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BACKGROUND AND AIMS: We investigated the ideal acetic acid (AA) concentration for AA-enhanced, narrow-band imaging (NBI) magnifying endoscopy (ANBI-ME) in the diagnosis of superficial colorectal neoplasms and evaluated its clinical efficacy. METHODS: During the exploratory phase, we investigated four concentrations (1.5%, 2.25%, 3.0%, and 4.5%) in rotation by performing ANBI-ME on 50 superficial colorectal neoplasms at each concentration. A favorable AA concentration was determined by evaluating the diagnostic accuracy, AA whitening duration (AD), peristalsis, and bleeding following endoscopic resection. In the validation phase, we assessed inter-observer agreements for ANBI-ME with the determined AA concentration and inter-methodological agreements between that and subsequently conducted crystal violet-stained magnifying endoscopy (CV-ME) with the exploratory set and 98 additional patients. RESULTS: The diagnostic accuracies were 89.3% (42/47) for 1.5% AA, 92.0% (46/50) for 2.25%, 96.8% (61/63) for 3.0%, and 97.8% (46/47) for 4.5% with no significant difference (p = 0.26). A significant positive correlation was observed between the AA concentrations and ADs (p < 0.001). No significant differences in hyperperistalsis or post-resection bleeding were observed. The optimal AA concentration was determined to be 4.5%. In the validation analysis, the accuracy rates were 72.4% (105/145) using AMBI-ME and 68.3% (99/145) using CV-ME (p = 0.43). Strong agreements were noted between two observers (κ, 0.87 for ANBI-ME; 0.83 for CV-ME) and between the methods (κ, 0.87 and 0.81 for each observer). CONCLUSION: For diagnosing colorectal lesions, an AA concentration of 4.5% in ANBI-ME was safe and effective. Its diagnostic performance was comparable to CV-ME, and future large-sample studies may confirm its potential as a reliable alternative endoscopic diagnostic method.
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Although esophageal cancers invading the muscularis mucosa (pT1a-MM) or submucosa (pT1b-SM) after endoscopic resection (ER) are associated with a risk of lymph node metastasis, details of metastatic recurrence after additional treatment remain unknown. We aimed to identify the risk factors for metastatic recurrence and recurrence patterns in patients receiving additional treatment after ER for esophageal cancer. Between 2006 and 2017, patients with pT1a-MM/pT1b-SM esophageal cancer who underwent ER with additional treatment (esophagectomy, chemoradiotherapy [CRT], and radiation therapy) at 21 institutions in Japan were enrolled. We evaluated the risk factors for metastatic recurrence after ER with additional treatment. Subsequently, the rate and pattern (locoregional or distant) of metastatic recurrence were investigated for each additional treatment. Of the 220 patients who received additional treatment, 57, 125, and 38 underwent esophagectomy, CRT, and radiation therapy, respectively. In the multivariate analysis, lymphatic invasion was the sole risk factor for metastatic recurrence after additional treatment (hazard ratio, 3.50; P = 0.029). Although the risk of metastatic recurrence with additional esophagectomy was similar to that with CRT (hazard ratio, 1.01; P = 0.986), the rate of locoregional recurrence tended to be higher with additional esophagectomy (80.0% (4/5) vs. 36.4% (4/11)), leading to a better prognosis in patients with metastatic recurrence after additional esophagectomy than CRT (survival rate, 80.0% (4/5) vs. 9.1% (1/11)). Patients with lymphatic invasion have a high risk of metastatic recurrence after ER with additional treatment for pT1a-MM/pT1b-SM esophageal cancer. Additional esophagectomy may result in a better prognosis after metastatic recurrence.
