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1.
Nucleic Acids Res ; 50(14): 8377-8391, 2022 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-35822842

RESUMO

The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.


Assuntos
Proteínas Associadas a CRISPR , Proteínas de Bactérias/metabolismo , Proteínas Associadas a CRISPR/metabolismo , Sistemas CRISPR-Cas , DNA/genética , Clivagem do DNA , DNA de Cadeia Simples/genética
2.
Mol Cell ; 60(6): 953-65, 2015 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-26626484

RESUMO

We report the development of a next-generation sequencing-based technology that entails construction of a DNA library comprising up to at least 4(7) (∼ 16,000) barcoded sequences, production of RNA transcripts, and analysis of transcript ends and transcript yields (massively systematic transcript end readout, "MASTER"). Using MASTER, we define full inventories of transcription start sites ("TSSomes") of Escherichia coli RNA polymerase for initiation at a consensus core promoter in vitro and in vivo; we define the TSS-region DNA sequence determinants for TSS selection, reiterative initiation ("slippage synthesis"), and transcript yield; and we define effects of DNA topology and NTP concentration. The results reveal that slippage synthesis occurs from the majority of TSS-region DNA sequences and that TSS-region DNA sequences have profound, up to 100-fold, effects on transcript yield. The results further reveal that TSSomes depend on DNA topology, consistent with the proposal that TSS selection involves transcription-bubble expansion ("scrunching") and transcription-bubble contraction ("anti-scrunching").


Assuntos
Escherichia coli/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sítio de Iniciação de Transcrição , Código de Barras de DNA Taxonômico , DNA Bacteriano/análise , Regiões Promotoras Genéticas , RNA Bacteriano/análise , Análise de Sequência de DNA/métodos , Análise de Sequência de RNA/métodos , Transcrição Gênica
3.
Int J Clin Pract ; 75(6): e14153, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33735532

RESUMO

BACKGROUND: Red cell distribution width (RDW) is recently emerging as a prognostic indicator in many cardiovascular diseases. However, less is known about its predictive role in patients undergoing transcatheter aortic valve implantation (TAVI). METHODS: We retrospectively included very high-risk patients with severe aortic valve stenosis undergoing TAVI between February 2012 and December 2019. Patients were classified according to RDW tertiles. Our primary endpoint was long-term all-cause mortality. The secondary endpoint was a composite of in-hospital major adverse events as defined by the Valve Academic Research Consortium 2 criteria and/or long-term all-cause mortality. RESULTS: A total of 424 patients [median age 83.5 years, 52.6% females] were analysed. After a median follow-up of 1.55 years, all-cause mortality was 25.5%. At the multivariate-adjusted Cox regression analysis, patients in the highest RDW tertile were associated with a higher risk for all-cause mortality [hazard ratio [HR] 1.73, 95%confidence interval [CI] 1.02-2.95] compared with the lowest tertile. When considering RDW as a continuous variable, we found an 11% increased risk in overall mortality [HR 1.11, 95% CI 1.00-1.24] for each increased point in RDW. The highest RDW tertile was also independently associated with the occurrence of the composite endpoint [odds ratio [OR] 2.10, 95% CI 1.17-3.76] compared with lower tertiles. CONCLUSIONS: In our cohort, elevated basal RDW values were independent predictors of increased long-term mortality and higher rate of in-hospital adverse events. The inclusion of a routinely available biomarker as RDW, may help the pre-operative risk assessment in potential TAVI candidates and optimise their management.


