Geraniol prevents CCl4-induced hepatotoxicity via suppression of hepatic oxidative stress, pro-inflammation and apoptosis in rats

Carbon tetrachloride (CCl4) is a classic chemical hepatotoxicant that triggers liver damage through hepatic exacerbation of oxidative stress. Geraniol (GRL) is a natural bioactive acyclic monoterpene with several pharmacological effects. We thus explored whether GRL could prevent CCl4-triggered hepatic toxicity. Rats were divided and administered GRL (100 mg/kg) and/or CCl4 (1 ml/kg of 1:1 v/v CCl4: olive oil) in Control group, GRL group, CCl4 group, GRL + CCl4 groups 2 times per week for 4 consecutive weeks. CCl4 caused significantly (p < 0.05) elevated serum activities of alkaline phosphatase (ALP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), and total bilirubin (TB), whereas the albumin (ALB) and total protein (TP) levels were significantly (p < 0.05) reduced relative to the control group. The liver activities of catalase (CAT), glutathione peroxidase (GPx), and superoxide dismutase (SOD) decreased significantly (p < 0.05), while malondialdehyde (MDA) level evidently elevated in comparison to the control group. The CCl4 exposure caused significant increases in proinflammatory interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α), apoptotic caspase-3 and caspase-9 levels, whereas the anti-inflammatory interleukin-4 (IL-4) and interleukin-10 (IL-10) were reduced in consistent with histopathological changes compared to the control. On the contrary, the GRL administration prevented the hepatic toxicity and lesions through restoration of liver status markers, antioxidant enzyme activities, MDA, cytokines and apoptosis in comparison to the CCl4 group. Altogether, the findings reveal that GRL could abrogate CCl4-provoked hepatic toxicity via inhibition of hepatic oxidative stress, inflammation and apoptosis in rats.

Properties of Recycled Nanomaterials and Their Effect on Biological Activity and Yield of Canola in Degraded Soils

Recycling waste, such as rice straw and water treatment residuals, is important to reduce harmful effects on the environment and to improve canola yield and soil quality in degraded soils. Nanotechnology for the production of nanomaterials from biochar and water treatment residues will be a future revolution for improving soil quality and increasing canola yield in degraded soil. Therefore, this study aims to identify the properties of some recycled nanomaterials, such as nanobiochar (nB) and nanowater treatment residue (nWTR), and their effect on the biological activity and productivity of canola in degraded soils. The results showed that the nWTR and nB contain many functional groups and minerals, and they also have high negative zeta potential. The addition of the studied soil amendments significantly improved microbial biomass carbon (MBC) and biological activity, which played a major role in increasing canola yield. The highest dehydrogenase (DHA) and catalase (CLA) activity was found in nWTR-treated soil at 50 mg kg−1, with increases of 32.8% and 566.7% compared to the control, respectively. The addition of nB greatly improved the growth of canola plants in the soil. This was evident from the increase in the weight of seeds, the weight of 1000 grains, the number of pods per plant, and the highest increase was for nB added at the rate of 250 mg per kg−1 soil. The addition of 50 mg kg−1 of nWTR gave the best results in seed yield by 150.64% compared to the control. These results indicate that recycled nWTR and nB are some of the best waste recycling treatments, in addition to good soil health, in increasing soil biology and canola yield in degraded soils. In the future, research on recycled nanomaterials should examine the residual effect they have on yield, soil quality, and soil fauna in the long term.

Beneficial role of naringin against methotrexate-induced injury to rat testes: biochemical and ultrastructural analyses

Background

Methotrexate (MTX) is a commonly used chemotherapeutic drug that has adverse toxic effects on germ cells. Naringin (NG) is a natural flavanone glycoside, with different phytotherapeutic applications, and its possible protective effects against MTX-induced testicular tissue damage were investigated in this study.

Methods

Low and high doses of NG (40 and 80 mg/kg/day) were given for 10 days by intraperitoneal (i.p.) injection and MTX (20 mg/kg i.p.) was given at the 4th day of the experiment, with or without NG in rats.

