scholarly journals Functional Analysis of the Streptomyces coelicolor NrdR ATP-Cone Domain: Role in Nucleotide Binding, Oligomerization, and DNA Interactions

2008 ◽  
Vol 191 (4) ◽  
pp. 1169-1179 ◽  
Author(s):  
Inna Grinberg ◽  
Tatyana Shteinberg ◽  
A. Quamrul Hassan ◽  
Yair Aharonowitz ◽  
Ilya Borovok ◽  
...  
Keyword(s):  
Dna Binding ◽  
De Novo ◽  
Streptomyces Coelicolor ◽  
Nucleotide Binding ◽  
Class I ◽  
Protein Oligomerization ◽  
Class Iii ◽  
Mutant Proteins ◽  
Pleiotrophic Effects ◽  
Zinc Ribbon

ABSTRACT Ribonucleotide reductases (RNRs) are essential enzymes in all living cells, providing the only known de novo pathway for the biosynthesis of deoxyribonucleotides (dNTPs), the immediate precursors of DNA synthesis and repair. RNRs catalyze the controlled reduction of all four ribonucleotides to maintain a balanced pool of dNTPs during the cell cycle. Streptomyces species contain genes, nrdAB and nrdJ, coding for oxygen-dependent class I and oxygen-independent class II RNRs, either of which is sufficient for vegetative growth. Both sets of genes are transcriptionally repressed by NrdR. NrdR contains a zinc ribbon DNA-binding domain and an ATP-cone domain similar to that present in the allosteric activity site of many class I and class III RNRs. Purified NrdR contains up to 1 mol of tightly bound ATP or dATP per mol of protein and binds to tandem 16-bp sequences, termed NrdR-boxes, present in the upstream regulatory regions of bacterial RNR operons. Previously, we showed that the ATP-cone domain alone determines nucleotide binding and that an NrdR mutant defective in nucleotide binding was unable to bind to DNA probes containing NrdR-boxes. These observations led us to propose that when NrdR binds ATP/dATP it undergoes a conformational change that affects DNA binding and hence RNR gene expression. In this study, we analyzed a collection of ATP-cone mutant proteins containing changes in residues inferred to be implicated in nucleotide binding and show that they result in pleiotrophic effects on ATP/dATP binding, on protein oligomerization, and on DNA binding. A model is proposed to integrate these observations.

scholarly journals Class I and class III phosphoinositide 3-kinases are required for actin polymerization that propels phagosomes

2010 ◽  
Vol 191 (5) ◽  
pp. 999-1012 ◽  
Author(s):  
Michal Bohdanowicz ◽  
Gabriela Cosío ◽  
Jonathan M. Backer ◽  
Sergio Grinstein
Keyword(s):  
Plasma Membrane ◽  
Actin Polymerization ◽  
De Novo ◽  
Class I ◽  
Complement Receptors ◽  
Class Iii ◽  
Pi3k Activity ◽  
Phagosomal Membrane

Actin polymerization drives the extension of pseudopods that trap and engulf phagocytic targets. The polymerized actin subsequently dissociates as the phagocytic vacuole seals and detaches from the plasma membrane. We found that phagosomes formed by engagement of integrins that serve as complement receptors (CR3) undergo secondary waves of actin polymerization, leading to the formation of “comet tails” that propel the vacuoles inside the cells. Actin tail formation was accompanied by and required de novo formation of PI(3,4)P2 and PI(3,4,5)P3 on the phagosomal membrane by class I phosphoinositide 3-kinases (PI3Ks). Although the phosphatidylinositide phosphatase Inpp5B was recruited to nascent phagosomes, it rapidly detached from the membrane after phagosomes sealed. Detachment of Inpp5B required the formation of PI(3)P. Thus, class III PI3K activity was also required for the accumulation of PI(4,5)P2 and PI(3,4,5)P3 and for actin tail formation. These experiments reveal a new PI(3)P-sensitive pathway leading to PI(3,4)P2 and PI(3,4,5)P3 formation and signaling in endomembranes.

scholarly journals Comparative Study of Pre-Market Approval Process and Denovo Process for Medical Devices

2013 ◽  
Vol 11 (01) ◽  
pp. 74-82
Author(s):  
Akash Dambal ◽  
Harrison Michael Zaphrey ◽  
M. P. Venkatesh ◽  
Kaushik Devaraju ◽  
T. M. Pramod Kumar
Keyword(s):  
High Risk ◽  
Medical Devices ◽  
De Novo ◽  
The United States ◽  
Class I ◽  
Class Iii ◽  
Moderate Risk ◽  
Risk Class ◽  
Market Approval ◽  
Novel Devices