Assuntos
Estenose da Valva Aórtica , Substituição da Valva Aórtica Transcateter , Idoso de 80 Anos ou mais , Valva Aórtica/cirurgia , Estenose da Valva Aórtica/cirurgia , Índices de Eritrócitos , Eritrócitos , Feminino , Humanos , Masculino , Estudos Retrospectivos , Fatores de Risco , Substituição da Valva Aórtica Transcateter/efeitos adversos , Resultado do Tratamento
4.
J Enzyme Inhib Med Chem ; 36(1): 85-97, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33121288

RESUMO

SNAP-tag ® is a powerful technology for the labelling of protein/enzymes by using benzyl-guanine (BG) derivatives as substrates. Although commercially available or ad hoc produced, their synthesis and purification are necessary, increasing time and costs. To address this limitation, here we suggest a revision of this methodology, by performing a chemo-enzymatic approach, by using a BG-substrate containing an azide group appropriately distanced by a spacer from the benzyl ring. The SNAP-tag ® and its relative thermostable version (SsOGT-H5 ) proved to be very active on this substrate. The stability of these tags upon enzymatic reaction makes possible the exposition to the solvent of the azide-moiety linked to the catalytic cysteine, compatible for the subsequent conjugation with DBCO-derivatives by azide-alkyne Huisgen cycloaddition. Our studies propose a strengthening and an improvement in terms of biotechnological applications for this self-labelling protein-tag.


Assuntos
Azidas/química , Metilases de Modificação do DNA/metabolismo , Corantes Fluorescentes/química , Azidas/síntese química , Metilases de Modificação do DNA/química , Corantes Fluorescentes/síntese química , Células HEK293 , Humanos , Modelos Moleculares , Estrutura Molecular , Relação Estrutura-Atividade , Especificidade por Substrato
5.
Extremophiles ; 24(1): 81-91, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31555904

RESUMO

The specific labelling of proteins in recent years has made use of self-labelling proteins, such as the SNAP-tag® and the Halotag®. These enzymes, by their nature or suitably engineered, have the ability to specifically react with their respective substrates, but covalently retaining a part of them in the catalytic site upon reaction. This led to the synthesis of substrates conjugated with, e.g., fluorophores (proposing them as alternatives to fluorescent proteins), but also with others chemical groups, for numerous biotechnological applications. Recently, a mutant of the OGT from Saccharolobus solfataricus (H5) very stable to high temperatures and in the presence of physical and chemical denaturing agents has been proposed as a thermostable SNAP-tag® for in vivo and in vitro harsh reaction conditions. Here, we show two new thermostable OGTs from Thermotoga neapolitana and Pyrococcus furiosus, which, respectively, display a higher catalytic activity and thermostability respect to H5, proposing them as alternatives for in vivo studies in these extreme model organisms.


Assuntos
Biotecnologia , Estabilidade Enzimática , Temperatura Alta , Pyrococcus furiosus
6.
J Enzyme Inhib Med Chem ; 35(1): 1363-1371, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32552137

RESUMO

Cancer is a major health issue adsorbing the attention of a biomedical research. To fight this disease, new drugs are developed, specifically tailored to target biological pathways or peculiar components of the tumour cells. Particularly interesting is the use of intercalating agents as drugs capable to bind DNA and inhibit enzymes involved in DNA metabolism. Anthracyclines are the most commonly used anticancer drugs. In particular, daunomycin is used to cancer treatment by exploiting its ability to intercalate DNA and inhibit the activity of DNA topoisomerases implicated in the replication processes. Unfortunately, clinical application of anthracyclines is limited by their side effects. The conjugation with specific carriers could affect the selectivity and reduce side effect by improving stability and/or cellular uptake properties. We here report the biochemical characterisation of a daunomycin oligopeptide conjugate containing six residues of arginine, by the analysis of its fluorescence properties, DNA interaction and topoisomerases inhibitory effects.


Assuntos
Antineoplásicos/farmacologia , DNA/química , Daunorrubicina/farmacologia , Peptídeos/química , Inibidores da Topoisomerase II/farmacologia , Antineoplásicos/química , Cromatografia Líquida de Alta Pressão , Dicroísmo Circular , Daunorrubicina/química , Espectrometria de Fluorescência , Espectrometria de Massas por Ionização por Electrospray , Inibidores da Topoisomerase II/química
7.
Int J Mol Sci ; 21(8)2020 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-32326075

