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1.
Mol Cell ; 53(5): 766-78, 2014 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-24606919

RESUMEN

In bacteria, translation-transcription coupling inhibits RNA polymerase (RNAP) stalling. We present evidence suggesting that, upon amino acid starvation, inactive ribosomes promote rather than inhibit RNAP stalling. We developed an algorithm to evaluate genome-wide polymerase progression independently of local noise and used it to reveal that the transcription factor DksA inhibits promoter-proximal pausing and increases RNAP elongation when uncoupled from translation by depletion of charged tRNAs. DksA has minimal effect on RNAP elongation in vitro and on untranslated RNAs in vivo. In these cases, transcripts can form RNA structures that prevent backtracking. Thus, the effect of DksA on transcript elongation may occur primarily upon ribosome slowing/stalling or at promoter-proximal locations that limit the potential for RNA structure. We propose that inactive ribosomes prevent formation of backtrack-blocking mRNA structures and that, in this circumstance, DksA acts as a transcription elongation factor in vivo.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Regulación Enzimológica de la Expresión Génica , Ribosomas/metabolismo , Algoritmos , Inmunoprecipitación de Cromatina , ARN Polimerasas Dirigidas por ADN/química , ARN Polimerasas Dirigidas por ADN/metabolismo , Escherichia coli/enzimología , Eliminación de Gen , Sistemas de Lectura Abierta , ARN de Transferencia/metabolismo , Ribosomas/química , Factor sigma/química , Transcripción Genética , Factores de Elongación Transcripcional/metabolismo
2.
Genes Dev ; 26(23): 2621-33, 2012 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-23207917

RESUMEN

Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its cofactor, NusG, is suppression of ubiquitous antisense transcription genome-wide. Rho binds C-rich unstructured nascent RNA (high C/G ratio) prior to its ATP-dependent dissociation of transcription complexes. NusG is required for efficient termination at minority subsets (~20%) of both antisense and sense Rho-dependent terminators with lower C/G ratio sequences. In contrast, a widely studied nusA deletion proposed to compromise Rho-dependent termination had no effect on antisense or sense Rho-dependent terminators in vivo. Global colocalization of the histone-like nucleoid-structuring protein (H-NS) with Rho-dependent terminators and genetic interactions between hns and rho suggest that H-NS aids Rho in suppression of antisense transcription. The combined actions of Rho, NusG, and H-NS appear to be analogous to the Sen1-Nrd1-Nab3 and nucleosome systems that suppress antisense transcription in eukaryotes.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Factores de Elongación de Péptidos/metabolismo , Factores de Transcripción/metabolismo , Secuencia de Bases , Proteínas de Escherichia coli/genética , Eliminación de Gen , Genoma Bacteriano , Factores de Elongación de Péptidos/genética , Unión Proteica , Factores de Transcripción/genética , Transcripción Genética
3.
Proc Natl Acad Sci U S A ; 111(25): E2576-85, 2014 Jun 24.
Artículo en Inglés | MEDLINE | ID: mdl-24927582

RESUMEN

The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and have revealed multiple mechanisms of tolerance, but it remains difficult to separate the direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, and then characterized mechanisms of toxicity and resistance using genome-scale DNAseq, RNAseq, and ribosome profiling coupled with specific assays of ribosome and RNA polymerase function. Evolved alleles of metJ, rho, and rpsQ recapitulated most of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. Ethanol induced miscoding errors during protein synthesis, from which the evolved rpsQ allele protected cells by increasing ribosome accuracy. Ribosome profiling and RNAseq analyses established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis through direct effects on ribosomes and RNA polymerase conformations are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ help protect these central dogma processes in the presence of ethanol.


Asunto(s)
Farmacorresistencia Bacteriana , Escherichia coli K12 , Proteínas de Escherichia coli , Etanol/farmacología , Biosíntesis de Proteínas , Solventes/farmacología , Transcripción Genética , Alelos , Farmacorresistencia Bacteriana/efectos de los fármacos , Farmacorresistencia Bacteriana/genética , Escherichia coli K12/genética , Escherichia coli K12/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Estudio de Asociación del Genoma Completo , Biosíntesis de Proteínas/efectos de los fármacos , Biosíntesis de Proteínas/genética , Transcripción Genética/efectos de los fármacos , Transcripción Genética/genética
4.
Blood ; 117(18): 4769-72, 2011 May 05.
Artículo en Inglés | MEDLINE | ID: mdl-21398579