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OBJECTIVES: Clinical outcomes of endoscopic submucosal dissection (ESD) for esophageal squamous cell carcinoma (ESCC) with esophageal varices (EVs) are obscure. We aimed to elucidate the clinical outcomes of ESD for ESCC with EVs in a multicenter, retrospective study. METHODS: We established a retrospective cohort of 30 patients with ESCC complicating EVs, who underwent ESD at 11 Japanese institutions. Rates of en bloc resection and R0 resection, procedure time, and adverse events were evaluated as indicators of the feasibility and safety of ESD. Additional treatment, recurrence, and metastasis of the lesions were evaluated as indicators of the long-term efficacy of ESD. RESULTS: Portal hypertension was caused by cirrhosis, of which alcohol was the most common cause. En bloc resection was achieved in 93.3% and R0 resection in 80.0% of the patients. The median procedure time was 92 min. Adverse events included a case of uncontrolled intraoperative bleeding leading to discontinuation of ESD and a case of esophageal stricture due to extensive resection. During the follow-up period of a median for 42 months, a patient with local recurrence and another patient with liver metastasis were observed. One patient died of liver failure after receiving chemoradiotherapy as an additional treatment after ESD. No patient died of ESCC. CONCLUSION: This multicenter, retrospective cohort study demonstrated the safety and efficacy of ESD for ESCC with EVs. Further studies are needed to establish appropriate treatment methods for EVs before ESD and additional treatments for patients with insufficient ESD.
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Carcinoma de Células Escamosas , Resección Endoscópica de la Mucosa , Neoplasias Esofágicas , Carcinoma de Células Escamosas de Esófago , Várices Esofágicas y Gástricas , Humanos , Carcinoma de Células Escamosas/complicaciones , Carcinoma de Células Escamosas/cirugía , Resección Endoscópica de la Mucosa/efectos adversos , Resección Endoscópica de la Mucosa/métodos , Várices Esofágicas y Gástricas/complicaciones , Várices Esofágicas y Gástricas/cirugía , Neoplasias Esofágicas/complicaciones , Neoplasias Esofágicas/cirugía , Carcinoma de Células Escamosas de Esófago/complicaciones , Carcinoma de Células Escamosas de Esófago/cirugía , Esofagoscopía/métodos , Estudios Retrospectivos , Resultado del TratamientoRESUMEN
Escherichia coli is a useful platform for producing valuable materials through the implementation of synthetic gene(s) derived from other organisms. The production of lactate (LA)-based polyester poly[LA-co-3-hydroxybutyrate (3HB)] was carried out in E. coli using a set of five other species-derived genes: Pseudomonas sp. 61-3-derived phaC1STQK (for polymerization), Cupriavidus necator-derived phaAB (for 3HB-CoA generation), and Megasphaera elsdenii-derived pct (for LA-CoA generation) cloned into pTV118NpctphaC1ps(ST/QK)AB. Here, we aimed to optimize the expression level and timing of these genes to improve the production of P(LA-co-3HB) and to manipulate the LA fraction by replacing the promoters with various promoters in E. coli. Evaluation of the effects of 21 promoter replacement plasmids revealed that the phaC1STQK-AB operon is critical for the stationary phase for P(LA-co-3HB) production. Interestingly, the effects of the promoters depended on the composition of the medium. In glucose-supplemented LB medium, the dps promoter replacement plasmid resulted in the greatest effect, increasing the accumulation to 8.8 g/L and an LA fraction of 14.1 mol% of P(LA-co-3HB), compared to 2.7 g/L and 8.1 mol% with the original plasmid. In xylose-supplemented LB medium, the yliH promoter replacement plasmid resulted in the greatest effect, with production of 5.6 g/L and an LA fraction of 40.2 mol% compared to 3.6 g/L and 22.6 mol% with the original plasmid. These results suggest that the selection of an appropriate promoter for expression of the phaC1STQK-AB operon could improve the production and LA fraction of P(LA-co-3HB). Here, we propose that the selection of cell-growth phase-dependent promoters is a versatile biotechnological strategy for effective intracellular production of polymeric materials such as P(LA-co-3HB), in combination with the selection of sugar-based carbon sources.
