Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

FOLD TYPE II PYRIDOXAL 5 `-PHOSPHATE DEPENDENT ENZYMES: STRUCTURE, SUBSTRATE RECOGNITION AND CATALYSIS

Enzymes utilizing pyridoxal 5'-phosphate dependent mechanism for catalysis are observed in all cellular forms of living organisms. PLP-dependent enzymes catalyze a wide variety of reactions involving amino acid substrates and their analogs. Structurally, these ubiquitous enzymes have been classified into four major fold types. We have carried out investigations on the structure and function of fold type I enzymes serine hydroxymethyl transferase and acetylornithine amino transferase, fold type n enzymes catabolic threonine deaminase, D-serine deaminase, D-cysteine desulfhydrase and diaminopropionate ammonia lyase. This review summarizes the major findings of investigations on fold type II enzymes in the context of similar studies on other PLP-dependent enzymes. Fold type II enzymes participate in pathways of both degradation and synthesis of amino acids. Polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity are briefly described. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance.

Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor

We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.

Food composition and digestive enzymes in the gut of the African electric catfish Malapterurus electricus (Gmelin 1789) (Malapteruridae)

Analyses of stomach contents of 330 Malapterurus electricus (standard length, 10.1-30.5 cm) in Mahin Lagoon (southwestern Nigeria) established it as a bottom feeder. There was a preponderance of insects accounting for >80% occurrence and >25% of total volume in stomachs of specimens, suggesting a stenophagous predatory habit. Qualitative and quantitative assays of digestive enzymes in the different regions of the gut (oesophagus, stomach, duodenum, ileum, rectum) were investigated. Carbohydrases (amylase, maltase), chitinase, proteases (pepsin, chymotrypsin, trypsin) and lipases were detected in different gut regions with different activity. The pattern of distribution and relative activity of the enzymes correlated with the predatory diet

Olefin cyclopropanation and carbon-hydrogen amination via carbene and nitrene transfers catalyzed by engineered cytochrome P450 enzymes

Synthetic biology promises to transform organic synthesis by enabling artificial catalysis in living cells. I start by reviewing the state of the art in this young field and recognizing that new approaches are required for designing enzymes that catalyze nonnatural reactions, in order to expand the scope of biocatalytic transformations. Carbene and nitrene transfers to C=C and C-H bonds are reactions of tremendous synthetic utility that lack biological counterparts. I show that various heme proteins, including cytochrome P450BM3, will catalyze promiscuous levels of olefin cyclopropanation when provided with the appropriate synthetic reagents (e.g., diazoesters and styrene). Only a few amino acid substitutions are required to install synthetically useful levels of stereoselective cyclopropanation activity in P450BM3. Understanding that the ferrous-heme is the active species for catalysis and that the artificial reagents are unable to induce a spin-shift-dependent increase in the redox potential of the ferric P450, I design a high-potential serine-heme ligated P450 (P411) that can efficiently catalyze cyclopropanation using NAD(P)H. Intact E. coli whole-cells expressing P411 are highly efficient asymmetric catalysts for olefin cyclopropanation. I also show that engineered P450s can catalyze intramolecular amination of benzylic C-H bonds from arylsulfonyl azides. Finally, I review other examples of where synthetic reagents have been used to drive the evolution of novel enzymatic activity in the environment and in the laboratory. I invoke preadaptation to explain these observations and propose that other man-invented reactions may also be transferrable to natural enzymes by using a mechanism-based approach for choosing the enzymes and the reagents. Overall, this work shows that existing enzymes can be readily adapted for catalysis of synthetically important reactions not previously observed in nature.

Engineering and Characterization of Cytochrome P450 Enzymes for Nitrogen-Atom Transfer Reactions

The creation of novel enzyme activity is a great challenge to protein engineers, but nature has done so repeatedly throughout the process of natural selection. I begin by outlining the multitude of distinct reactions catalyzed by a single enzyme class, cytochrome P450 monooxygenases. I discuss the ability of cytochrome P450 to generate reactive intermediates capable of diverse reactivity, suggesting this enzyme can also be used to generate novel reactive intermediates in the form of metal-carbenoid and nitrenoid species. I then show that cytochrome P450 from Bacillus megaterium (P450_BM3) and its isolated cofactor can catalyze metal-nitrenoid transfer in the form of intramolecular C–H bond amination. Mutations to the protein sequence can enhance the reactivity and selectivity of this transformation significantly beyond that of the free cofactor. Next, I demonstrate an intermolecular nitrene transfer reaction catalyzed by P450_BM3 in the form of sulfide imidation. Understanding that sulfur heteroatoms are strong nucleophiles, I show that increasing the sulfide nucleophilicity through substituents on the aryl sulfide ring can dramatically increase reaction productivity. To explore engineering nitrenoid transfer in P450BM3, active site mutagenesis is employed to tune the regioselectivity intramolecular C–H amination catalysts. The solution of the crystal structure of a highly selective variant demonstrates that hydrophobic residues in the active site strongly modulate reactivity and regioselectivity. Finally, I use a similar strategy to develop P450-based catalysts for intermolecular olefin aziridination, demonstrating that active site mutagenesis can greatly enhance this nitrene transfer reaction. The resulting variant can catalyze intermolecular aziridination with more than 1000 total turnovers and enantioselectivity of up to 99% ee.