RESUMEN

Master transcriptional regulators of development often function through dispersed cis elements at endogenous target genes. While cis-elements are routinely studied in transfection and transgenic reporter assays, it is challenging to ascertain how they function in vivo. To address this problem in the context of the locus encoding the critical hematopoietic transcription factor Gata2, we engineered mice lacking a cluster of GATA motifs 2.8 kb upstream of the Gata2 transcriptional start site. We demonstrate that the -2.8 kb site confers maximal Gata2 expression in hematopoietic stem cells and specific hematopoietic progenitors. By contrast to our previous demonstration that a palindromic GATA motif at the neighboring -1.8 kb site maintains Gata2 repression in terminally differentiating erythroid cells, the -2.8 kb site was not required to initiate or maintain repression. These analyses reveal qualitatively distinct functions of 2 GATA motif-containing regions in vivo.


Asunto(s)
Factor de Transcripción GATA2/genética , Factor de Transcripción GATA2/metabolismo , Hematopoyesis/genética , Hematopoyesis/fisiología , Secuencias de Aminoácidos , Animales , Eritropoyesis/genética , Eritropoyesis/fisiología , Factor de Transcripción GATA2/química , Expresión Génica , Técnicas de Sustitución del Gen , Genes de Cambio , Células Madre Hematopoyéticas/citología , Células Madre Hematopoyéticas/metabolismo , Ratones , Ratones Transgénicos , Modelos Biológicos , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Sitio de Iniciación de la Transcripción
5.
PLoS Genet ; 6(9): e1001103, 2010 Sep 09.
Artículo en Inglés | MEDLINE | ID: mdl-20838598

RESUMEN

In development, lineage-restricted transcription factors simultaneously promote differentiation while repressing alternative fates. Molecular dissection of this process has been challenging as transcription factor loci are regulated by many trans-acting factors functioning through dispersed cis elements. It is not understood whether these elements function collectively to confer transcriptional regulation, or individually to control specific aspects of activation or repression, such as initiation versus maintenance. Here, we have analyzed cis element regulation of the critical hematopoietic factor Gata2, which is expressed in early precursors and repressed as GATA-1 levels rise during terminal differentiation. We engineered mice lacking a single cis element -1.8 kb upstream of the Gata2 transcriptional start site. Although Gata2 is normally repressed in late-stage erythroblasts, the -1.8 kb mutation unexpectedly resulted in reactivated Gata2 transcription, blocked differentiation, and an aberrant lineage-specific gene expression pattern. Our findings demonstrate that the -1.8 kb site selectively maintains repression, confers a specific histone modification pattern and expels RNA Polymerase II from the locus. These studies reveal how an individual cis element establishes a normal developmental program via regulating specific steps in the mechanism by which a critical transcription factor is repressed.


Asunto(s)
Factor de Transcripción GATA2/genética , Regulación del Desarrollo de la Expresión Génica , Regiones Promotoras Genéticas , Proteínas Represoras/metabolismo , Animales , Emparejamiento Base/genética , Islas de CpG/genética , Metilación de ADN/genética , Células Eritroides/metabolismo , Eritropoyesis/genética , Factor de Transcripción GATA2/metabolismo , Eliminación de Gen , Marcación de Gen , Sitios Genéticos/genética , Histonas/metabolismo , Ratones , Ratones Mutantes , Nucleoproteínas/metabolismo , Unión Proteica , ARN Polimerasa II/metabolismo , Estrés Fisiológico/genética
6.
Appl Environ Microbiol ; 78(9): 3442-57, 2012 May.
Artículo en Inglés | MEDLINE | ID: mdl-22389370

RESUMEN

The physiology of ethanologenic Escherichia coli grown anaerobically in alkali-pretreated plant hydrolysates is complex and not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pretreated by ammonia fiber expansion. Despite the high sugar content (∼6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses during an exponential growth phase, a transition phase, and the glycolytically active stationary phase. During the exponential and transition phases, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate. However, after the majority of amino acids were depleted, the cells entered stationary phase, and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin, and ethanol stress collectively limits growth, sugar utilization rates, and ethanol yields in alkali-pretreated lignocellulosic hydrolysates.


