Hādhihi al-Maqāmāt al-Suyūṭīyah

li-Jalāl al-Dīn Sayyidī ʻAbd al-Raḥmān al-Suyūṭī. Mudhayyalah bi-Maqāmah li-Ḥasan al-ʻAṭṭār.

Distinctive contributions of the ribosomal P-site elements m(2)G966, m(5)C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli

The accuracy of pairing of the anticodon of the initiator tRNA (tRNA(fMet)) and the initiation codon of an mRNA, in the ribosomal P-site, is crucial for determining the translational reading frame. However, a direct role of any ribosomal element(s) in scrutinizing this pairing is unknown. The P-site elements, m(2)G966 (methylated by RsmD), m(5)C967 (methylated by RsmB) and the C-terminal tail of the protein S9 lie in the vicinity of tRNA(fMet). We investigated the role of these elements in initiation from various codons, namely, AUG, GUG, UUG, CUG, AUA, AUU, AUC and ACG with tRNA(CAU)(fmet) (tRNA(fMet) with CAU anticodon); CAC and CAU with tRNA(GUG)(fme); UAG with tRNA(GAU)(fMet) using in vivo and computational methods. Although RsmB deficiency did not impact initiation from most codons, RsmD deficiency increased initiation from AUA, CAC and CAU (2- to 3.6-fold). Deletion of the S9 C-terminal tail resulted in poorer initiation from UUG, GUG and CUG, but in increased initiation from CAC, CAU and UAC codons (up to 4-fold). Also, the S9 tail suppressed initiation with tRNA(CAU)(fMet)lacking the 3GC base pairs in the anticodon stem. These observations suggest distinctive roles of 966/967 methylations and the S9 tail in initiation.

Role of the Ribosomal P-Site Elements of m(2)G966, m(5)C967, and the S9 C-Terminal Tail in Maintenance of the Reading Frame during Translational Elongation in Escherichia coli

The ribosomal P-site hosts the peptidyl-tRNAs during translation elongation. Which P-site elements support these tRNA species to maintain codon-anticodon interactions has remained unclear. We investigated the effects of P-site features of methylations of G966, C967, and the conserved C-terminal tail sequence of Ser, Lys, and Arg (SKR) of the S9 ribosomal protein in maintenance of the translational reading frame of an mRNA. We generated Escherichia coli strains deleted for the SKR sequence in S9 ribosomal protein, RsmB (which methylates C967), and RsmD (which methylates G966) and used them to translate LacZ from its +1 and -1 out-of-frame constructs. We show that the S9 SKR tail prevents both the +1 and -1 frameshifts and plays a general role in holding the P-site tRNA/peptidyl-tRNA in place. In contrast, the G966 and C967 methylations did not make a direct contribution to the maintenance of the translational frame of an mRNA. However, deletion of rsmB in the S9 Delta 3 background caused significantly increased -1 frameshifting at 37 degrees C. Interestingly, the effects of the deficiency of C967 methylation were annulled when the E. coli strain was grown at 30 degrees C, supporting its context-dependent role.

The molecular characterization of RNA segment S9 of grass carp hemorrhage virus (GCHV), an aquareovirus

Although reovirus infection is one of the major virus diseases of grass carp in China, the available knowledge on the structure and function of genes and proteins of the virus is limited. The complete sequence of the S9 genome segment of grass carp hemorrhage virus (GCHV) was determined. The segment consists of 1130 nucleotides and has a large open reading frame (ORF) encoding a protein of 352 amino acids with predicted molecular mass of 37.7 kDa. Amino acid sequence comparison revealed that the deduced protein encoded by GCHV S9 is closely related to the sigma NS proteins of mammalian reovirus (MRV) and avian reovirus (ARV). Secondary structure analysis displayed that the form of alpha -helices (40.1%) and beta -sheets (49.4%) are the richest two contents in the protein encoded by S9, and this protein is predicted to be a nonstructural protein. (C) 2001 Elsevier Science B.V. All rights reserved.

In Vitro Ketamine CYP3A Mediated Metabolism Study using Mammalian Liver S9 Fractions, cDNA Expressed Enzymes and Liquid Chromatography Tandem Mass Spectrometry

