Fluorescent photoaffinity labeling of cytochrome P450 3A4 by lapachenole: identification of modification sites by mass spectrometry

While photoaffinity ligands (PALs) have been widely used to probe the structures of many receptors and transporters, their effective use in the study of membrane-bound cytochrome P450s is less established. Here, lapachenole has been used as an effective photoaffinity ligand of human P450 3A4, and mass spectrometry data demonstrating the efficient and specific photoaffinity labeling of CYP3A4 by this naturally occurring benzochromene compound is presented. Without photolysis, lapachenole is a substrate of CYP3A4 and can be metabolized to hydroxylated products by this enzyme. A high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) procedure was developed to analyze small amounts of intact purified CYP3A4, and analysis of the labeled protein showed the presence of one molecule of lapachenole bound per monomer of protein. Photolabeled CYP3A4 peptide adducts were further characterized by mass spectrometric analysis after proteolytic digestion and isolation of fluorescent photolabeled peptides. Two peptide adducts accounting for >95% of the labeled peptides were isolated by HPLC, and both peptides, ECYSVFTNR (positions 97-105) and VLQNFSFKPCK (positions 459-469), were identified by nano-LC/ESI quadrupole time-of-flight (QTOF) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. The sites of modification were further localized to positions Cys-98 and Cys-468 for each peptide by nano-LC/ESI QTOF tandem mass spectrometry (MS/MS). The results provided the first direct evidence for interaction between the PAL and the putative B-B' loop region, which may serve as a substrate access channel or as a part of the CYP3A4 active site. In conclusion, benzochromene analogues are effective PALs, which may be used in the study of other cytochrome P450 structures.     

-1 frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222

The discovery of programmed -1 frameshifting at the hexanucleotide shift site CGA_AAG, in addition to the classical X_XXY_YYZ heptanucleotide shift sequences, prompted a search for instances among eubacterial insertion sequence elements. IS1222 has a CGA_AAG shift site. A genetic analysis revealed that frameshifting at this site is required for transposition.     

血液磁极化疗法对糖尿病兔胰岛功能的影响

目的观察血液磁极化疗法(简称血磁治疗)对糖尿病(DM)的治疗效果和对胰岛功能的影响。方法制备了四氧嘧啶DM兔模型20只,随机分为两组,即DM模型血磁治疗组及DM模型未治疗组,同时设立正常对照组10只,分别测定治疗前后空腹血糖(FPG)、糖化血红蛋白(HbA1c)、胰岛素(INS)及C-肽(C-P),并于观察期结束后处死动物取胰腺组织常规石蜡包埋切片,行HE及Mallory三色法特殊染色观察3组胰岛形态学变化。结果血磁治疗显著降低DM兔的FPG(P<0.001)。DM治疗组INS及C-P水平较治疗前明显升高(P<0.01),与未治疗组相比差异显著(P<0.05)。胰岛病理改变可见治疗组β细胞数量明显多于DM未治疗组,提示血磁疗法具有促进胰岛修复,改善胰岛功能的作用。结论血磁疗法能够促进DM时受损胰岛组织的修复,改善胰岛β细胞分泌功能,降血糖作用明显。     

Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

Background  

While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria, there are two RFs with overlapping specificity, RF1 recognizes UA(A/G) and RF2 recognizes U(A/G)A.     

Time-resolved fluorescence studies of heterotropic ligand binding to cytochrome P450 3A4

Cytochrome P450 3A4 (CYP3A4) is a major enzymatic determinant of drug and xenobiotic metabolism that demonstrates remarkable substrate diversity and complex kinetic properties. The complex kinetics may result, in some cases, from multiple binding of ligands within the large active site or from an effector molecule acting at a distal allosteric site. Here, the fluorescent probe TNS (2-p-toluidinylnaphthalene-6-sulfonic acid) was characterized as an active site fluorescent ligand. UV-vis difference spectroscopy revealed a TNS-induced low-spin heme absorbance spectrum with an apparent K(d) of 25.4 +/- 2 microM. Catalytic turnover using 7-benzyloxyquinoline (7-BQ) as a substrate demonstrated TNS-dependent inhibition with an IC(50) of 9.9 +/- 0.1 microM. These results suggest that TNS binds in the CYP3A4 active site. The steady-state fluorescence of TNS increased upon binding to CYP3A4, and fluorescence titrations yielded a K(d) of 22.8 +/- 1 microM. Time-resolved frequency-domain measurement of TNS fluorescence lifetimes indicates a testosterone (TST)-dependent decrease in the excited-state lifetime of TNS, concomitant with a decrease in the steady-state fluorescence intensity. In contrast, the substrate erythromycin (ERY) had no effect on TNS lifetime, while it decreased the steady-state fluorescence intensity. Together, the results suggest that TNS binds in the active site of CYP3A4, while the first equivalent of TST binds at a distant allosteric effector site. Furthermore, the results are the first to indicate that TST bound to the effector site can modulate the environment of the heterotropic ligand.     