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Escherichia coli , Ácido Láctico , Escherichia coli/genética , Escherichia coli/metabolismo , Poliésteres/metabolismo , Hidroxibutiratos/metabolismoRESUMEN
BACKGROUND: Although additional treatment is considered for patients with esophageal squamous cell carcinoma (ESCC) invading into the muscularis mucosa (pT1a-MM) or submucosa (pT1b-SM) after endoscopic submucosal dissection (ESD), the actual benefits of this method remain to be elucidated. AIMS: We aimed to evaluate the prognostic benefits of additional treatment in such patients. METHODS: Between 2006 and 2017, we enrolled patients with pT1a-MM/pT1b-SM ESCC after ESD at 21 institutions in Japan. Overall survival (OS) and disease-specific survival (DSS) were compared between the additional treatment and follow-up groups after propensity score matching, to reduce the bias of baseline characteristics. A subgroup analysis was performed according to the pathological findings: category A, pT1a-MM but negative for lymphovascular invasion (LVI) and vertical margin (VM); category B, tumor invasion into the submucosa ≤ 200 µm but negative for LVI and VM; category C, others. RESULTS: Of 593 patients with pT1a-MM/pT1b-SM ESCC after ESD, 101 matched pairs were extracted after propensity score matching. The OSs were similar between the additional treatment and follow-up groups (80.6% vs. 78.6% in 5 years; P = 0.972). In a subgroup analysis, the OS in the additional treatment group was significantly lower than that in the follow-up group (65.7% vs. 95.2% in 5 years; P = 0.037) in category A, whereas OS did not significantly differ in category C (76.8% vs. 69.5% in 5 years; P = 0.360). CONCLUSIONS: Additional treatment after ESD in patients with pT1a-MM/pT1b-SM ESCC was not associated with an improved prognosis.
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Resección Endoscópica de la Mucosa , Neoplasias Esofágicas , Carcinoma de Células Escamosas de Esófago , Humanos , Carcinoma de Células Escamosas de Esófago/cirugía , Carcinoma de Células Escamosas de Esófago/patología , Pronóstico , Neoplasias Esofágicas/patología , Resección Endoscópica de la Mucosa/métodos , Estudios Retrospectivos , Resultado del TratamientoRESUMEN
So far, the genome sequences of more than tens of thousands of organisms have been determined, and the overall picture of the genes that make up one organism has been clarified [https://www [...].
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Bacterias , Genoma Bacteriano , Bacterias/genéticaRESUMEN
Bacteria exposed to stress survive by regulating the expression of several genes at the transcriptional and translational levels. For instance, in Escherichia coli, when growth is arrested in response to stress, such as nutrient starvation, the anti-sigma factor Rsd is expressed to inactivate the global regulator RpoD and activate the sigma factor RpoS. However, ribosome modulation factor (RMF) expressed in response to growth arrest binds to 70S ribosomes to form inactive 100S ribosomes and inhibit translational activity. Moreover, stress due to fluctuations in the concentration of metal ions essential for various intracellular pathways is regulated by a homeostatic mechanism involving metal-responsive transcription factors (TFs). Therefore, in this study, we examined the binding of a few metal-responsive TFs to the promoter regions of rsd and rmf through promoter-specific TF screening and studied the effects of these TFs on the expression of rsd and rmf in each TF gene-deficient E. coli strain through quantitative PCR, Western blot imaging, and 100S ribosome formation analysis. Our results suggest that several metal-responsive TFs (CueR, Fur, KdpE, MntR, NhaR, PhoP, ZntR, and ZraR) and metal ions (Cu2+, Fe2+, K+, Mn2+, Na+, Mg2+, and Zn2+) influence rsd and rmf gene expression while regulating transcriptional and translational activities.
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Proteínas de Escherichia coli , Escherichia coli , Escherichia coli/metabolismo , Proteínas Ribosómicas/metabolismo , Proteínas de Escherichia coli/metabolismo , Dimerización , Factores de Transcripción/metabolismo , Factor sigma/metabolismo , Ribosomas/metabolismo , Proteínas Bacterianas/metabolismoRESUMEN
Flagella are vital bacterial organs that allow microorganisms to move to favorable environments. However, their construction and operation consume a large amount of energy. The master regulator FlhDC mediates all flagellum-forming genes in E. coli through a transcriptional regulatory cascade, the details of which remain elusive. In this study, we attempted to uncover a direct set of target genes in vitro using gSELEX-chip screening to re-examine the role of FlhDC in the entire E. coli genome regulatory network. We identified novel target genes involved in the sugar utilization phosphotransferase system, sugar catabolic pathway of glycolysis, and other carbon source metabolic pathways in addition to the known flagella formation target genes. Examining FlhDC transcriptional regulation in vitro and in vivo and its effects on sugar consumption and cell growth suggested that FlhDC activates these new targets. Based on these results, we proposed that the flagella master transcriptional regulator FlhDC acts in the activation of a set of flagella-forming genes, sugar utilization, and carbon source catabolic pathways to provide coordinated regulation between flagella formation, operation and energy production.