Ketamine is widely used in medicine in combination with several benzodiazepines including midazolam. The objectives of this study were to develop a novel HPLC-MS/SRM method capable of quantifying ketamine and norketamine using an isotopic dilution strategy in biological matrices and study the formation of norketamine, the principal metabolite of ketamine with and without the presence of midazolam, a well-known CYP3A substrate. The chromatographic separation was achieved using a Thermo Betasil Phenyl 100 x 2 mm column combined with an isocratic mobile phase composed of acetonitrile, methanol, water and formic acid (60:20:20:0.4) at a flow rate of 300 μL/min. The mass spectrometer was operating in selected reaction monitoring mode and the analytical range was set at 0.05–50 μM. The precision (%CV) and accuracy (%NOM) observed were ranging from 3.9–7.8 and 95.9.2–111.1% respectively. The initial rate of formation of norketamine was determined using various ketamine concentration and Km values of 18.4 μM, 13.8 μM and 30.8 μM for rat, dog and human liver S9 fractions were observed respectively. The metabolic stability of ketamine on liver S9 fractions was significantly higher in human (T1/2 = 159.4 min) compared with rat (T1/2 = 12.6 min) and dog (T1/2 = 7.3 min) liver S9 fractions. Moreover significantly lower IC50 and Ki values observed in human compared with rat and dog liver S9 fractions. Experiments with cDNA expressed CYP3A enzymes showed the formation of norketamine is mediated by CYP3A but results suggest an important contribution from others isoenzymes, most likely CYP2C particularly in rat.

Effects of liver S9 enzymes on somalargine and solasodine cytotoxicity and mass spectrometric fragmentation

The steroidal glycoalkaloid solamargine and its parent aglycone solasodine, isolated from Solanum palinacanthum, were studied in vitro for cytotoxicity and biotransformation by the hepatic S9 fraction as the metabolic activating system. The MTT uptake assay was used to determine viability after 24 h in RAW 264.7 mouse macrophage-like and SiHa cells exposed to various concentrations of the alkaloids in the presence and absence of the hepatic S9 microsomal fraction. The dose-response curves were established for solamargine and solasodine in the presence and absence of external metabolizing system. From these data, the cytotoxic index (CI50) was calculated with mean values of 7.2 and 13.6 μg/mL for Raw cells and 8.6 and 26.0 μg/mL for SiHa cells, respectively. Mass spectrometry was performed to compare the fragmentation patterns of the alkaloids to predict metabolism by the S9 fraction. The mass spectra demonstrated a distinct fragmentation patterns for solamargine and solasodine after the addition of the S9 fraction. In the present study, we demonstrate that the cytotoxic effect of solamargine and solasodine and their metabolites prepared in vitro by biotransformation with the S9 fraction are comparable. These findings suggest that the metabolic activation system S9 fraction may fail to suppress the cytotoxicity of these alkaloids. © 2013 Springer-Verlag Berlin Heidelberg.

Effect of biotransformation by liver S9 enzymes on the mutagenicity and cytotoxicity of melanin extracted from Aspergillus nidulans

A mutant that exhibited increased melanin pigment production was isolated from Aspergillus nidulans fungus. This pigment has aroused biotechnological interest due to its photoprotector and antioxidant properties. In a recent study, we showed that melanin from A. nidulans also inhibits NO and TNF-α production. The present study evaluates the mutagenicity and cytotoxicity of melanin extracted from A. nidulans after its exposure to liver S9 enzymes. The cytotoxicity of multiple concentrations of melanin (31.2-500 μg/mL) against the McCoy cell line was evaluated using the Neutral Red assay, after incubation for 24 h. Mutagenicity was assessed using the Ames test with the Salmonella typhimurium strains TA98, TA97a, TA100, and TA102 at concentrations ranging from 125 μg/plate to 1 mg/plate after incubation for 48 h. The cytotoxicity of A. nidulans melanin after incubation with S9 enzymes was less than (CI50 value= 413.4 ± 3.1 μg/mL) that of other toxins, such as cyclophosphamide (CI50 value = 15 ± 1.2 μg/mL), suggesting that even the metabolised pigment does not cause significant damage to cellular components at concentrations up to 100 μg/mL. In addition, melanin did not exhibit mutagenic properties against the TA 97a, TA 98, TA 100, or TA 102 strains of S. typhimurium, as shown by a mutagenic index (MI)  <2 in all assays. The significance of these results supports the use of melanin as a therapeutic reagent because it possesses low cytotoxicity and mutagenic potential, even when processed through an external metabolising system.

Assessment of metabolic stability using the rainbow trout (Oncorhynchus mykiss) liver S9 fraction

Standard protocols are given for assessing metabolic stability in rainbow trout using the liver S9 fraction. These protocols describe the isolation of S9 fractions from trout livers, evaluation of metabolic stability using a substrate depletion approach, and expression of the result as in vivo intrinsic clearance. Additional guidance is provided on the care and handling of test animals, design and interpretation of preliminary studies, and development of analytical methods. Although initially developed to predict metabolism impacts on chemical accumulation by fish, these procedures can be used to support a broad range of scientific and risk assessment activities including evaluation of emerging chemical contaminants and improved interpretation of toxicity testing results. These protocols have been designed for rainbow trout and can be adapted to other species as long as species-specific considerations are modified accordingly (e.g., fish maintenance and incubation mixture temperature). Rainbow trout is a cold-water species. Protocols for other species (e.g., carp, a warm-water species) can be developed based on these procedures as long as the specific considerations are taken into account.