Results

The obtained results showed that exposure to MTX increased malondialdehyde (MDA) levels and nitric oxide (NO) production compared with the control. In the meantime, MTX depleted catalse (CAT), superoxide dismutase (SOD), glutathione reductase (GR), glutathione peroxidase (GPx), and reduced glutathione (GSH) in the testicular tissue. Further, serum testosterone levels were significantly decreased in the MTX group. NG significantly counteracted the aforementioned effects of MTX; however, NG80 was more effective in restoring SOD, GR, MDA and NO. Interestingly, NG80 achieved a better improvement in the ultrastructural pattern of the testicular cells in MTX-exposed rats.

Conclusion

These results indicated, for the first time, that NG could be a potential candidate therapy against MTX-reprotoxic impacts.

Acacetin Inhibits Cell Proliferation and Induces Apoptosis in Human Hepatocellular Carcinoma Cell Lines

Human hepatocellular carcinoma (HCC) is the fifth most common cancer and the third leading cause of death across the world. Recent evidence suggests that STAT3 regulates proliferative, survival, metastasis, and angiogenesis genes in HCC. Novel agents that suppress STAT3 activation can be used to prevent or treat HCC. We used a functional proteomics tumor pathway technology platform and multiple HCC cell lines to investigate the effects of acacetin (ACN) on STAT3 activation, protein kinases, phosphatases, products of STAT3-regulated genes, and apoptosis. ACN was found to inhibit STAT3 activation in a dose- and time-dependent manner in HCC cells. Upstream kinases c-Src, Janus-activated kinase 1, and Janus-activated kinase 2 were also inhibited. The ACN inhibition of STAT3 was abolished by vanadate treatment, suggesting the involvement of tyrosine phosphatase activity. ACN was found to suppress the protein expression of genes involved in proliferation, survival, and angiogenesis via STAT3 inhibition. ACN appears to be a novel STAT3 inhibitor and may be a promising therapeutic compound for application in the treatment of HCC and other cancers.

Color-switchable and photoluminescent poly (vinyl chloride) for multifunctional smart applications

Recycled poly (vinyl chloride) (PVC) waste was used to prepare transparent material with long-lasting phosphorescence, photochromic activity, hydrophobicity, strong optical transmission, ultraviolet (UV) protection, and stiffness. Lanthanide-activated aluminate (LaA) microparticles were prepared via the high temperature solid state procedure, which were subjected to the top-down grinding technology to afford LaA nanoparticles (LaAN). Laminated poly (vinyl chloride) bottles were shredded into a transparent plastic matrix, which was combined with LaAN and drop-casted to produce smart materials for a variety of applications. Smart window and photochromic film for smart packaging can be made from recycled poly (vinyl chloride) waste by immobilizing it with various ratios of LaAN. Long-lasting phosphorescent translucent poly (vinyl chloride) smart window and films need LaAN to be evenly dispersed in PVC without clumping. Different analytical methods were employed to assess the materials' morphological structure and chemical composition. Photoluminescence and decay spectra were all employed to investigate the luminescence characteristics. In addition, the mechanical performance was studied. According to CIE Lab (Commission Internationale de L'éclairage) color measurements, this transparent PVC smart material becomes a bright green under UV rays and turns a greenish-yellow in the dark. The PVC luminescence was observed to exhibit an apparent emission bands at 429 and 513 nm when excited at 367 nm. Improvements have been monitored in the UV shielding and hydrophobicity with increasing the phosphor concentration. LaAN-immobilized PVC exhibited reversible photochromism. The present approach can be applied for a variety of applications, such as anticounterfeiting films for smart packaging, smart window, and warning lightening marks.

Design, Synthesis, and Biological Evaluations of Novel Azothiazoles Based on Thioamide

Herein we studied the preparation of different thiazoles via the reaction of 2-(3,4-dimethoxybenzylidene)hydrazine-1-carbothioamide (1) with hydrazonoyl halides under base-catalyzed conditions. The reactions proceed through nucleophilic substitution attack at the halogen atom of the hydrazonoyl halides by the thiol nucleophile to form an S-alkylated intermediate. The latter intermediate undergoes cyclization by the loss of water to afford the final products. The structures of the azo compounds were confirmed by FTIR, MS, NMR, and elemental analyses. Indeed, the newly synthesized azo compounds were estimated for their potential anticancer activities by an MTT assay against different human cancer cells, such as lung adenocarcinoma (A549) and colorectal adenocarcinoma (DLD-1). The caspase-3 levels were also estimated using Western blotting and the dual staining technique to evaluate the potency of the titled compounds to promote apoptosis.