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Proteínas de Escherichia coli , Escherichia coli , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas Bacterianas/metabolismo , Transactivadores/metabolismo , Genómica , Flagelos/metabolismo , Azúcares/metabolismo , Regulación Bacteriana de la Expresión GénicaRESUMEN
Genomic SELEX screening was performed to identify the binding sites of YiaU, an uncharacterized LysR family transcription factor, on the Escherichia coli K-12 genome. Five high-affinity binding targets of YiaU were identified, all of which were involved in the structures of the bacterial cell surface such as outer and inner membrane proteins, and lipopolysaccharides. Detailed in vitro and in vivo analyses suggest that YiaU activates these target genes. To gain insight into the effects of YiaU in vivo on physiological properties, we used phenotype microarrays, biofilm screening assays and the sensitivity against serum complement analysed using a yiaU deletion mutant or YiaU expression strain. Together, these results suggest that the YiaU regulon confers resistance to some antibiotics, and increases biofilm formation and complement sensitivity. We propose renaming YiaU as CsuR (regulator of cell surface).
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Escherichia coli K12 , Proteínas de Escherichia coli , Biopelículas , Escherichia coli/genética , Escherichia coli K12/genética , Escherichia coli K12/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Propiedades de SuperficieRESUMEN
The biogenesis of the photosynthetic apparatus in developing seedlings requires the assembly of proteins encoded on both nuclear and chloroplast genomes. To coordinate this process there needs to be communication between these organelles, but the retrograde signals by which the chloroplast communicates with the nucleus at this time are still essentially unknown. The Arabidopsis thaliana genomes uncoupled (gun) mutants, that show elevated nuclear gene expression after chloroplast damage, have formed the basis of our understanding of retrograde signaling. Of the 6 reported gun mutations, 5 are in tetrapyrrole biosynthesis proteins and this has led to the development of a model for chloroplast-to-nucleus retrograde signaling in which ferrochelatase 1 (FC1)-dependent heme synthesis generates a positive signal promoting expression of photosynthesis-related genes. However, the molecular consequences of the strongest of the gun mutants, gun1, are poorly understood, preventing the development of a unifying hypothesis for chloroplast-to-nucleus signaling. Here, we show that GUN1 directly binds to heme and other porphyrins, reduces flux through the tetrapyrrole biosynthesis pathway to limit heme and protochlorophyllide synthesis, and can increase the chelatase activity of FC1. These results raise the possibility that the signaling role of GUN1 may be manifested through changes in tetrapyrrole metabolism, supporting a role for tetrapyrroles as mediators of a single biogenic chloroplast-to-nucleus retrograde signaling pathway.
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Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Proteínas de Unión al ADN/metabolismo , Fotosíntesis/fisiología , Tetrapirroles/biosíntesis , Proteínas de Arabidopsis/genética , Vías Biosintéticas/genética , Vías Biosintéticas/fisiología , Núcleo Celular/metabolismo , Cloroplastos/metabolismo , Proteínas de Unión al ADN/genética , Ferroquelatasa , Regulación de la Expresión Génica de las Plantas , Hemo/metabolismo , Complejos de Proteína Captadores de Luz/metabolismo , Mutación , Transducción de Señal/fisiologíaRESUMEN
OBJECTIVES: We aimed to clarify the prognostic factors for patients with esophageal squamous cell carcinoma (ESCC) invading into the muscularis mucosa (pT1a-MM) or submucosa (pT1b-SM) after endoscopic submucosal dissection (ESD). METHODS: This retrospective study enrolled such patients at 21 institutions in Japan between 2006 and 2017. We evaluated 15 factors, including pathological risk categories for ESCC-specific mortality, six non-cancer-related indices, and treatment strategies. RESULTS: In the analysis of 593 patients, the 5-year overall and disease-specific survival rates were 83.0% and 97.6%, respectively. In a multivariate Cox analysis, male sex (hazard ratio [HR] 3.56), Charlson comorbidity index (CCI) ≥3 (HR 2.53), ages of 75-79 (HR 1.61) and ≥80 years (HR 2.04), prognostic nutrition index (PNI) <45 (HR 1.69), and pathological intermediate-risk (HR 1.63) and high-risk (HR 1.89) were prognostic factors. Subsequently, we developed a clinical risk classification for non-ESCC-related mortality based on the number of prognostic factors (age ≥75 years, male sex, CCI ≥3, PNI <45): low-risk, 0; intermediate-risk, 1-2; and high-risk, 3-4. The 5-year non-ESCC-related mortality rates for patients without additional treatment were 0.0%, 10.2%, and 45.8% in the low-, intermediate-, and high-risk groups, respectively. Meanwhile, the 5-year ESCC-specific mortality rates for the pathological low-, intermediate-, and high-risk groups were 0.3%, 5.3%, and 18.2%, respectively. CONCLUSIONS: We clarified prognostic factors for patients with pT1a-MM/pT1b-SM ESCC after ESD. The combined assessment of non-ESCC- and ESCC-related mortalities by the two risk classifications might help clinicians in deciding treatment strategies for such patients.