FDA’s Center for Devices and Radiological Health (CDRH) is responsible for regulating firms who manufacture, repackage, relabel, and/or import medical devices sold in the United States. Regulatory control increases from Class I to Class III. Most Class I devices are exempt from Premarket Notification 510(k); most Class II devices require Pre-market Notification 510(k); and most Class III devices require Pre-market Approval.The Food and Drug Administration Modernization Act of 1997 (FDAMA) added the De Novo classification option as an alternate pathway to classify novel medical devices that had automatically been placed in Class III after receiving a “not substantially equivalent” determination in response to a pre-market notification [510(k)] submission.Class III Devices are those considered as high risk along these lines requiring the regularly lengthier Pre-market Approval (PMA) process. The new De Novo process was designed to usher through any new device that was both Unprecedented (novel) and Low to moderate risk (or with a risk that was easily mitigated). The most inventive gadgets are considered high-hazard due to the non-attendance of equivalent items and follow either the De Novo or PMA path. Truly high-risk devices, in which deficient data exists to decide if general and special controls are sufficient to give sensible attestation of the item’s safety and effectiveness, follow the PMA pathway. Novel devices that do not have a predicate are classified in the highest risk class,despite the level of genuine risk it postures or the capacity of general and special controls to guarantee safety and effectiveness. The De Novo process allows these novel devices with low to moderate risk to be reclassified from a high-risk class, which requires a PMA.

scholarly journals The Streptomyces NrdR Transcriptional Regulator Is a Zn Ribbon/ATP Cone Protein That Binds to the Promoter Regions of Class Ia and Class II Ribonucleotide Reductase Operons

2006 ◽  
Vol 188 (21) ◽  
pp. 7635-7644 ◽  
Author(s):  
Inna Grinberg ◽  
Tanya Shteinberg ◽  
Batia Gorovitz ◽  
Yair Aharonowitz ◽  
Gerald Cohen ◽  
...  
Keyword(s):  
Biochemical Characterization ◽  
De Novo ◽  
Streptomyces Coelicolor ◽  
Regulatory Region ◽  
Direct Repeat ◽  
Class Ii ◽  
Promoter Regions ◽  
Specific Sequence ◽  
Sequence Elements ◽  
Zinc Ribbon

ABSTRACT Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides and are essential for de novo DNA synthesis and repair. Streptomyces spp. contain genes coding for two RNRs, either of which is sufficient for vegetative growth. The class Ia RNR is encoded by the nrdAB genes, and the class II RNR is encoded by nrdJ, which is coexpressed with nrdR. We previously showed that the Streptomyces coelicolor nrdR gene encodes a protein, NrdR, which represses transcription of both sets of RNR genes. NrdR is a member of a highly conserved family of proteins that is confined exclusively to prokaryotes. In this report, we describe a physical and biochemical characterization of the S. coelicolor NrdR protein and show that it is a zinc-ATP/dATP-containing protein that binds to the promoter regions of both Streptomyces RNR operons. The NrdR N terminus contains a zinc ribbon motif that is necessary for binding to the upstream regulatory region of both RNR operons. The latter contains two 16-bp direct repeat sequences, termed NrdR boxes, which are located proximal to, or overlap with, the promoter regions. These experiments support the view that NrdR controls the transcription of RNR genes by binding to the NrdR box sequences. We also show that the central NrdR ATP cone domain binds ATP and dATP and that mutations that abolish ATP/dATP binding significantly reduce DNA binding, suggesting that the ATP cone domain may allosterically regulate NrdR binding. We conclude that NrdR is a widely conserved regulator of RNR genes, binding to specific sequence elements in the promoter region and thereby modulating transcription.

scholarly journals Functional Analysis of the Carboxy-Terminal Region of Bacillus subtilis TnrA, a MerR Family Protein

2006 ◽  
Vol 189 (1) ◽  
pp. 20-27 ◽  
Author(s):  
Lewis V. Wray ◽  
Susan H. Fisher
Keyword(s):  
Bacillus Subtilis ◽  
Dna Binding ◽  
Glutamine Synthetase ◽  
Complex Mixture ◽  
Class Ii ◽  
Terminal Region ◽  
Class I ◽  
Class Iii ◽  
Dimerization Domain ◽  
Alanine Scanning Mutagenesis