Asunto(s)
Escherichia coli K12/metabolismo , Etanol/metabolismo , Etanol/toxicidad , Estrés Fisiológico , Zea mays/metabolismo , Aminoácidos/metabolismo , Anaerobiosis , Escherichia coli K12/crecimiento & desarrollo , Fermentación , Perfilación de la Expresión Génica , Glucosa/metabolismo
7.
Proc Natl Acad Sci U S A ; 105(31): 10907-12, 2008 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-18669654

RESUMEN

Increased alpha-synuclein gene (SNCA) dosage due to locus multiplication causes autosomal dominant Parkinson's disease (PD). Variation in SNCA expression may be critical in common, genetically complex PD but the underlying regulatory mechanism is unknown. We show that SNCA and the heme metabolism genes ALAS2, FECH, and BLVRB form a block of tightly correlated gene expression in 113 samples of human blood, where SNCA naturally abounds (validated P = 1.6 x 10(-11), 1.8 x 10(-10), and 6.6 x 10(-5)). Genetic complementation analysis revealed that these four genes are co-induced by the transcription factor GATA-1. GATA-1 specifically occupies a conserved region within SNCA intron-1 and directly induces a 6.9-fold increase in alpha-synuclein. Endogenous GATA-2 is highly expressed in substantia nigra vulnerable to PD, occupies intron-1, and modulates SNCA expression in dopaminergic cells. This critical link between GATA factors and SNCA may enable therapies designed to lower alpha-synuclein production.


Asunto(s)
Factores de Transcripción GATA/metabolismo , Regulación de la Expresión Génica/fisiología , Enfermedad de Parkinson/metabolismo , alfa-Sinucleína/metabolismo , 5-Aminolevulinato Sintetasa/metabolismo , Animales , Northern Blotting , Western Blotting , Células Cultivadas , Biología Computacional , Ensayo de Inmunoadsorción Enzimática , Prueba de Complementación Genética , Humanos , Inmunohistoquímica , Ratones , Análisis por Micromatrices , ARN Interferente Pequeño/genética
8.
Mol Cell Biol ; 26(19): 7056-67, 2006 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-16980610

RESUMEN

The reciprocal expression of GATA-1 and GATA-2 during hematopoiesis is an important determinant of red blood cell development. Whereas Gata2 is preferentially transcribed early in hematopoiesis, elevated GATA-1 levels result in GATA-1 occupancy at sites upstream of the Gata2 locus and transcriptional repression. GATA-2 occupies these sites in the transcriptionally active locus, suggesting that a "GATA switch" abrogates GATA-2-mediated positive autoregulation. Chromatin immunoprecipitation (ChIP) coupled with genomic microarray analysis and quantitative ChIP analysis with GATA-1-null cells expressing an estrogen receptor ligand binding domain fusion to GATA-1 revealed additional GATA switches 77 kb upstream of Gata2 and within intron 4 at +9.5 kb. Despite indistinguishable GATA-1 occupancy at -77 kb and +9.5 kb versus other GATA switch sites, GATA-1 functioned uniquely at the different regions. GATA-1 induced histone deacetylation at and near Gata2 but not at the -77 kb region. The -77 kb region, which was DNase I hypersensitive in both active and inactive states, conferred equivalent enhancer activities in GATA-1- and GATA-2-expressing cells. By contrast, the +9.5 kb region exhibited considerably stronger enhancer activity in GATA-2- than in GATA-1-expressing cells, and other GATA switch sites were active only in GATA-1- or GATA-2-expressing cells. Chromosome conformation capture analysis demonstrated higher-order interactions between the -77 kb region and Gata2 in the active and repressed states. These results indicate that dispersed GATA factor complexes function via long-range chromatin interactions and qualitatively distinct activities to regulate Gata2 transcription.