RESUMO

The genome of living cells is continuously exposed to endogenous and exogenous attacks, and this is particularly amplified at high temperatures. Alkylating agents cause DNA damage, leading to mutations and cell death; for this reason, they also play a central role in chemotherapy treatments. A class of enzymes known as AGTs (alkylguanine-DNA-alkyltransferases) protects the DNA from mutations caused by alkylating agents, in particular in the recognition and repair of alkylated guanines in O6-position. The peculiar irreversible self-alkylation reaction of these enzymes triggered numerous studies, especially on the human homologue, in order to identify effective inhibitors in the fight against cancer. In modern biotechnology, engineered variants of AGTs are developed to be used as protein tags for the attachment of chemical ligands. In the last decade, research on AGTs from (hyper)thermophilic sources proved useful as a model system to clarify numerous phenomena, also common for mesophilic enzymes. This review traces recent progress in this class of thermozymes, emphasizing their usefulness in basic research and their consequent advantages for in vivo and in vitro biotechnological applications.


Assuntos
Reparo do DNA , O(6)-Metilguanina-DNA Metiltransferase/metabolismo , Alquilação , Biotecnologia , Dano ao DNA , Replicação do DNA , Terapia de Alvo Molecular , Neoplasias/tratamento farmacológico , Neoplasias/etiologia , Neoplasias/metabolismo , Neoplasias/patologia , O(6)-Metilguanina-DNA Metiltransferase/química , O(6)-Metilguanina-DNA Metiltransferase/genética , Relação Estrutura-Atividade , Termodinâmica , Thermoproteus/genética , Thermoproteus/metabolismo
8.
J Enzyme Inhib Med Chem ; 34(1): 946-954, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31039618

RESUMO

Carbonic anhydrases (CAs, EC 4.2.1.1) are a superfamily of ubiquitous metalloenzymes present in all living organisms on the planet. They are classified into seven genetically distinct families and catalyse the hydration reaction of carbon dioxide to bicarbonate and protons, as well as the opposite reaction. CAs were proposed to be used for biotechnological applications, such as the post-combustion carbon capture processes. In this context, there is a great interest in searching CAs with robust chemical and physical properties. Here, we describe the enhancement of thermostability of the α-CA from Sulfurihydrogenibium yellowstonense (SspCA) by using the anchoring-and-self-labelling-protein-tag system (ASLtag). The anchored chimeric H5-SspCA was active for the CO2 hydration reaction and its thermostability increased when the cells were heated for a prolonged period at high temperatures (e.g. 70 °C). The ASLtag can be considered as a useful method for enhancing the thermostability of a protein useful for biotechnological applications, which often need harsh operating conditions.


Assuntos
Anidrases Carbônicas/química , Anidrases Carbônicas/metabolismo , Bactérias Gram-Negativas Quimiolitotróficas/enzimologia , Coloração e Rotulagem/métodos , Temperatura , Estabilidade Enzimática , Modelos Moleculares , Relação Estrutura-Atividade
9.
J Enzyme Inhib Med Chem ; 34(1): 490-499, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30724623

RESUMO

The use of natural systems, such as outer membrane protein A (OmpA), phosphoporin E (PhoE), ice nucleation protein (INP), etc., has been proved very useful for the surface exposure of proteins on the outer membrane of Gram-negative bacteria. These strategies have the clear advantage of unifying in a one-step the production, the purification and the in vivo immobilisation of proteins/biocatalysts onto a specific biological support. Here, we introduce the novel Anchoring-and-Self-Labelling-protein-tag (ASLtag), which allows the in vivo immobilisation of enzymes on E. coli surface and the labelling of the neosynthesised proteins with the engineered alkylguanine-DNA-alkyl-transferase (H5) from Sulfolobus solfataricus. Our results demonstrated that this tag enhanced the overexpression of thermostable enzymes, such as the carbonic anhydrase (SspCA) from Sulfurihydrogenibium yellowstonense and the ß-glycoside hydrolase (SsßGly) from S. solfataricus, without affecting their folding and catalytic activity, proposing a new tool for the improvement in the utilisation of biocatalysts of biotechnological interest.