ABSTRACT The Bacillus subtilis TnrA transcription factor belongs to the MerR family of proteins and regulates gene expression during nitrogen-limited growth. When B. subtilis cells are grown with excess nitrogen, feedback-inhibited glutamine synthetase forms a protein-protein complex with TnrA that prevents TnrA from binding to DNA. The C-terminal region of TnrA is required for the interaction with glutamine synthetase. Alanine scanning mutagenesis of the C-terminal region of TnrA identified three classes of mutants that altered the regulation by glutamine synthetase. While expression of the TnrA-regulated amtB gene was expressed constitutively in the class I (M96A, Q100A, and A103G) and class II (L97A, L101A, and F105A) mutants, the class II mutants were unable to grow on minimal medium unless a complex mixture of amino acids was present. The class III tnrA mutants (R93A, G99A, N102A, H104A, and Y107A mutants) were partially defective in the regulation of TnrA activity. In vitro experiments showed that feedback-inhibited glutamine synthetase had a significantly reduced ability to inhibit the DNA-binding activity of several class I and class II mutant TnrA proteins. A coiled-coil homology model of the C-terminal region of TnrA is used to explain the properties of the class I and II mutant proteins. The C-terminal region of TnrA corresponds to a dimerization domain in other MerR family proteins. Surprisingly, gel filtration and cross-linking analysis showed that a truncated TnrA protein which contained only the N-terminal DNA binding domain was dimeric. The implications of these results for the structure of TnrA are discussed.

Chemometric Analysis of Substituent Effects. VIII. Alternative Interpretation of Substituent Effects (AISE)

1995 ◽  
Vol 60 (9) ◽  
pp. 1502-1528 ◽  
Author(s):  
Oldřich Pytela
Keyword(s):  
Multiple Bond ◽  
Substituent Effects ◽  
Alternative Interpretation ◽  
Class I ◽  
Reaction Centre ◽  
Correlation Equations ◽  
Class Iii ◽  
Substituent Constant ◽  
Chemical Models ◽  
The Individual

Alternative interpretation of substituent effects (AISE) starts from the presumption that a substituent only possesses a single property described by a single substituent constant. This property is transmitted to the reaction centre by three different ways depending on the interaction type in the triad reaction centre - basic skeleton - substituent. For interpretation it is substantial whether or not the substituent has p electrons at the atom adjacent to the basic skeleton. If it has none, the substituent belongs to class I and operates only by its basic effect described by the mentioned single substituent constant. Substituents of class II possess a free electron pair at the atom adjacent to the basic skeleton, and those of class III have a multiple bond between the first and the second atoms which is polarized in the direction from the basic skeleton. Substituent effects in class I are described by a substituent constant identical with σI constant. Substituents in classes II and III show additional effects proportional to the same constant. Hence, a separate treatment of substituent effects in the individual classes provides three straight lines intersecting in a common point. Mathematically, the description of substituent effects in this approach is expressed by a family of lines with a single explaining variable. The point of intersection, which is referred to as the iso-effect point, is not identical with the classic standard substituent - hydrogen - but is near to CN substituent. The approach given has the advantage of adopting a single substituent constant whose scale can be adjusted relatively precisely. Its drawback (like in the case of the correlation equations derived from the principle of separation of substituent effects) lies in a more extensive set of substituents needed for a correlation. The AISE principle has been applied to 318 series of experimental data describing effects of 32 substituents in a large variety of chemical models (aliphatic, alicyclic, aromatic, heteroaromatic, with or without direct conjugation between reaction centre and substituent) in both chemical reactions and equilibria. A comparison with two other correlation relations with two and three substituent constants for interpretation of substituent effects based on the principle of separation of the individual substituent effects showed that the closeness of AISE based correlations is comparable with that of the correlation equations currently used. It was somewhat less successful in the models with direct conjugation between reaction centre and substituent but the AISE principle can be used even in these cases.

scholarly journals Environmental Cadmium Exposure and Dental Indices in Orthodontic Patients

Healthcare ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 413
Author(s):  
Hui-Ling Chen ◽  
Jason Chen-Chieh Fang ◽  
Chia-Jung Chang ◽  
Ti-Feng Wu ◽  
I-Kuan Wang ◽  
...  
Keyword(s):  
Cadmium Concentration ◽  
Class Ii ◽  
Cadmium Exposure ◽  
Class I ◽  
P Value ◽  
Tooth Decay ◽  
Class Iii ◽  
Orthodontic Patients ◽  
Urine Cadmium ◽  
The Mean