Asunto(s)
Factor de Transcripción GATA1/genética , Factor de Transcripción GATA1/metabolismo , Factor de Transcripción GATA2/genética , Factor de Transcripción GATA2/metabolismo , Acetilación , Animales , Emparejamiento Base/genética , Secuencia de Bases , Cromatina/metabolismo , Inmunoprecipitación de Cromatina , Secuencia Conservada/genética , Desoxirribonucleasa I/metabolismo , Elementos de Facilitación Genéticos/genética , Humanos , Ratones , Datos de Secuencia Molecular , Proteínas Nucleares/metabolismo , Regiones Promotoras Genéticas/genética , Receptores de Estrógenos/metabolismo , Factores de Transcripción p300-CBP/metabolismo
9.
Biotechnol J ; 14(9): e1800441, 2019 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-31297978

RESUMEN

Currently, microbial conversion of lignocellulose-derived glucose and xylose to biofuels is hindered by the fact that most microbes (including Escherichia coli [E. coli], Saccharomyces cerevisiae, and Zymomonas mobilis) preferentially consume glucose first and consume xylose slowly after glucose is depleted in lignocellulosic hydrolysates. In this study, E. coli strains are developed that simultaneously utilize glucose and xylose in lignocellulosic biomass hydrolysate using genome-scale models and adaptive laboratory evolution. E. coli strains are designed and constructed that coutilize glucose and xylose and adaptively evolve them to improve glucose and xylose utilization. Whole-genome resequencing of the evolved strains find relevant mutations in metabolic and regulatory genes and the mutations' involvement in sugar coutilization is investigated. The developed strains show significantly improved coconversion of sugars in lignocellulosic biomass hydrolysates and provide a promising platform for producing next-generation biofuels.


Asunto(s)
Escherichia coli/metabolismo , Ingeniería Metabólica/métodos , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Glucosa/metabolismo , Lignina/metabolismo , Xilosa/metabolismo
10.
Mol Cell Biol ; 25(4): 1458-74, 2005 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-15684396

RESUMEN

The process whereby the primitive vascular network develops into the mature vasculature, known as angiogenic vascular remodeling, is controlled by the Notch signaling pathway. Of the two mammalian Notch receptors expressed in vascular endothelium, Notch1 is broadly expressed in diverse cell types, whereas Notch4 is preferentially expressed in endothelial cells. As mechanisms that confer Notch4 expression were unknown, we investigated how NOTCH4 transcription is regulated in human endothelial cells and in transgenic mice. The NOTCH4 promoter and the 5' portion of NOTCH4 assembled into an endothelial cell-specific histone modification pattern. Analysis of NOTCH4 primary transcripts in human umbilical vein endothelial cells by RNA fluorescence in situ hybridization revealed that 36% of the cells transcribed one or both NOTCH4 alleles. The NOTCH4 promoter was sufficient to confer endothelial cell-specific transcription in transfection assays, but intron 1 or upstream sequences were required for expression in the vasculature of transgenic mouse embryos. Cell-type-specific activator protein 1 (AP-1) complexes occupied NOTCH4 chromatin and conferred endothelial cell-specific transcription. Vascular angiogenic factors activated AP-1 and reprogrammed the endogenous NOTCH4 gene in HeLa cells from a repressed to a transcriptionally active state. These results reveal an AP-1-Notch4 pathway, which we propose to be crucial for transducing angiogenic signals and to be deregulated upon aberrant signal transduction in cancer.


Asunto(s)
Alelos , Células Endoteliales/metabolismo , Proteínas Proto-Oncogénicas/metabolismo , Receptores de Superficie Celular/metabolismo , Factores de Transcripción/metabolismo , Transcripción Genética/genética , Región de Flanqueo 5'/genética , Animales , Células Cultivadas , Embrión de Mamíferos/citología , Embrión de Mamíferos/metabolismo , Células HeLa , Histonas/genética , Histonas/metabolismo , Humanos , Hibridación Fluorescente in Situ , Intrones/genética , Ratones , Ratones Transgénicos , Regiones Promotoras Genéticas , Proteínas Proto-Oncogénicas/genética , Receptor Notch1 , Receptor Notch4 , Receptores de Superficie Celular/genética , Receptores Notch , Factor de Transcripción AP-1/genética , Factor de Transcripción AP-1/metabolismo , Factores de Transcripción/genética
11.
Mol Cell Biol ; 23(18): 6484-93, 2003 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-12944475

RESUMEN

RNA polymerase II (Pol II) can associate with regulatory elements far from promoters. For the murine beta-globin locus, Pol II binds the beta-globin locus control region (LCR) far upstream of the beta-globin promoters, independent of recruitment to and activation of the betamajor promoter. We describe here an analysis of where Pol II resides within the LCR, how it is recruited to the LCR, and the functional consequences of recruitment. High-resolution analysis of the distribution of Pol II revealed that Pol II binding within the LCR is restricted to the hypersensitive sites. Blocking elongation eliminated the synthesis of genic and extragenic transcripts and eliminated Pol II from the betamajor open reading frame. However, the elongation blockade did not redistribute Pol II at the hypersensitive sites, suggesting that Pol II is recruited to these sites. The distribution of Pol II did not strictly correlate with the distributions of histone acetylation and methylation. As Pol II associates with histone-modifying enzymes, Pol II tracking might be critical for establishing and maintaining broad histone modification patterns. However, blocking elongation did not disrupt the histone modification pattern of the beta-globin locus, indicating that Pol II tracking is not required to maintain the pattern.