Assuntos
Proteínas da Membrana Bacteriana Externa/metabolismo , Enzimas Imobilizadas/metabolismo , Escherichia coli/enzimologia , Transferases/metabolismo , Enzimas Imobilizadas/química , Escherichia coli/metabolismo , Humanos , Coloração e Rotulagem , Propriedades de Superfície , Transferases/química
10.
Biochem Biophys Res Commun ; 500(3): 698-703, 2018 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-29684348

RESUMO

The self-labeling protein tags are robust and versatile tools for studying different molecular aspects of cell biology. In order to be suitable for a wide spectrum of experimental conditions, it is mandatory that these systems are stable after the fluorescent labeling reaction and do not alter the properties of the fusion partner. SsOGT-H5 is an engineered variant alkylguanine-DNA-alkyl-transferase (OGT) of the hyperthermophilic archaeon Sulfolobus solfataricus, and it represents an alternative solution to the SNAP-tag® technology under harsh reaction conditions. Here we present the crystal structure of SsOGT-H5 in complex with the fluorescent probe SNAP-Vista Green® (SsOGT-H5-SVG) that reveals the conformation adopted by the protein upon the trans-alkylation reaction with the substrate, which is observed covalently bound to the catalytic cysteine residue. Moreover, we identify the amino acids that contribute to both the overall protein stability in the post-reaction state and the coordination of the fluorescent moiety stretching-out from the protein active site. We gained new insights in the conformational changes possibly occurring to the OGT proteins upon reaction with modified guanine base bearing bulky adducts; indeed, our structural analysis reveals an unprecedented conformation of the active site loop that is likely to trigger protein destabilization and consequent degradation. Interestingly, the SVG moiety plays a key role in restoring the interaction between the N- and C-terminal domains of the protein that is lost following the new conformation adopted by the active site loop in the SsOGT-H5-SVG structure. Molecular dynamics simulations provide further information into the dynamics of SsOGT-H5-SVG structure, highlighting the role of the fluorescent ligand in keeping the protein stable after the trans-alkylation reaction.


Assuntos
Corantes Fluorescentes/metabolismo , O(6)-Metilguanina-DNA Metiltransferase/química , O(6)-Metilguanina-DNA Metiltransferase/metabolismo , Proteínas Recombinantes de Fusão/metabolismo , Coloração e Rotulagem , Sulfolobus solfataricus/enzimologia , Sequência de Aminoácidos , Domínio Catalítico , Cristalografia por Raios X , Corantes Fluorescentes/química , Metilação , Simulação de Dinâmica Molecular , Mutação/genética , Análise de Componente Principal , Conformação Proteica , Sulfolobus solfataricus/química , Sulfolobus solfataricus/genética
11.
Biochim Biophys Acta Gen Subj ; 1861(2): 86-96, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-27777086

RESUMO

BACKGROUND: Alkylated DNA-protein alkyltransferases (AGTs) are conserved proteins that repair alkylation damage in DNA by using a single-step mechanism leading to irreversible alkylation of the catalytic cysteine in the active site. Trans-alkylation induces inactivation and destabilization of the protein, both in vitro and in vivo, likely triggering conformational changes. A complete picture of structural rearrangements occurring during the reaction cycle is missing, despite considerable interest raised by the peculiarity of AGT reaction, and the contribution of a functional AGT in limiting the efficacy of chemotherapy with alkylating drugs. METHODS: As a model for AGTs we have used a thermostable ortholog from the archaeon Sulfolobus solfataricus (SsOGT), performing biochemical, structural, molecular dynamics and in silico analysis of ligand-free, DNA-bound and mutated versions of the protein. RESULTS: Conformational changes occurring during lesion recognition and after the reaction, allowed us to identify a novel interaction network contributing to SsOGT stability, which is perturbed when a bulky adduct between the catalytic cysteine and the alkyl group is formed, a mandatory step toward the permanent protein alkylation. CONCLUSIONS: Our data highlighted conformational changes and perturbation of intramolecular interaction occurring during lesion recognition and catalysis, confirming our previous hypothesis that coordination between the N- and C-terminal domains of SsOGT is important for protein activity and stability. GENERAL SIGNIFICANCE: A general model of structural rearrangements occurring during the reaction cycle of AGTs is proposed. If confirmed, this model might be a starting point to design strategies to modulate AGT activity in therapeutic settings.