In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury

Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid peroxidation, and inhibition of inflammation and cardiac cell death.

Ruscogenin protects against deoxynivalenol-Induced hepatic injury by inhibiting oxidative stress, inflammation, and apoptosis through the Nrf2 signaling pathway: An In vitro study

Background

Deoxynivalenol (DON) is a trichothecene mycotoxin with demonstrated cytotoxicity in several cell lines and animals, primarily owing to inflammation and reactive oxygen species accumulation. Ruscogenin (RGN), a steroidal sapogenin of Radix Ophiopogon japonicus, has significant anti-thrombotic/anti-inflammatory effects.

Objective:

The aim of this study was to assess the protective role of RGN against DON-induced oxidative stress, which occurs through the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway and is regulated by phosphoinositide 3-kinases/protein kinase B (PI3K/AKT).

Methods:

The effects were examined using the HepG2 cell line. RGN and DON were suspended in serum-free medium. Cells were seeded onto plates, and then RGN, DON, or both were added over 24 h in triplicates for each group.

Results:

RGN conferred protection against DON-exhibited cytotoxicity against HepG2 cells. RGN pretreatment downregulated the expression of DON-induced TNF-α and COX-2 and the formation of reactive oxygen species in a dose-dependent manner. RGN upregulated the expression of Nrf2 and its antioxidant proteins as well as mRNA levels of HO-1/NQO-1/HO-1/Nrf2. Similarly, treatment with DON + RGN resulted in upregulation of the pI3K/pAKT signaling pathway in a dose-dependent manner. Finally, RGN was also found to inhibit the DON-induced apoptosis by upregulating the levels of cleaved proteins and downregulating the expression of Bcl2.

Conclusion:

The study demonstrates that RGN suppresses hepatic cell injury induced by oxidative stress through Nrf2 via activation of the pI3K/AKT signaling pathway.

Nephroprotective effect of naringin in methotrexate induced renal toxicity in male rats

The current work aims to study the nephroprotective potential of naringin (NG), a flavanone derived from citrus fruits, in methotrexate (MTX)-induced renal toxicity. Thirty male rats were divided into five groups; control group (IP saline), MTX group (IP single dose, 20 mg/kg), and three groups co-treated with MTX and naringin (IP daily dose; 20, 40, and 80 mg/kg, respectively). Kidney tissues were used to investigate renal function, oxidative stress, lipid peroxidation, and caspase-3 activity. Biochemical cytokine analysis was performed in addition to ultrastructural examinations of kidney tissue. When compared to the MTX-treated rats, MTX+NG significantly reduced the levels of urea, creatinine, MDA, NO, TNFα, IL-6, and caspase-3 activity. A significant increase in the levels of the antioxidant enzymes and GSH were also noted. Additionally, naringin ameliorated the apparent ultrastructural changes observed in the glomeruli and renal tubules of MTX-intoxicated rats. Noticeable structural improvements of glomerular lesions, proximal, and distal convoluted tubular epithelium were observed in MTX+NG treated animals, including podocytes with regular foot processes, perfectly organized filtration barrier, no signs of GBM thickening, organized brush border, and normal architecture of microvilli. Naringin (80 mg/kg) had the maximum amelioration effect. To the best of our knowledge, this is the first study to investigate the ultrastructural manifestations of naringin and/or MTX on the kidney of rats. Taken all, naringin has a potent therapeutic effect and can be used in adjuvant therapy to prevent MTX-induced nephrotoxicity. Nevertheless, the molecular mechanism underlying the nephroprotective capacity of naringin needs further investigation.

Analysis of silymarin-modulating effects against acrylamide-induced cerebellar damage in male rats: Biochemical and pathological markers

BACKGROUND

Acrylamide (ACR) is a well-proven neurotoxin and potential food carcinogen in humans and rodent models. Silymarin (SIL) is a flavonoid mixture isolated from seeds, leaves, and fruits of Silymarin marianum (milk thistle) that possesses a free-radical scavenging effect.

OBJECTIVE

In this work, the primary focus was to investigate the efficacy of SIL to mitigate ACR-induced subacute neurotoxic effects and oxidative changes in rat cerebellum.