Asunto(s)
Cromatina/metabolismo , Región de Control de Posición/fisiología , ARN Polimerasa II/metabolismo , Acetilación , Animales , Sitios de Unión , Células Cultivadas , Células Precursoras Eritroides/fisiología , Globinas/genética , Globinas/metabolismo , Histona Acetiltransferasas , Histonas/metabolismo , Metilación , Ratones , Especificidad de Órganos , Extensión de la Cadena Peptídica de Translación , Regiones Promotoras Genéticas , ARN Polimerasa II/genética , Factores Asociados con la Proteína de Unión a TATA/inmunología , Factores Asociados con la Proteína de Unión a TATA/metabolismo , Factor de Transcripción TFIID/inmunología , Factor de Transcripción TFIID/metabolismo , Transcripción Genética
12.
Methods Mol Biol ; 284: 129-46, 2004.
Artículo en Inglés | MEDLINE | ID: mdl-15173613

RESUMEN

Elucidating mechanisms controlling nuclear processes requires an understanding of the nucleoprotein structure of genes at endogenous chromosomal loci. Traditional approaches to measuring protein-DNA interactions in vitro have often failed to provide insights into physiological mechanisms. Given that most transcription factors interact with simple DNA sequence motifs, which are abundantly distributed throughout a genome, it is essential to pinpoint the small subset of sites bound by factors in vivo. Signaling mechanisms induce the assembly and modulation of complex patterns of histone acetylation, methylation, phosphorylation, and ubiquitination, which are crucial determinants of chromatin accessibility. These seemingly complex issues can be directly addressed by a powerful methodology termed the chromatin immunoprecipitation (ChIP) assay. ChIP analysis involves covalently trapping endogenous proteins at chromatin sites, thereby yielding snapshots of protein-DNA interactions and histone modifications within living cells. The chromatin is sonicated to generate small fragments, and an immunoprecipitation is conducted with an antibody against the desired factor or histone modification. Crosslinks are reversed, and polymerase chain reaction (PCR) is used to assess whether DNA sequences are recovered immune-specifically. Chromatin-domain scanning coupled with quantitative analysis is a powerful means of dissecting mechanisms by which signaling pathways target genes within a complex genome.


Asunto(s)
Cromatina/química , Proteínas de Unión al ADN/análisis , Pruebas de Precipitina/métodos , Transducción de Señal , Factores de Transcripción/análisis , Acetilación , Animales , Núcleo Celular/genética , Cromatina/metabolismo , ADN/análisis , ADN/química , ADN/metabolismo , Proteínas de Unión al ADN/inmunología , Proteínas de Unión al ADN/metabolismo , Histonas/química , Histonas/inmunología , Histonas/metabolismo , Metilación , Reacción en Cadena de la Polimerasa , Procesamiento Proteico-Postraduccional , Reproducibilidad de los Resultados , Factores de Transcripción/inmunología , Factores de Transcripción/metabolismo
13.
J Clin Anesth ; 14(8): 571-7, 2002 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-12565114