Efeito protetor do extrato hidroalcoólico de Euterpe oleracea Mart. (Açaí) nas alterações renais, cardiovasculares e metabólicas induzidas pela restrição protéica materna durante a gestação

Alguns trabalhos demonstraram que a planta, Euterpe oleracea Mart. (açaí) é rica em polifenóis e que uma dieta rica em polifenóis pode estar envolvida na proteção contra o risco cardiovascular. Desta forma, o objetivo deste estudo foi avaliar o efeito do tratamento com o extrato hidroalcoólico do caroço do açaí (ASE) (200mg/Kg/dia), sobre as alterações renais, cardiovasculares, metabólicas, morfológicas e o estresse oxidativo na prole adulta com dezesseis semanas, cujas mães foram submetidas a uma dieta hipoprotéica durante a gestação. Quatro grupos de ratas foram alimentados com dietas experimentais: controle (20% de proteínas); controle + ASE (20% de proteína + ASE); hipoprotéica (6% de proteína); hipoprotéica + ASE (6% de proteína + ASE) durante a gestação. Após o desmame, todos os filhotes passaram a ser alimentados com uma dieta controle e foram sacrificados com 4 meses de idade. A pressão arterial sistólica (PAS) foi medida por pletismografia de cauda e o efeito vasodilatador da acetilcolina (ACh) e nitroglicerina (NG) foi avaliado em leito arterial mesentérico (LAM) perfundido. Foram determinados o peso corporal, níveis séricos de colesterol total, triglicerídeos, lipoproteína de alta densidade (HDL), albumina, uréia, creatinina, glicose, insulina, resistência à insulina (índice de Homa IR), sódio, potássio e a renina plasmática. Foi avaliada a depuração de creatinina, volume de urina, excreção fracionada de sódio (EFNa) e o número de glomérulos renais. O dano oxidativo, níveis de nitrito e a atividade das enzimas antioxidantes: superóxido dismutase, catalase e glutationa peroxidase foram dosados no plasma e homogenato de rim. O peso corporal foi menor no grupo hipoprotéico e recuperado com ASE. A PAS foi aumentada no grupo hipoprotéico e revertida pelo tratamento com ASE. Os níveis de renina plasmática foram aumentados no grupo hipoprotéico e reduzidos com ASE. A resposta vasodilatadora à ACh em LAM estava reduzida no grupo hipoprotéico com ASE houve uma melhora dessa resposta.O efeito vasodilatador da NG não foi diferente entre os grupos. No grupo hipoprotéico também foi observado o aumento dos níveis de triglicerídeos, colesterol total, uréia, creatinina, glicose e insulina, os mesmos foram reduzidos pelo ASE. Não houve diferença nos níveis de HDL, sódio, potássio, depuração de creatinina e volume urinário nos grupos estudados. Os níveis de malondialdeído e carbonilação de proteínas estavam aumentados e os níveis de nitrito reduzidos no grupo hipoprotéico e foram revertidos pelo ASE. As atividades das enzimas antioxidantes no plasma e no rim foram reduzidas no grupo hipoprotéico e aumentadas pelo ASE, com exceção da catalase que não apresentou diferença entre os grupos. Os animais hipoprotéicos apresentaram redução no número de glomérulos renais e aumento da EFNa e o tratamento com ASE preveniu as alterações renais encontradas neste modelo. Em conclusão, o ASE parece proteger a prole, cujas mães foram expostas a uma dieta com pouca proteína durante a gestação, através do efeito anti-hipertensivo, vasodilatador e antioxidante observado neste trabalho.

Studies on phenolase enzymes in prawns. Pt. 1. The distribution and physical properties of phenolases in Penaeid prawns

The distribution of phenolases in certain species of Penaeid prawns has been studied. Attempts were made to locate the regions of maximum enzyme activity in the prawns. The relative dopase activity has been examined in extracts from head, tail, shell with cuticles and muscle. The head juice and tail extracts were found to register very high order of enzyme activity. Metapenaeus affinis, Metapenaeus monoceros and Penaeus indicus record comparatively higher enzyme activity than Parapenaeopsis stylifera and Metapenaeus dobsoni, no definite relationship has been found between the relative activity of the enzyme and size grade at least in one species examined. Experiments were done to determine the pH optima of the enzyme and the influence of pH on its deactivation. Exposure to higher temperatures up to 55°c was shown to activate the crude enzyme considerably. The possible implications of the observations have been discussed.