Assuntos
Alquil e Aril Transferases/metabolismo , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Alquilantes/metabolismo , Alquilação/fisiologia , Catálise , Reparo do DNA/fisiologia , Domínios Proteicos , Estabilidade Proteica , Sulfolobus solfataricus/metabolismo
12.
Nucleic Acids Res ; 43(18): 8801-16, 2015 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-26227971

RESUMO

Alkylated DNA-protein alkyltransferases repair alkylated DNA bases, which are among the most common DNA lesions, and are evolutionary conserved, from prokaryotes to higher eukaryotes. The human ortholog, hAGT, is involved in resistance to alkylating chemotherapy drugs. We report here on the alkylated DNA-protein alkyltransferase, SsOGT, from an archaeal species living at high temperature, a condition that enhances the harmful effect of DNA alkylation. The exceptionally high stability of SsOGT gave us the unique opportunity to perform structural and biochemical analysis of a protein of this class in its post-reaction form. This analysis, along with those performed on SsOGT in its ligand-free and DNA-bound forms, provides insights in the structure-function relationships of the protein before, during and after DNA repair, suggesting a molecular basis for DNA recognition, catalytic activity and protein post-reaction fate, and giving hints on the mechanism of alkylation-induced inactivation of this class of proteins.


Assuntos
Alquil e Aril Transferases/química , Alquil e Aril Transferases/metabolismo , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Reparo do DNA , Alquil e Aril Transferases/genética , Alquilação , Proteínas Arqueais/genética , DNA/metabolismo , Estabilidade Enzimática , Modelos Moleculares , Mutação , Relação Estrutura-Atividade , Sulfolobus solfataricus/enzimologia
13.
Int J Mol Sci ; 18(12)2017 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-29206193

RESUMO

O6-DNA-alkyl-guanine-DNA-alkyl-transferases (OGTs) are evolutionarily conserved, unique proteins that repair alkylation lesions in DNA in a single step reaction. Alkylating agents are environmental pollutants as well as by-products of cellular reactions, but are also very effective chemotherapeutic drugs. OGTs are major players in counteracting the effects of such agents, thus their action in turn affects genome integrity, survival of organisms under challenging conditions and response to chemotherapy. Numerous studies on OGTs from eukaryotes, bacteria and archaea have been reported, highlighting amazing features that make OGTs unique proteins in their reaction mechanism as well as post-reaction fate. This review reports recent functional and structural data on two prokaryotic OGTs, from the pathogenic bacterium Mycobacterium tuberculosis and the hyperthermophilic archaeon Sulfolobus solfataricus, respectively. These studies provided insight in the role of OGTs in the biology of these microorganisms, but also important hints useful to understand the general properties of this class of proteins.


Assuntos
Reparo do DNA/fisiologia , Síncrotrons , Alquil e Aril Transferases/genética , Reparo do DNA/genética , Mycobacterium tuberculosis/enzimologia , Mycobacterium tuberculosis/metabolismo , Estabilidade Proteica , Sulfolobus solfataricus/enzimologia , Sulfolobus solfataricus/metabolismo
14.
Extremophiles ; 20(1): 1-13, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26499124

RESUMO

In the last decade, a powerful biotechnological tool for the in vivo and in vitro specific labeling of proteins (SNAP-tag™ technology) was proposed as a valid alternative to classical protein-tags (green fluorescent proteins, GFPs). This was made possible by the discovery of the irreversible reaction of the human alkylguanine-DNA-alkyl-transferase (hAGT) in the presence of benzyl-guanine derivatives. However, the mild reaction conditions and the general instability of the mesophilic SNAP-tag™ make this new approach not fully applicable to (hyper-)thermophilic and, in general, extremophilic organisms. Here, we introduce an engineered variant of the thermostable alkylguanine-DNA-alkyl-transferase from the Archaea Sulfolobus solfataricus (SsOGT-H5), which displays a catalytic efficiency comparable to the SNAP-tag™ protein, but showing high intrinsic stability typical of proteins from this organism. The successful heterologous expression obtained in a thermophilic model organism makes SsOGT-H5 a valid candidate as protein-tag for organisms living in extreme environments.