METHODS

Adult male rats were treated intraperitoneally with ACR (50 mg/kg) with or without SIL (160 mg/kg). The neuropathology and biochemical parameters viz. lipid peroxidation (measured as levels of malondialdehyde or MDA), catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), serotonin (5-hydroxytryptamine; 5-HT), dopamine (DA), and cathepsin D (CTSD) in the cerebellum have been evaluated.

RESULTS

The data showed that ACR induced redox disruptions as measured by increased MDA levels and inhibition of CAT, SOD, and GPx antioxidant enzyme activities. Besides, cerebellar monoamine neurotransmitters, 5-HT and DA, were depleted in ACR-treated rats. Furthermore, ACR administration caused a significant elevation of CTSD activity, indicating that ACR could trigger apoptosis or apoptosis-like death. At the tissue level, cerebellar cortex sections from ACR-treated animals were characterized by severe neuronal damage. The administration of SIL to ACR-treated rats remarkably alleviated all the aforementioned ACR-induced effects.

CONCLUSION

SIL has a potent therapeutic effect against ACR-induced cerebellar neurotoxicity in experimental rats via the attenuation of oxidative/antioxidative responses and the inhibition of CTSD-activity.

Somatic Cancer Mutations in the SUV420H1 Protein Lysine Methyltransferase Modulate Its Catalytic Activity

SUV420H1 is a protein lysine methyltransferase that introduces di- and trimethylation of H4K20 and is frequently mutated in human cancers. We investigated the functional effects of eight somatic cancer mutations on SUV420H1 activity in vitro and in cells. One group of mutations (S255F, K258E, A269V) caused a reduction of the catalytic activity on peptide and nucleosome substrates. The mutated amino acids have putative roles in AdoMet binding and recognition of H4 residue D24. Group 2 mutations (E238V, D249N, E320K) caused a reduction of activity on peptide substrates, which was partially recovered when using nucleosomal substrates. The corresponding residues could have direct or indirect roles in peptide and AdoMet binding, but the effects of the mutations can be overcome by additional interactions between SUV420H1 and the nucleosome substrate. The third group of mutations (S283L, S304Y) showed enhanced activity with peptide substrates when compared with nucleosomal substrates, suggesting that these residues are involved in nucleosomal interaction or allosteric activation of SUV420H1 after nucleosome binding. Group 2 and 3 mutants highlight the role of nucleosomal contacts for SUV420H1 regulation in agreement with the high activity of this enzyme on nucleosomal substrates. Strikingly, seven of the somatic cancer mutations studied here led to a reduction of the catalytic activity of SUV420H1 in cells, suggesting that SUV420H1 activity might have a tumor suppressive function. This could be explained by the role of H4K20me2/3 in DNA repair, suggesting that loss or reduction of SUV420H1 activity could contribute to a mutator phenotype in cancer cells.

Rutin ameliorates carbon tetrachloride (CCl4)-induced hepatorenal toxicity and hypogonadism in male rats

Rutin, a food derived-polyphenolic bioflavonoid, has been acknowledged for several health benefits. This study aims to explore the ameliorative effects of rutin against carbon tetrachloride (CCl4) toxicity in male rats. Adult male rats were given either CCl4 (30% in olive oil, 3 ml/kg b.w. intraperitoneally) alone or in combination with rutin (70 mg/kg intragastrically) twice a week for 4 weeks. Our data showed that rutin mitigated CCl4 hepatorenal damage, as indicated by diagnostic markers (i.e., transaminases, alkaline phosphatase, total bilirubin, total protein, albumin, urea, uric acid and creatinine), and histopathological findings. In addition, CCl4 induced profound elevation of free radical generation and oxidative stress, as evidenced by increasing lipid peroxidation and reducing catalase, superoxide dismutase and glutathione peroxidase activities in liver, kidney and testicular tissues; these effects were suppressed by coexposure with rutin. Moreover, the increase in the levels of serum triglycerides, cholesterol, low-density lipoprotein cholesterol, and very-low-density lipoprotein cholesterol induced by CCl4 was effectively counteracted by rutin. The decrease in the level of high-density lipoprotein cholesterol in the CCl4 group was also counteracted by rutin treatment. Interestingly, the decreased levels of hormonal mediators associated with sperm production, including serum testosterone, luteinizing hormone and follicle-stimulating hormone, and the impaired sperm quality induced by CCl4 were reversed by rutin. Data from the current study clearly demonstrated that rutin supplementation could at least partly overcome CCl4-induced hepatotoxicity, nephrotoxicity and reproductive toxicity by antioxidant and antidyslipidemic effects.