RESUMEN

STUDY OBJECTIVE: To compare the effects of ropivacaine-fentanyl patient-controlled epidural analgesia (PCEA) with morphine intravenous (IV) patient-controlled analgesia (PCA). DESIGN: Prospective, randomized, multicenter trial. SETTING: Five university-affiliated hospitals. PATIENTS: 41 patients undergoing colon surgery. INTERVENTION: Patients were randomized to receive either standardized combined epidural/general anesthesia followed by PCEA with ropivacaine 0.2% and fentanyl (2 microg/mL) or standardized general anesthesia followed by morphine IV PCA. All patients participated in a standardized postoperative clinical pathway. MEASUREMENTS AND MAIN RESULTS: Analgesia was assessed with visual analog scale (VAS) scores. Postoperative recovery was assessed by completion of prospectively defined discharge milestones and time until discharge. Statistical analyses included nonparametric and contingency table analyses. The PCEA group had better analgesia (> 50% reduction in pain scores, assessed both at rest and during a cough) for the first 3 days after surgery (p < 0.0,005). The PCEA group achieved discharge milestones approximately 36 hours faster (p < 0.002), but time until discharge was similar between groups. CONCLUSIONS: Ropivacaine-fentanyl PCEA provides superior analgesia, reduced opioid requirement, and more rapid recovery after colon surgery.


Asunto(s)
Amidas , Analgesia Epidural , Analgesia Controlada por el Paciente , Analgésicos Opioides , Anestésicos Locales , Colon/cirugía , Procedimientos Quirúrgicos del Sistema Digestivo , Morfina , Analgésicos Opioides/administración & dosificación , Antiinflamatorios no Esteroideos/uso terapéutico , Tos/complicaciones , Método Doble Ciego , Femenino , Humanos , Inyecciones Intravenosas , Masculino , Persona de Mediana Edad , Morfina/administración & dosificación , Dimensión del Dolor , Alta del Paciente , Medicación Preanestésica , Estudios Prospectivos , Ropivacaína
14.
Front Microbiol ; 5: 402, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25177315

RESUMEN

Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts.

15.
Mol Cell Biol ; 31(16): 3312-25, 2011 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-21670157

RESUMEN

The flap domain of multisubunit RNA polymerases (RNAPs), also called the wall, forms one side of the RNA exit channel. In bacterial RNAP, the mobile part of the flap is called the flap tip and makes essential contacts with initiation and elongation factors. Cocrystal structures suggest that the orthologous part of eukaryotic RNAPII, called the flap loop, contacts transcription factor IIB (TFIIB), but the function of the flap loop has not been assessed. We constructed and tested a deletion of the flap loop in human RNAPII (subunit RPB2 Δ873-884) that removes the flap loop interaction interface with TFIIB. Genome-wide analysis of the distribution of the RNAPII with the flap loop deletion expressed in a human embryonic kidney cell line (HEK 293) revealed no effect of the flap loop on global transcription initiation, RNAPII occupancy within genes, or the efficiency of promoter escape and productive elongation. In vitro, the flap loop deletion had no effect on promoter binding, abortive initiation or promoter escape, TFIIS-stimulated transcript cleavage, or inhibition of transcript elongation by the complex of negative elongation factor (NELF) and 5,6-dichloro-1-ß-d-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor (DSIF). A modest effect on transcript elongation and pausing was suppressed by TFIIF. Although similar to the flap tip of bacterial RNAP, the RNAPII flap loop is not equivalently essential.


Asunto(s)
ARN Polimerasa II/química , ARN Polimerasa II/genética , Transcripción Genética , Sitios de Unión/genética , Línea Celular , Humanos , Proteínas Nucleares , Regiones Promotoras Genéticas , Ingeniería de Proteínas , Estructura Terciaria de Proteína , Eliminación de Secuencia , Factor de Transcripción TFIIB , Factores de Transcripción , Factores de Transcripción TFII , Factores de Elongación Transcripcional
16.
Biochemistry ; 47(3): 859-69, 2008 Jan 22.
Artículo en Inglés | MEDLINE | ID: mdl-18154321

RESUMEN

Whereas the transcription factors GATA-1 and GATA-2 function both uniquely and redundantly to control blood cell development, the process termed hematopoiesis, mechanisms underlying their unique versus common functions are poorly understood. We used two independent assays to demonstrate that GATA-1 is considerably more stable than GATA-2 in multiple cellular contexts, even though both factors are subject to degradation via the ubiquitin-proteasome system. Studies with GATA factor mutants and novel chimeric GATA factors provided evidence that both GATA-1 and GATA-2 have highly unstable zinc finger core modules. The GATA-1 and GATA-2 N-termini both confer stabilization to their respective zinc finger core modules. In contrast, the GATA-1 and GATA-2 C-termini confer stabilization and destabilization, respectively. As GATA-2 stabilization via proteasome inhibition impairs the capacity of GATA-1 to displace GATA-2 from endogenous chromatin sites, we propose that differential GATA factor stability is an important determinant of chromatin target site occupancy and therefore the establishment of genetic networks that control hematopoiesis.