Background. Previous studies have shown that environmental cadmium exposure could disrupt salivary gland function and is associated with dental caries and reduced bone density. Therefore, this cross-sectional study attempted to determine whether tooth decay with tooth loss following cadmium exposure is associated with some dental or skeletal traits such as malocclusions, sagittal skeletal pattern, and tooth decay. Methods. Between August 2019 and June 2020, 60 orthodontic patients with no history of previous orthodontics, functional appliances, or surgical treatment were examined. The patients were stratified into two groups according to their urine cadmium concentrations: high (>1.06 µg/g creatinine, n = 28) or low (<1.06 µg/g creatinine, n = 32). Results. The patients were 25.07 ± 4.33 years old, and most were female (female/male: 51/9 or 85%). The skeletal relationship was mainly Class I (48.3%), followed by Class II (35.0%) and Class III (16.7%). Class I molar relationships were found in 46.7% of these patients, Class II molar relationships were found in 15%, and Class III molar relationships were found in 38.3%. The mean decayed, missing, and filled surface (DMFS) score was 8.05 ± 5.54, including 2.03 ± 3.11 for the decayed index, 0.58 ± 1.17 for the missing index, and 5.52 ± 3.92 for the filled index. The mean index of complexity outcome and need (ICON) score was 53.35 ± 9.01. The facial patterns of these patients were within the average low margin (26.65 ± 5.53 for Frankfort–mandibular plane angle (FMA)). There were no significant differences in the above-mentioned dental indices between patients with high urine cadmium concentrations and those with low urine cadmium concentrations. Patients were further stratified into low (<27, n = 34), average (27–34, n = 23), and high (>34, n = 3) FMA groups. There were no statistically significant differences in the urine cadmium concentration among the three groups. Nevertheless, a marginally significant p-value of 0.05 for urine cadmium concentration was noted between patients with low FMA and patients with high FMA. Conclusion. This analysis found no association between environmental cadmium exposure and dental indices in our orthodontic patients.

RUNX1 DNA-binding mutations and RUNX1-PRDM16 cryptic fusions in BCR-ABL+ leukemias are frequently associated with secondary trisomy 21 and may contribute to clonal evolution and imatinib resistance

Blood ◽  
2008 ◽  
Vol 111 (7) ◽  
pp. 3735-3741 ◽  
Author(s):  
Catherine Roche-Lestienne ◽  
Lauréline Deluche ◽  
Sélim Corm ◽  
Isabelle Tigaud ◽  
Sami Joha ◽  
...  
Keyword(s):  
Dna Binding ◽  
High Frequency ◽  
Trisomy 21 ◽  
De Novo ◽  
Blast Crisis ◽  
Clonal Evolution ◽  
Chronic Phase ◽  
Chromosome 21 ◽  
Imatinib Resistance ◽  
Molecular Abnormalities

Abstract Acquired molecular abnormalities (mutations or chromosomal translocations) of the RUNX1 transcription factor gene are frequent in acute myeloblastic leukemias (AMLs) and in therapy-related myelodysplastic syndromes, but rarely in acute lymphoblastic leukemias (ALLs) and chronic myelogenous leukemias (CMLs). Among 18 BCR-ABL+ leukemias presenting acquired trisomy of chromosome 21, we report a high frequency (33%) of recurrent point mutations (4 in myeloid blast crisis [BC] CML and one in chronic phase CML) within the DNA-binding region of RUNX1. We did not found any mutation in de novo BCR-ABL+ ALLs or lymphoid BC CML. Emergence of the RUNX1 mutations was detected at diagnosis or before the acquisition of trisomy 21 during disease progression. In addition, we also report a high frequency of cryptic chromosomal RUNX1 translocation to a novel recently described gene partner, PRDM16 on chromosome 1p36, for 3 (21.4%) of 14 investigated patients: 2 myeloid BC CMLs and, for the first time, 1 therapy-related BCR-ABL+ ALL. Two patients presented both RUNX1 mutations and RUNX1-PRDM16 fusion. These events are associated with a short survival and support the concept of a cooperative effect of BCR-ABL with molecular RUNX1 abnormalities on the differentiation arrest phenotype observed during progression of CML and in BCR-ABL+ ALL.

scholarly journals DNA Binding by the Methanothermobacter thermautotrophicus Cdc6 Protein Is Inhibited by the Minichromosome Maintenance Helicase

2006 ◽  
Vol 188 (12) ◽  
pp. 4577-4580 ◽  
Author(s):  
Rajesh Kasiviswanathan ◽  
Jae-Ho Shin ◽  
Zvi Kelman
Keyword(s):  
Dna Binding ◽  
Binding Activity ◽  
Minichromosome Maintenance ◽  
Single Stranded Dna ◽  
Mutant Proteins ◽  
Dna Binding Activity ◽  
Double Stranded Dna ◽  
Mcm Helicase ◽  
Methanothermobacter Thermautotrophicus

ABSTRACT The Cdc6 proteins from the archaeon Methanothermobacter thermautotrophicus were previously shown to bind double-stranded DNA. It is shown here that the proteins also bind single-stranded DNA. Using minichromosome maintenance (MCM) helicase mutant proteins unable to bind DNA, it was found that the interaction of MCM with Cdc6 inhibits the DNA binding activity of Cdc6.