Protective effects of quercetin supplementation against short-term toxicity of cadmium-induced hematological impairment, hypothyroidism, and testicular disturbances in albino rats

The aim of this study was to evaluate the probable protective effect of quercetin (QUE) against cadmium (Cd)-induced sub-chronic toxicity in rats. Adult male rats were given either Cd (as cadmium chloride; 5 mg/kg) alone or in combination with QUE (50 mg/kg) daily for 4 weeks by oral gavage. At the end of the experimental period, Cd accumulation, and selected hematological, thyroid, and reproductive markers were assessed. Results revealed that Cd treatment significantly increased Cd concentrations in blood, thyroid gland, and testicular tissue of rats. Cd also caused a decline in hemoglobin content, hematocrit value, and total erythrocyte and leucocyte counts. Further, significant suppressions in the blood levels of hormones related to thyroid gland function, and male reproductive hormones (i.e., testosterone, luteinizing hormone and follicle-stimulating hormone), were observed in Cd-treated rats compared to the control. In parallel, low sperm count and sperm motility, increased sperm abnormalities, and marked pathology occurred in testis. Combination with QUE recorded amelioration of the deleterious effects of Cd, involving regulation of hematological toxicity and thyroid hormonal levels and subsequently modulation of testicular function. In conclusion, it appears that dietary QUE can rescue from Cd-induced hematological dysfunctions and testicular damage by reversing the hypothyroid state.

Monitoring metal levels in water and multiple biomarkers in the grouper ( Epinephelus tauvina) to assess environmental stressors on the Arabian Gulf coast of Saudi Arabia

In this field study, the levels of heavy metals (Pb, Fe, Co, Cu, and Zn) in water and a suite of biochemical and histological biomarkers in the grouper ( Epinephelus tauvina) were assessed at four sites in the Arabian Gulf. Samples were taken from a relatively non-urban reference site, called Salwa (S1), and three effluent-dominated sites, namely Al-aziziyah in southern Dammam city (S2), the Al-Jubail coast (S3), and Manifa (S4). Toxic metals, namely Pb and Co (at all sites) and Fe (at S3), were elevated in water samples relative to the internationally permissible limits. In fish, induced levels of heat shock protein 70 (HSP70) in the liver at S3 and S4 were higher than those of the reference fish at S1. Additionally, the level of the lipid peroxidation (LPO) product (malondialdehyde (MDA)) was significantly increased in gills (at S3) and liver (at S2 and S3). There was an inhibition of catalase activities in the gills of fish from S2 to S4 and significantly higher activity levels of superoxide dismutase in the gills of fish from S4. Histopathological features such as aneurysms in gill vessels, deformed gill lamellae, increases in liver melano-macrophage centers, and hepatocellular necrosis were most abundant at sites where significant pollution problems exist (i.e. S2-S4). The results reveal that the eastern coast of Saudi Arabia, in the Arabian Gulf, is still contaminated, as indicated by elevated HSP70, LPO content and numbers of histological lesions, and that monitoring of contaminants and their effects should be continued in this region.

Synthesis, antimicrobial, DNA cleavage and antioxidant activities of tricyclic sultams derived from saccharin

Two series of fused tricyclic sultams (carboxylates, 3a, b and 5a, f, g and anilides 5b-e) were synthesized from saccharin and their chemical structures were confirmed by spectroscopic tools. Then, their antibacterial activities and MIC were evaluated against two strains of gram positive and gram-negative bacteria. The MIC values of the tested compounds are in the of range 8-33 μg/ml. In addition, their DNA cleavage ability, binding affinity and their anticancer activities against hepatic cancer cell were tested. And their antioxidant activities were also measured. Four carboxylate derivatives (3a, 5a, 5f and 5g) and one anilide (5d) of the tested compounds proved to be the highest activity all over the study.