Asunto(s)
Cromatina/metabolismo , Factor de Transcripción GATA1/metabolismo , Factor de Transcripción GATA2/metabolismo , Animales , Línea Celular Tumoral , Núcleo Celular/metabolismo , Inmunoprecipitación de Cromatina , Cicloheximida/farmacología , Inhibidores de Cisteína Proteinasa/farmacología , Factor de Transcripción GATA1/genética , Factor de Transcripción GATA2/genética , Expresión Génica/efectos de los fármacos , Humanos , Células K562 , Leupeptinas/farmacología , Ratones , Mutación/fisiología , Proteínas Nucleares/genética , Complejo de la Endopetidasa Proteasomal/metabolismo , Inhibidores de Proteasoma , Biosíntesis de Proteínas/efectos de los fármacos , Procesamiento Proteico-Postraduccional/fisiología , Proteínas Recombinantes de Fusión/metabolismo , Tamoxifeno/farmacología , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Transfección
17.
J Biol Chem ; 282(19): 14665-74, 2007 May 11.
Artículo en Inglés | MEDLINE | ID: mdl-17347142

RESUMEN

GATA factors are fundamental components of developmentally important transcriptional networks. By contrast to common mechanisms in which transacting factors function directly at promoters, the hematopoietic GATA factors GATA-1 and GATA-2 often assemble dispersed complexes over broad chromosomal regions. For example, GATA-1 and GATA-2 occupy five conserved regions over approximately 100 kb of the Gata2 locus in the transcriptionally repressed and active states, respectively, in erythroid cells. Since it is unknown whether the individual complexes exert qualitatively distinct or identical functions to regulate Gata2 transcription in vivo, we compared the activity of the -3.9 and +9.5 kb sites of the Gata2 locus in transgenic mice. The +9.5 site functioned as an autonomous enhancer in the endothelium and fetal liver of embryonic day 11 embryos, whereas the -3.9 site lacked such activity. Mechanistic studies demonstrated critical requirements for a GATA motif and a neighboring E-box within the +9.5 site for enhancer activity in endothelial and hematopoietic cells. Surprisingly, whereas this GATA-E-box composite motif was sufficient for enhancer activity in an erythroid precursor cell line, its enhancer function in primary human endothelial cells required additional regulatory modules. These results identify the first molecular determinant of Gata2 transcription in vascular endothelium, composed of a core enhancer module active in both endothelial and hematopoietic cells and regulatory modules preferentially required in endothelial cells.


Asunto(s)
Endotelio Vascular/metabolismo , Factor de Transcripción GATA1/genética , Factor de Transcripción GATA2/genética , Regulación de la Expresión Génica , Sistema Hematopoyético/metabolismo , Transcripción Genética , Animales , Aorta/citología , Aorta/metabolismo , Secuencia de Bases , Células Cultivadas , Endotelio Vascular/citología , Elementos de Facilitación Genéticos , Factor de Transcripción GATA1/metabolismo , Factor de Transcripción GATA2/metabolismo , Sistema Hematopoyético/citología , Humanos , Ratones , Ratones Transgénicos , Datos de Secuencia Molecular , Secuencias Reguladoras de Ácidos Nucleicos , Homología de Secuencia de Ácido Nucleico , Activación Transcripcional , Venas Umbilicales/citología , Venas Umbilicales/metabolismo
18.
J Biol Chem ; 281(49): 37345-52, 2006 Dec 08.
Artículo en Inglés | MEDLINE | ID: mdl-16963445

RESUMEN

The hematopoietic GATA factors GATA-1 and GATA-2, which have distinct and overlapping roles to regulate blood cell development, are reciprocally expressed during erythropoiesis. GATA-1 directly represses Gata2 transcription, and reduced GATA-2 synthesis promotes red blood cell development. Gata2 repression involves "GATA switches" in which GATA-1 displaces GATA-2 from Gata2 regulatory regions. We show that extragenic GATA switch sites occupied by GATA-2 associate with as much RNA polymerase II (Pol II) and basal transcription factors as present at the active Gata2 promoters. Pol II bound to GATA switch sites in the active locus was phosphorylated on serine 5 of the carboxyl-terminal domain, indicative of elongation competence. GATA-1-mediated displacement of GATA-2 from GATA switch sites reduced Pol II recruitment to all sites except the far upstream -77-kb region. Surprisingly, TFIIB occupancy persisted at most sites upon repression. These results indicate that GATA-2-bound extragenic regulatory elements recruit Pol II, GATA-1 binding expels Pol II, and despite the persistent TFIIB-chromatin complexes, Pol II recruitment is blocked.