Assuntos
Alquil e Aril Transferases/metabolismo , Proteínas Arqueais/metabolismo , Sulfolobus solfataricus/enzimologia , Alquil e Aril Transferases/química , Alquil e Aril Transferases/genética , Sequência de Aminoácidos , Proteínas Arqueais/química , Proteínas Arqueais/genética , DNA/metabolismo , Estabilidade Enzimática , Temperatura Alta , Dados de Sequência Molecular , Ligação Proteica , Engenharia de Proteínas , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Sulfolobus solfataricus/genética
16.
JAMA ; 316(18): 1906-1912, 2016 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-27825009

RESUMO

Importance: Anakinra, an interleukin 1ß recombinant receptor antagonist, may have potential to treat colchicine-resistant and corticosteroid-dependent recurrent pericarditis. Objective: To determine the efficacy of anakinra for colchicine-resistant and corticosteroid-dependent recurrent pericarditis. Design, Setting, and Participants: The Anakinra-Treatment of Recurrent Idiopathic Pericarditis (AIRTRIP) double-blind, placebo-controlled, randomized withdrawal trial (open label with anakinra followed by a double-blind withdrawal step with anakinra or placebo until recurrent pericarditis occurred) conducted among 21 consecutive patients enrolled at 3 Italian referral centers between June and November 2014 (end of follow-up, October 2015). Included patients had recurrent pericarditis (with ≥3 previous recurrences), elevation of C-reactive protein, colchicine resistance, and corticosteroid dependence. Interventions: Anakinra was administered at 2 mg/kg per day, up to 100 mg, for 2 months, then patients who responded with resolution of pericarditis were randomized to continue anakinra (n = 11) or switch to placebo (n = 10) for 6 months or until a pericarditis recurrence. Main Outcomes and Measures: The primary outcomes were recurrent pericarditis and time to recurrence after randomization. Results: Eleven patients (7 female) randomized to anakinra had a mean age of 46.5 (SD, 16.3) years; 10 patients (7 female) randomized to placebo had a mean age of 44 (SD, 12.5) years. All patients were followed up for 12 months. Median follow-up was 14 (range, 12-17) months. Recurrent pericarditis occurred in 9 of 10 patients (90%; incidence rate, 2.06% of patients per year) assigned to placebo and 2 of 11 patients (18.2%; incidence rate, 0.11% of patients per year) assigned to anakinra, for an incidence rate difference of -1.95% (95% CI, -3.3% to -0.6%). Median flare-free survival (time to flare) was 72 (interquartile range, 64-150) days after randomization in the placebo group and was not reached in the anakinra group (P <.001). During anakinra treatment, 20 of 21 patients (95.2%) experienced transient local skin reactions: 1 (4.8%) herpes zoster, 3 (14.3%) transaminase elevation, and 1 (4.8%) ischemic optic neuropathy. No patient permanently discontinued the active drug. No adverse events occurred during placebo treatment. Conclusion and Relevance: In this preliminary study of patients with recurrent pericarditis with colchicine resistance and corticosteroid dependence, the use of anakinra compared with placebo reduced the risk of recurrence over a median of 14 months. Larger studies are needed to replicate these findings as well as to assess safety and longer-term efficacy. Trial Registration: clinicaltrials.gov Identifier: NCT02219828.