Reduced Efficacy of the Pipeline Embolization Device in the Treatment of Posterior Communicating Region Aneurysms with Fetal Posterior Cerebral Artery Configuration

Neurosurgery ◽  
2017 ◽  
Vol 82 (5) ◽  
pp. 695-700 ◽  
Author(s):  
Anil K Roy ◽  
Brian M Howard ◽  
Diogo C Haussen ◽  
Joshua W Osbun ◽  
Sameer H Halani ◽  
...  
Keyword(s):  
Cerebral Artery ◽  
Clinical Symptoms ◽  
Posterior Cerebral Artery ◽  
Neurological Complications ◽  
Class I ◽  
Class Iii ◽  
Pipeline Embolization Device ◽  
Independent Association ◽  
Incomplete Occlusion

Abstract BACKGROUND Aneurysms at the origin of the posterior communicating artery (PcommA) have been demonstrated to be effectively treated with the pipeline embolization device (PED). Much less is known about the efficacy of the PED for aneurysms associated with a fetal posterior cerebral artery (fPCA) variant. OBJECTIVE To study PED treatment efficacy of PcommA aneurysms, including fPCA aneurysms. METHODS A prospectively maintained university database of aneurysm patients treated with the PED was retrospectively reviewed. Demographics, treatment details, and imaging were reviewed for all PcommA and fPCA aneurysms. RESULTS Out of a total of 285 patients treated with PED, 50 patients (mean age 57.5 ± 12.2 yr, 42 females) with unruptured PcommA (9 fPCA) aneurysms were identified. Mean follow-up duration was 14.0 ± 11.6 mo (48 patients). Roy-Raymond class I occlusion on follow-up magnetic resonance or catheter angiography (mean time 11.7 ± 6.8 mo) was achieved in 30 patients (62.5%), class II occlusion in 11 patients (22.9%) and class III occlusion in 7 patients (14.5%). The PcommA was occluded in 56% of patients without any clinical symptoms. No deaths or permanent neurological complications occurred. In fPCA aneurysms, class I occlusion was seen in 1 patient, class 2 occlusion in 2 patients, and class III occlusion in 6 patients. Multivariate analysis revealed an independent association between incomplete occlusion and fPCA configuration (OR 73.65; 95% CI: 5.84-929.13; P = .001). CONCLUSION The PED is a safe and effective treatment for PcommA aneurysms, although fetal anatomy should increase consideration of traditional endovascular techniques or surgical clipping.

Effects of antiarrhythmic drugs on atrioventricular conduction in patients with preexisting bundle branch block

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Kochav ◽  
R.C Chen ◽  
J.M.D Dizon ◽  
J.A.R Reiffel
Keyword(s):  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Class I ◽  
Class Iii ◽  
Bundle Branch Block ◽  
Kaplan Meier ◽  
Cox Proportional Hazards Models ◽  
Hazard Ratios ◽  
History Of ◽  
Propensity Score Stratification

Abstract Background Theoretical concern exists regarding AV block (AVB) with class I antiarrhythmics (AADs) when bundle branch block (BBB) is present. Whether this is substantiated in real-world populations is unknown. Purpose To determine the relationship between type of AAD and incidence of AVB in patients with preexisting BBB. Methods We retrospectively studied all patients with BBB who received class I and III AADs between 1997–2019 to compare incidence of AVB. We defined index time as first exposure to either drug class and excluded patients with prior AVB or exposed to both classes. Time-at-risk window ended at first outcome occurrence or when patients were no longer observed in the database. We estimated hazard ratios for incident AVB using Cox proportional hazards models with propensity score stratification, adjusting for over 32,000 covariates from the electronic health record. Kaplan-Meier methods were used to determine treatment effects over time. Results Of 40,120 individuals with BBB, 148 were exposed to a class I AAD and 2401 to a class III AAD. Over nearly 4,200 person-years of follow up, there were 22 and 620 outcome events in the class I and class III cohorts, respectively (Figure). In adjusted analyses, AVB risk was markedly lower in patients exposed to class I AADs compared with class III (HR 0.48 [95% CI 0.30–0.75]). Conclusion Among patients with BBB, exposure to class III AADs was strongly associated with greater risk of incident AVB. This likely reflects differences in natural history of patients receiving class I vs class III AADs rather than adverse class III effects, however, the lack of worse outcomes acutely with class I AADs suggests that they may be safer in BBB than suspected. Funding Acknowledgement Type of funding source: None

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