppression of dna2-K1080E. Our findings suggest a novel Rad52/Rad59-dependent, but Rad51-independent recombination pathway that could ultimately lead to the removal of faulty flaps in conjunction with cohesion establishment factors.


Asunto(s)
Proteínas de Unión al ADN/metabolismo , ADN/metabolismo , Recombinación Homóloga , Proteína Recombinante y Reparadora de ADN Rad52/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , ADN/genética , ADN Helicasas/genética , ADN Helicasas/metabolismo , Reparación del ADN , Replicación del ADN , Proteínas de Unión al ADN/genética , Immunoblotting , Mutación , Proteína Recombinante y Reparadora de ADN Rad52/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética
18.
Nucleic Acids Res ; 41(6): 3576-87, 2013 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-23393192

RESUMEN

DNA repair helicases function in the cell to separate DNA duplexes or remodel nucleoprotein complexes. These functions are influenced by sensing and signaling; the cellular pool of a DNA helicase may contain subpopulations of enzymes carrying different post-translational modifications and performing distinct biochemical functions. Here, we report a novel experimental strategy, single-molecule sorting, which overcomes difficulties associated with comprehensive analysis of heterologously modified pool of proteins. This methodology was applied to visualize human DNA helicase F-box-containing DNA helicase (FBH1) acting on the DNA structures resembling a stalled or collapsed replication fork and its interactions with RAD51 nucleoprotein filament. Individual helicase molecules isolated from human cells with their native post-translational modifications were analyzed using total internal reflection fluorescence microscopy. Separation of the activity trajectories originated from ubiquitylated and non-ubiquitylated FBH1 molecules revealed that ubiquitylation affects FBH1 interaction with the RAD51 nucleoprotein filament, but not its translocase and helicase activities.


Asunto(s)
ADN Helicasas/metabolismo , Proteínas de Unión al ADN/metabolismo , Ubiquitinación , Sitios de Unión , ADN/metabolismo , ADN Helicasas/química , Replicación del ADN , Proteínas de Unión al ADN/química , Células HEK293 , Humanos , Estructura Terciaria de Proteína , Recombinasa Rad51/metabolismo
19.
J Biol Chem ; 288(13): 9468-81, 2013 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-23344960

RESUMEN

The removal of initiating primers from the 5'-ends of each Okazaki fragment, required for the generation of contiguous daughter strands, can be catalyzed by the combined action of DNA polymerase δ and Fen1. When the flaps generated by displacement of DNA synthesis activity of polymerase δ become long enough to bind replication protein A or form hairpin structures, the helicase/endonuclease enzyme, Dna2, becomes critical because of its ability to remove replication protein A-coated or secondary structure flaps. In this study, we show that the N-terminal 45-kDa domain of Dna2 binds hairpin structures, allowing the enzyme to target secondary structure flap DNA. We found that this activity was essential for the efficient removal of hairpin flaps by the endonuclease activity of Dna2 with the aid of its helicase activity. Thus, the efficient removal of hairpin structure flaps requires the coordinated action of all three functional domains of Dna2. We also found that deletion of the N-terminal 45-kDa domain of Dna2 led to a partial loss of the intra-S-phase checkpoint function and an increased rate of homologous recombination in yeast. We discuss the potential roles of the N-terminal domain of Dna2 in the maintenance of genomic stability.


Asunto(s)
ADN Helicasas/genética , ADN Helicasas/metabolismo , ADN/química , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Roturas del ADN de Doble Cadena , ADN Helicasas/química , Desoxirribonucleasas/química , Marcadores Genéticos , Genoma , Conformación de Ácido Nucleico , Oligonucleótidos/genética , Unión Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Recombinación Genética , Fase S
20.
J Lipid Res ; 53(9): 1864-76, 2012 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-22693256

RESUMEN

Acetylation is one of the most crucial post-translational modifications that affect protein function. Protein lysine acetylation is catalyzed by acetyltransferases, and acetyl-CoA functions as the source of the acetyl group. Additionally, acetyl-CoA plays critical roles in maintaining the balance between carbohydrate metabolism and fatty acid synthesis. Here, we sought to determine whether lysine acetylation is an important process for adipocyte differentiation. Based on an analysis of the acetylome during adipogenesis, various proteins displaying significant quantitative changes were identified by LC-MS/MS. Of these identified proteins, we focused on malate dehydrogenase 1 (MDH1). The acetylation level of MDH1 was increased up to 6-fold at the late stage of adipogenesis. Moreover, overexpression of MDH1 in 3T3-L1 preadipocytes induced a significant increase in the number of cells undergoing adipogenesis. The introduction of mutations to putative lysine acetylation sites showed a significant loss of the ability of cells to undergo adipogenic differentiation. Furthermore, the acetylation of MDH1 dramatically enhanced its enzymatic activity and subsequently increased the intracellular levels of NADPH. These results clearly suggest that adipogenic differentiation may be regulated by the acetylation of MDH1 and that the acetylation of MDH1 is one of the cross-talk mechanisms between adipogenesis and the intracellular energy level.


Asunto(s)
Adipogénesis , Malato Deshidrogenasa/metabolismo , Células 3T3-L1 , Acetilación , Adipocitos/citología , Adipocitos/enzimología , Adipocitos/metabolismo , Animales , Activación Enzimática , Regulación Enzimológica de la Expresión Génica , Humanos , Espacio Intracelular/metabolismo , Lisina/metabolismo , Malato Deshidrogenasa/química , Malato Deshidrogenasa/genética , Ratones , Mutagénesis Sitio-Dirigida , Mutación , NADP/metabolismo
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