Asunto(s)
Factor de Transcripción GATA1/metabolismo , Factor de Transcripción TFIIB/metabolismo , Animales , Secuencia de Bases , Sitios de Unión , Cromatina/genética , Cromatina/metabolismo , ADN Polimerasa II/metabolismo , Cartilla de ADN/genética , Eritropoyesis/genética , Eritropoyesis/fisiología , Factor de Transcripción GATA1/genética , Factor de Transcripción GATA2/genética , Factor de Transcripción GATA2/metabolismo , Hematopoyesis , Humanos , Técnicas In Vitro , Ratones , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Factor de Transcripción TFIIB/genética , Transcripción Genética
19.
Anesth Analg ; 101(5 Suppl): S44-S61, 2005 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-16334492

RESUMEN

One of the most common methods for providing postoperative analgesia is via patient-controlled analgesia (PCA). Although the typical approach is to administer opioids via a programmable infusion pump, other drugs and other modes of administration are available. This article reviews the history and practice of many aspects of PCA and provides extensive guidelines for the practice of PCA-administered opioids. In addition, potential adverse effects and recommendations for their monitoring and treatment are reviewed.


Asunto(s)
Analgesia Controlada por el Paciente , Analgesia Controlada por el Paciente/instrumentación , Analgesia Controlada por el Paciente/métodos , Analgésicos Opioides/administración & dosificación , Analgésicos Opioides/efectos adversos , Humanos , Bombas de Infusión , Infusiones Intravenosas/instrumentación , Selección de Paciente
20.
J Biol Chem ; 280(3): 1724-32, 2005 Jan 21.
Artículo en Inglés | MEDLINE | ID: mdl-15494394

RESUMEN

Given the simplicity of the DNA sequence that mediates binding of GATA transcription factors, GATA motifs reside throughout chromosomal DNA. However, chromatin immunoprecipitation analysis has revealed that GATA-1 discriminates exquisitely among these sites. GATA-2 selectively occupies the -2.8-kilobase (kb) region of the GATA-2 locus in the active state despite there being numerous GATA motifs throughout the locus. The GATA-1-mediated displacement of GATA-2 is tightly coupled to repression of GATA-2 transcription. We have used high resolution chromatin immunoprecipitation to show that GATA-1 and GATA-2 occupy two additional regions, -3.9 and -1.8 kb of the GATA-2 locus. GATA-1 and GATA-2 had distinct preferences for occupancy at these regions, with GATA-1 and GATA-2 occupancy highest at the -3.9- and -1.8-kb regions, respectively. Activation of an estrogen receptor fusion to GATA-1 (ER-GATA-1) induced similar kinetics of ER-GATA-1 occupancy and GATA-2 displacement at the sites. In the transcriptionally active state, DNase I hypersensitive sites (HSs) were detected at the -3.9- and -1.8-kb regions, with a weak HS at the -2.8-kb region. Whereas ER-GATA-1-instigated repression abolished the -1.8-kb HS, the -3.9-kb HS persisted in the repressed state. Transient transfection analysis provided evidence that the -3.9-kb region functions distinctly from the -2.8- and -1.8-kb regions. We propose that GATA-2 transcription is regulated via the collective actions of complexes assembled at the -2.8- and -1.8-kb regions, which share similar properties, and through a qualitatively distinct activity of the -3.9-kb complex.


Asunto(s)
Proteínas de Unión al ADN/genética , Secuencias Reguladoras de Ácidos Nucleicos , Factores de Transcripción/genética , Animales , Secuencia de Bases , Mapeo Cromosómico , Cartilla de ADN , Proteínas de Unión al ADN/metabolismo , Factores de Unión al ADN Específico de las Células Eritroides , Factor de Transcripción GATA1 , Factor de Transcripción GATA2 , Regulación de la Expresión Génica , Ratones , Células 3T3 NIH , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Factores de Transcripción/metabolismo , Transcripción Genética
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