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Resección Endoscópica de la Mucosa , Neoplasias Esofágicas , Carcinoma de Células Escamosas de Esófago , Humanos , Masculino , Anciano de 80 o más Años , Anciano , Carcinoma de Células Escamosas de Esófago/patología , Neoplasias Esofágicas/patología , Estudios Retrospectivos , Pronóstico , Membrana Mucosa/cirugía , Membrana Mucosa/patología , Resultado del TratamientoRESUMEN
Understanding the functional information of all genes and the biological mechanism based on the comprehensive genome regulation mechanism is an important task in life science. YgfI is an uncharacterized LysR family transcription factor in Escherichia coli. To identify the function of YgfI, the genomic SELEX (gSELEX) screening was performed for YgfI regulation targets on the E. coli genome. In addition, regulatory and phenotypic analyses were performed. A total of 10 loci on the E. coli genome were identified as the regulatory targets of YgfI with the YgfI binding activity. These predicted YgfI target genes were involved in biofilm formation, hydrogen peroxide resistance, and antibiotic resistance, many of which were expressed in the stationary phase. The TCAGATTTTGC sequence was identified as an YgfI box in in vitro gel shift assay and DNase-I footprinting assays. RT-qPCR analysis in vivo revealed that the expression of YgfI increased in the stationary phase. Physiological analyses suggested the participation of YgfI in biofilm formation and an increase in the tolerability against hydrogen peroxide. In summary, we propose to rename ygfI as srsR (a stress-response regulator in stationary phase).
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Escherichia coli K12 , Proteínas de Escherichia coli , Proteínas Bacterianas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Escherichia coli K12/genética , Escherichia coli K12/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Peróxido de Hidrógeno/metabolismo , Peróxido de Hidrógeno/farmacología , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
BACKGROUND/AIMS: For early gastric cancer (EGC) treated using endoscopic submucosal dissection (ESD) with poor curability defined by the Japanese Guidelines (non-curative EGC, N-EGC), additional gastrectomy has been recommended. However, N-EGC patients without additional gastrectomy often die of other diseases within a relatively short interval after ESD. It has been unclear whether additional gastrectomy is beneficial or not for such patients. The aim of this study was to clarify predictors for short-term survival of N-EGC patients without additional gastrectomy after ESD. METHODS: One hundred six N-EGC patients without additional gastrectomy were included in this study. Factors related to short-term survival, defined as death within 3 years after ESD, were evaluated using uni- and multivariate analyses by comparing patients with and without short-term survival (Groups S and C, respectively). RESULTS: During the mean follow-up period of 89 months, 39 patients died (14 patients died within 3 years, being Group S). The cause of death was gastric cancer for only 1 patient in the Group C. The 3- and 5-year overall survival rates were 86.8 and 81.8%, respectively, and the 3- and 5-years disease-specific survival rates were 100 and 98.9%, respectively. Univariate analyses showed that short-term survival was statistically associated with elevated morphology, high-risk status for lymph node metastases as defined by the eCura system, severe comorbidity (Charlson Comorbidity Index [CCI] ≥3), low level of activity in daily living (being unable to go out by oneself), habitation (a nursing home), and several poor nutritional prognostic indices (neutrophil to lymphocyte ratio ≥2.5, geriatric nutritional risk index <92, C-reactive protein ≥1.0). In the multivariate analysis, a high CCI (≥3) was the independent predictor for short-term survival after ESD (odds ratio, 8.1; 95% confidence interval, 1.53-43.0; p = 0.014). CONCLUSIONS: Severe comorbidity indicated by a high CCI score (≥3) was the independent predictor for short-term survival for EGC patients without additional gastrectomy after non-curative ESD. Since the cause of death for most patients was not gastric cancer, observational follow-ups without additional gastrectomy might be a reasonable option for patients with a poor general status indicated by a CCI ≥3.