Ameliorative potentials of quercetin against lead-induced hematological and testicular alterations in Albino rats

Lead is one of the oldest environmental and occupational toxins. Health hazards from increased lead exposure as a result of industrial and environmental pollution are recognized. The aim of the present study was to investigate the protective effects of quercetin as a model of an antioxidant drug against the toxic effects of lead acetate on the blood and the testis of rats. The lead concentrations were determined in blood and the testis. Testosterone (T), luteinizing hormone (LH) and follicle stimulating hormone (FSH) were assessed in serum. Hemoglobin (Hb) content, packed cell volume (PCV), white blood cell (WBC) and red blood cell (RBC) counts were evaluated in the whole blood. Our results showed that administration of lead acetate was associated with an increased lead levels in blood as well as in the testis. Lead acetate administration also caused a decrease in testicular function, Hb content, PCV and RBC count in comparison to the respective mean values of the control. In addition, lead acetate increased WBC count and induced alterations in sperm count, sperm motility and sperm abnormality and histopathology. In the contrary, administration of lead acetate along with quercetin partially restored the studied parameters to normal values. In conclusion, the treatment with quercetin may provide a partial protection against the toxic effects induced by lead acetate in blood and the testis of rats.

Increasing DNA substrate specificity of the EcoDam DNA-(adenine N(6))-methyltransferase by site-directed mutagenesis

DNA methylation catalyzed by DNA methyltransferases (MTases) is widespread in prokaryotes. In an attempt to find EcoDam variants with enhanced preference for hemimethylated DNA, the L122, P134, and V133 residues were replaced with other amino acids using site directed mutagenesis, and the catalytic activity of all variants on unmethylated and hemimethylated substrates was studied. Our results showed that, in addition to L122A, the L122S and L122A/V133L EcoDam variants were able to sense the methylation status of the 5'-GATC-3' double-stranded target recognition site and methylated only hemimethylated DNA.

Transition from EcoDam to T4Dam DNA recognition mechanism without loss of activity and specificity

The EcoDam and T4Dam DNA-(adenine N6)-methyltransferases both methylate the adenine residue in GATC sites. These enzymes are highly related in amino acid sequence, but they deviate in their contact to the first base pair of the target sequence. EcoDam contacts Gua1 with K9 (which corresponds to T4Dam A6), while T4Dam contacts Gua1 with R130 (which corresponds to EcoDam Y138). We have "transplanted" the T4Dam DNA recognition into EcoDam and show that the EcoDam K9A/Y138R double mutant is highly active and specific. We also studied the intermediates of this transition: The EcoDam K9A variant showed low activity and loss of recognition of Gua1 [Horton, et al., J. Mol. Biol. 2006, 358, 559-570]. In contrast, the EcoDam Y138R variant, which carries both Gua1 recognition elements (K9 from EcoDam and R138 corresponding to R130 from T4Dam), is fully active and specific. This result indicates that a smooth evolutionary pathway exists for changing the EcoDam DNA recognition mode to T4Dam without loss of activity and without generation of evolutionary intermediates with reduced activity. We consistently observed increased activity of EcoDam variants containing Y138R; this suggests that the transition from EcoDam (Gua1 recognition through K9) to T4Dam (Gua1 recognition through R130) was driven by selective pressure towards increased catalytic activity.

Changing the DNA recognition specificity of the EcoDam DNA-(adenine-N6)-methyltransferase by directed evolution

EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the Escherichia coli genome. We have changed the target specificity of EcoDam from GATC to GATT by directed evolution, combining different random mutagenesis methods with restriction protection at GATT sites for selection and screening. By co-evolution of an enzyme library and a substrate library, we identified GATT as the best non-GATC site and discover a double mutation, R124S/P134S, as the first step to increase enzyme activity at GATT sites. After four generations of mutagenesis and selection, we obtained enzyme variants with new specificity for GATT. While the wild-type EcoDam shows no detectable activity at GATT sites in E. coli cells, some variants prefer methylation at GATT over GATC sites by about 10-fold in cells. In vitro DNA methylation kinetics carried out under single-turnover conditions using a hemimethylated GATC and a GATT oligonucleotide substrate confirmed that the evolved proteins prefer methylation of GATT sites to a similar degree. They show up to 1600-fold change in specificity in vitro and methylate the new GATT target site with 20% of the rate of GATC methylation by the wild-type enzyme, indicating good activity. We conclude that the new methyltransferases are fully functional in vivo and in vitro but show a new target-site specificity.