Assuntos
Desenvolvimento Infantil , Cognição , Fórmulas Infantis , Recém-Nascido de muito Baixo Peso/crescimento & desenvolvimento , Leite Humano , Método Duplo-Cego , Feminino , Humanos , Lactente , Recém-Nascido , Recém-Nascido Prematuro , Desenvolvimento da Linguagem , Masculino , Ontário
17.
J Biol Chem ; 289(6): 3231-43, 2014 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-24347172

RESUMO

Reverse gyrase is a DNA topoisomerase specific for hyperthermophilic bacteria and archaea. It catalyzes the peculiar ATP-dependent DNA-positive supercoiling reaction and might be involved in the physiological adaptation to high growth temperature. Reverse gyrase comprises an N-terminal ATPase and a C-terminal topoisomerase domain, which cooperate in enzyme activity, but details of its mechanism of action are still not clear. We present here a functional characterization of PcalRG, a novel reverse gyrase from the archaeon Pyrobaculum calidifontis. PcalRG is the most robust and processive reverse gyrase known to date; it is active over a wide range of conditions, including temperature, ionic strength, and ATP concentration. Moreover, it holds a strong ATP-inhibited DNA cleavage activity. Most important, PcalRG is able to induce ATP-dependent unwinding of synthetic Holliday junctions and ATP-stimulated annealing of unconstrained single-stranded oligonucleotides. Combined DNA unwinding and annealing activities are typical of certain helicases, but until now were shown for no other reverse gyrase. Our results suggest for the first time that a reverse gyrase shares not only structural but also functional features with evolutionary conserved helicase-topoisomerase complexes involved in genome stability.


Assuntos
Proteínas Arqueais/química , DNA Topoisomerases Tipo I/química , DNA Arqueal/química , Pyrobaculum/enzimologia , Trifosfato de Adenosina/química , Trifosfato de Adenosina/genética , Trifosfato de Adenosina/metabolismo , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , DNA Topoisomerases Tipo I/genética , DNA Topoisomerases Tipo I/metabolismo , DNA Arqueal/genética , DNA Arqueal/metabolismo , Evolução Molecular , Instabilidade Genômica/fisiologia , Pyrobaculum/genética
18.
Extremophiles ; 18(5): 895-904, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25102812

RESUMO

Repair and defence of genome integrity from endogenous and environmental hazard is a primary need for all organisms. Natural selection has driven the evolution of multiple cell pathways to deal with different DNA damaging agents. Failure of such processes can hamper cell functions and induce inheritable mutations, which in humans may cause cancerogenicity or certain genetic syndromes, and ultimately cell death. A special case is that of hyperthermophilic bacteria and archaea, flourishing at temperatures higher than 80 °C, conditions that favor genome instability and thus call for specific, highly efficient or peculiar mechanisms to keep their genome intact and functional. Over the last few years, numerous studies have been performed on the activity, function, regulation, physical and functional interaction of enzymes and proteins from hyperthermophilic microorganisms that are able to bind, repair, bypass damaged DNA, or modify its structure or conformation. The present review is focused on two enzymes that act on DNA catalyzing unique reactions: reverse gyrase and DNA alkyltransferase. Although both enzymes belong to evolutionary highly conserved protein families present in organisms of the three domains (Eucarya, Bacteria and Archaea), recently characterized members from hyperthermophilic archaea show both common and peculiar features.


Assuntos
Alquil e Aril Transferases/genética , Archaea/genética , Proteínas Arqueais/genética , Bactérias/genética , Proteínas de Bactérias/genética , DNA Topoisomerases Tipo I/genética , Instabilidade Genômica , Alquil e Aril Transferases/química , Alquil e Aril Transferases/metabolismo , Sequência de Aminoácidos , Archaea/enzimologia , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Bactérias/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , DNA Topoisomerases Tipo I/química , DNA Topoisomerases Tipo I/metabolismo , Dados de Sequência Molecular
19.
JAMA ; 312(10): 1016-23, 2014 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-25172965