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Resección Endoscópica de la Mucosa , Neoplasias Gástricas , Anciano , Resección Endoscópica de la Mucosa/efectos adversos , Gastrectomía/efectos adversos , Mucosa Gástrica/cirugía , Humanos , Pronóstico , Estudios Retrospectivos , Neoplasias Gástricas/cirugía , Tasa de Supervivencia , Resultado del TratamientoRESUMEN
Under stressful conditions, Escherichia coli forms biofilm for survival by sensing a variety of environmental conditions. CsgD, the master regulator of biofilm formation, controls cell aggregation by directly regulating the synthesis of Curli fimbriae. In agreement of its regulatory role, as many as 14 transcription factors (TFs) have so far been identified to participate in regulation of the csgD promoter, each monitoring a specific environmental condition or factor. In order to identify the whole set of TFs involved in this typical multi-factor promoter, we performed in this study 'promoter-specific transcription-factor' (PS-TF) screening in vitro using a set of 198 purified TFs (145 TFs with known functions and 53 hitherto uncharacterized TFs). A total of 48 TFs with strong binding to the csgD promoter probe were identified, including 35 known TFs and 13 uncharacterized TFs, referred to as Y-TFs. As an attempt to search for novel regulators, in this study we first analysed a total of seven Y-TFs, including YbiH, YdcI, YhjC, YiaJ, YiaU, YjgJ and YjiR. After analysis of curli fimbriae formation, LacZ-reporter assay, Northern-blot analysis and biofilm formation assay, we identified at least two novel regulators, repressor YiaJ (renamed PlaR) and activator YhjC (renamed RcdB), of the csgD promoter.
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Biopelículas/crecimiento & desarrollo , Escherichia coli K12/crecimiento & desarrollo , Escherichia coli K12/genética , Proteínas de Escherichia coli/genética , Regiones Promotoras Genéticas , Transactivadores/genética , Factores de Transcripción/metabolismo , Sitios de Unión , Escherichia coli K12/metabolismo , Proteínas de Escherichia coli/metabolismo , Fimbrias Bacterianas/fisiología , Regulación Bacteriana de la Expresión Génica , Genes Bacterianos , Transactivadores/metabolismo , Factores de Transcripción/genéticaRESUMEN
The identification of regulatory targets of all TFs is critical for understanding the entire network of the genome regulation. The lac regulon of Escherichia coli K-12 W3110 is composed of the lacZYA operon and its repressor lacI gene, and has long been recognized as the seminal model of transcription regulation in bacteria with only one highly preferred target. After the Genomic SELEX screening in vitro of more than 200 transcription factors (TFs) from E. coli K-12, however, we found that most TFs regulate multiple target genes. With respect to the number of regulatory targets, a total of these 200 E. coli TFs form a hierarchy ranging from a single target to as many as 1000 targets. Here we focus a total of 13 single-target TFs, 9 known TFs (BetI, KdpE, LacI, MarR, NanR, RpiR, TorR, UlaR and UxuR) and 4 uncharacterized TFs (YagI, YbaO, YbiH and YeaM), altogether forming only a minor group of TFs in E. coli. These single-target TFs were classified into three groups based on their functional regulation.