RESUMO

IMPORTANCE: Postpericardiotomy syndrome, postoperative atrial fibrillation (AF), and postoperative effusions may be responsible for increased morbidity and health care costs after cardiac surgery. Postoperative use of colchicine prevented these complications in a single trial. OBJECTIVE: To determine the efficacy and safety of perioperative use of oral colchicine in reducing postpericardiotomy syndrome, postoperative AF, and postoperative pericardial or pleural effusions. DESIGN, SETTING, AND PARTICIPANTS: Investigator-initiated, double-blind, placebo-controlled, randomized clinical trial among 360 consecutive candidates for cardiac surgery enrolled in 11 Italian centers between March 2012 and March 2014. At enrollment, mean age of the trial participants was 67.5 years (SD, 10.6 years), 69% were men, and 36% had planned valvular surgery. Main exclusion criteria were absence of sinus rhythm at enrollment, cardiac transplantation, and contraindications to colchicine. INTERVENTIONS: Patients were randomized to receive placebo (n=180) or colchicine (0.5 mg twice daily in patients ≥70 kg or 0.5 mg once daily in patients <70 kg; n=180) starting between 48 and 72 hours before surgery and continued for 1 month after surgery. MAIN OUTCOMES AND MEASURES: Occurrence of postpericardiotomy syndrome within 3 months; main secondary study end points were postoperative AF and pericardial or pleural effusion. RESULTS: The primary end point of postpericardiotomy syndrome occurred in 35 patients (19.4%) assigned to colchicine and in 53 (29.4%) assigned to placebo (absolute difference, 10.0%; 95% CI, 1.1%-18.7%; number needed to treat = 10). There were no significant differences between the colchicine and placebo groups for the secondary end points of postoperative AF (colchicine, 61 patients [33.9%]; placebo, 75 patients [41.7%]; absolute difference, 7.8%; 95% CI, -2.2% to 17.6%) or postoperative pericardial/pleural effusion (colchicine, 103 patients [57.2%]; placebo, 106 patients [58.9%]; absolute difference, 1.7%; 95% CI, -8.5% to 11.7%), although there was a reduction in postoperative AF in the prespecified on-treatment analysis (placebo, 61/148 patients [41.2%]; colchicine, 38/141 patients [27.0%]; absolute difference, 14.2%; 95% CI, 3.3%-24.7%). Adverse events occurred in 21 patients (11.7%) in the placebo group vs 36 (20.0%) in the colchicine group (absolute difference, 8.3%; 95% CI; 0.76%-15.9%; number needed to harm = 12), but discontinuation rates were similar. No serious adverse events were observed. CONCLUSIONS AND RELEVANCE: Among patients undergoing cardiac surgery, perioperative use of colchicine compared with placebo reduced the incidence of postpericardiotomy syndrome but not of postoperative AF or postoperative pericardial/pleural effusion. The increased risk of gastrointestinal adverse effects reduced the potential benefits of colchicine in this setting. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01552187.


Assuntos
Fibrilação Atrial/prevenção & controle , Procedimentos Cirúrgicos Cardíacos , Colchicina/uso terapêutico , Complicações Pós-Operatórias/prevenção & controle , Síndrome Pós-Pericardiotomia/prevenção & controle , Moduladores de Tubulina/uso terapêutico , Idoso , Colchicina/efeitos adversos , Método Duplo-Cego , Feminino , Gastroenteropatias/induzido quimicamente , Humanos , Masculino , Pessoa de Meia-Idade , Derrame Pericárdico/prevenção & controle , Assistência Perioperatória , Derrame Pleural/prevenção & controle , Moduladores de Tubulina/efeitos adversos
20.
Int J Mol Sci ; 15(9): 17162-87, 2014 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-25257534

RESUMO

In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.


Assuntos
Archaea/fisiologia , Proteínas Arqueais/fisiologia , Cromatina/ultraestrutura , DNA Topoisomerases/fisiologia , Temperatura Alta , Archaea/genética , Proteínas Arqueais/química , Proteínas Arqueais/genética , Cromatina/metabolismo , Clima , DNA Topoisomerases/genética , DNA Topoisomerases Tipo I/química , DNA Topoisomerases Tipo I/fisiologia , DNA Arqueal/química , DNA Arqueal/genética , DNA Arqueal/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/fisiologia , Regulação da Expressão Gênica em Archaea , Genes Arqueais , Histonas/química , Histonas/genética , Histonas/fisiologia , Conformação de Ácido Nucleico , Nucleossomos/metabolismo , Nucleossomos/ultraestrutura , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade
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