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Escherichia coli K12/genética , Escherichia coli K12/metabolismo , Proteínas de Escherichia coli/clasificación , Proteínas de Escherichia coli/metabolismo , Factores de Transcripción/clasificación , Factores de Transcripción/metabolismo , Proteínas de Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Redes Reguladoras de Genes , Genoma Bacteriano , Operón Lac , Represoras Lac/clasificación , Represoras Lac/genética , Represoras Lac/metabolismo , Modelos Biológicos , Regulón , Técnica SELEX de Producción de Aptámeros , Factores de Transcripción/genéticaRESUMEN
A 15-mm whitish, depressed lesion was observed in the stomach of a 39-year-old using screening esophagogastroduodenoscopy. The lesion had grown to a size of 40mm and had a cobblestone-like appearance at an 11-year endoscopic follow-up. Using endoscopic submucosal dissection (ESD) as a diagnostic therapy, gastric mucosa-associated lymphoid tissue (MALT) lymphoma with MALT translocation gene 1 without Helicobacter pylori infection was detected. Although the patient did not undergo additional treatments, he remained alive without for recurrence 5 years after ESD.
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Resección Endoscópica de la Mucosa , Infecciones por Helicobacter , Helicobacter pylori , Linfoma de Células B de la Zona Marginal , Neoplasias Gástricas , Adulto , Mucosa Gástrica , Humanos , Tejido Linfoide , Masculino , Recurrencia Local de NeoplasiaRESUMEN
The binding sites of YihW, an uncharacterized DeoR-family transcription factor (TF) of Escherichia coli K-12, were identified using Genomic SELEX screening at two closely located sites, one inside the spacer between the bidirectional transcription units comprising the yihUTS operon and the yihV gene, and another one upstream of the yihW gene itself. Recently the YihUTS and YihV proteins were identified as catalysing the catabolism of sulfoquinovose (SQ), a hydrolysis product of sulfoquinovosyl diacylglycerol (SQDG) derived from plants and other photosynthetic organisms. Gel shift assay in vitro and reporter assay in vivo indicated that YihW functions as a repressor for all three transcription units. De-repression of the yih operons was found to be under the control of SQ as inducer, but not of lactose, glucose or galactose. Furthermore, a mode of its cooperative DNA binding was suggested for YihW by atomic force microscopy. Hence, as a regulator of the catabolism of SQ, we renamed YihW as CsqR.
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Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Metilglucósidos/metabolismo , Proteínas Represoras/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas Represoras/genética , Azúcares/metabolismo , Transcripción GenéticaRESUMEN
Bacteria and other organisms, including cyanobacteria, employ two-component signal transducing modules comprising histidine kinases and response regulators to acclimate to changing environments. While the number and composition of these modules differ among cyanobacteria, two response regulators that contain DNA binding domains, RpaB and Rre1, are conserved in all sequenced cyanobacterial genomes and are essential for viability. Although RpaB negatively or positively regulates high light and other stress-responsive gene expression, little is known about the function of Rre1. Here, they investigated the direct regulatory targets of Rre1 in the cyanobacterium Synechococcus elongatus PCC 7942. Chromatin immunoprecipitation and high-density tiling array analysis were used to map Rre1 binding sites. The sites included promoter regions for chaperone genes such as dnaK2, groESL-1, groEL-2, hspA and htpG, as well as the group 2 sigma factor gene rpoD2. In vivo and in vitro analyses revealed that Rre1 phosphorylation level, DNA binding activity and adjacent gene transcription increased in response to heat stress. These responses were much diminished in a knock-out mutant of Hik34, a previously identified heat shock regulator. Based on our results, we propose Hik34-Rre1 is the heat shock-responsive signaling module that positively regulates major chaperone and other genes in cyanobacteria.
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Respuesta al Choque Térmico/fisiología , Synechococcus/metabolismo , Proteínas Bacterianas/metabolismo , Secuencia de Bases , Inmunoprecipitación de Cromatina , Cianobacterias/genética , Expresión Génica , Regulación Bacteriana de la Expresión Génica/genética , Histidina Quinasa/metabolismo , Calor , Luz , Chaperonas Moleculares/metabolismo , Fosforilación , Proteínas Quinasas/metabolismo , Factor sigma/metabolismo , Transducción de Señal , Synechococcus/genéticaRESUMEN
Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, 'Transcription Profile of Escherichia coli' (www.shigen.nig.ac.jp/ecoli/tec/).