NMR studies of ligand binding to P450(eryF) provides insight into the mechanism of cooperativity

Cytochrome P450's (P450's) catalyze the oxidative metabolism of most drugs and toxins. Although extensive studies have proven that some P450's demonstrate both homotropic and heterotropic cooperativity toward a number of substrates, the mechanistic and molecular details of P450 allostery are still not well-established. Here, we use UV/vis and heteronuclear nuclear magnetic resonance (NMR) spectroscopic techniques to study the mechanism and thermodynamics of the binding of two 9-aminophenanthrene (9-AP) and testosterone (TST) molecules to the erythromycin-metabolizing bacterial P450(eryF). UV/vis absorbance spectra of P450(eryF) demonstrated that binding occurs with apparent negative homotropic cooperativity for TST and positive homotropic cooperativity for 9-AP with Hill-equation-derived dissociation constants of K(S) = 4 and 200 microM, respectively. The broadening and shifting observed in the 2D-{1H,15N}-HSQC-monitored titrations of 15N-Phe-labeled P450(eryF) with 9-AP and TST indicated binding on intermediate and fast chemical exchange time scales, respectively, which was consistent with the Hill-equation-derived K(S) values for these two ligands. Regardless of the type of spectral perturbation observed (broadening for 9-AP and shifting for TST), the 15N-Phe NMR resonances most affected were the same in each titration, suggesting that the two ligands "contact" the same phenylalanines within the active site of P450(eryF). This finding is in agreement with X-ray crystal structures of bound P450(eryF) showing different ligands occupying similar active-site niches. Complex spectral behavior was additionally observed for a small collection of resonances in the TST titration, interpreted as multiple binding modes for the low-affinity TST molecule or multiple TST-bound P450(eryF) conformational substates. A structural and energetic model is presented that combines the energetics and structural aspects of 9-AP and TST binding derived from these observations.     

Economy of Carbon and Nitrogen in a Nodulated and Nonnodulated (NO(3)-grown) Legume

Partitioning and utilization of assimilated C and N were compared in nonnodulated, NO₃-fed and nodulated, N₂-fed plants of white lupin (Lupinus albus L.). The NO₃ regime used (5 millimolar NO₃) promoted closely similar rates of growth and N assimilation as in the symbiotic plants. Over 90% of the N absorbed by the NO₃-fed plants was judged to be reduced in roots. Empirically based models of C and N flow demonstrated that patterns of incorporation of C and N into dry matter and exchange of C and N among plant parts were essentially similar in the two forms of nutrition. NO₃-fed and N₂-fed plants transported similar types and proportions of organic solutes in xylem and phloem. Withdrawal of NO₃ supply from NO₃-fed plants led to substantial changes in assimilate partitioning, particularly in increased translocation of N from shoot to root. Nodulated plants showed a lower (57%) conversion of C or net photosynthate to dry matter than did NO₃-fed plants (69%), and their stems were only half as effective as those of NO₃-fed plants in xylem to phloem transfer of N supplied from the root. Below-ground parts of symbiotic plants consumed a larger share (58%) of the plants' net photosynthate than did NO₃-fed roots (50%), thus reflecting a higher CO₂ loss per unit of N assimilated (10.2 milligrams C/milligram N) by the nodulated root than by the root of the NO₃-fed plant (8.1 milligrams C/milligram N). Theoretical considerations indicated that the greater CO₂ output of the nodulated root involved a slightly greater expenditure for N₂ than for NO₃ assimilation, a small extra cost due to growth and maintenance of nodule tissue, and a considerably greater nonassimilatory component of respiration in root tissue of the symbiotic plant than in the root of the NO₃-fed plant.     

Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5

An AUG in an optimal nucleotide context is the preferred translation initiation site in eukaryotic cells. Interactions among translation initiation factors, including eIF1 and eIF5, govern start codon selection. Experiments described here showed that high intracellular eIF5 levels reduced the stringency of start codon selection in human cells. In contrast, high intracellular eIF1 levels increased stringency. High levels of eIF5 induced translation of inhibitory upstream open reading frames (uORFs) in eIF5 mRNA that initiate with AUG codons in conserved poor contexts. This resulted in reduced translation from the downstream eIF5 start codon, indicating that eIF5 autoregulates its own synthesis. As with eIF1, which is also autoregulated through translation initiation, features contributing to eIF5 autoregulation show deep evolutionary conservation. The results obtained provide the basis for a model in which auto- and cross-regulation of eIF5 and eIF1 translation establish a regulatory feedback loop that would stabilize the stringency of start codon selection.     

Risk assessment studies on succinate dehydrogenase inhibitors, the new weapons in the battle to control Septoria leaf blotch in wheat

Chemical control of Septoria leaf blotch, caused by Mycosphaerella graminicola, is essential to ensure wheat yield and food security in most European countries. Mycosphaerella graminicola has developed resistance to several classes of fungicide and, with the efficacy of azoles gradually declining over time, new modes of action and/or improvements in host varietal resistance are urgently needed to ensure future sustainable disease control. Several new‐generation carboxamide fungicides with broad‐spectrum activity have recently been introduced into the cereal market. Carboxamides inhibit succinate dehydrogenase (Sdh) of the mitochondrial respiratory chain (complex II) but, because of their single‐site specificity, these fungicides may be prone to resistance development. The objective of this study was to assess the risk of resistance development to different Sdh inhibitor (SDHI) fungicides in M. graminicola. UV mutagenesis was conducted to obtain a library of carboxin‐resistant mutants. A range of SDHI resistance‐conferring mutations was found in Sdh subunits B, C and D. Pathogenicity studies with a range of Sdh variants did not detect any fitness costs associated with these mutations. Most of the amino acid residues identified (e.g. B‐S221P/T, B‐H267F/L/N/Y, B‐I269V and D‐D129E/G/T) are directly involved in forming the cavity in which SDHI fungicides bind. Docking studies of SDHI fungicides in structural models of wild‐type and mutated Sdh complexes also indicated which residues were important for the binding of different SDHI fungicides and showed a different binding for fluopyram. The predictive power of the model was also shown. Further diagnostic development, enabling the detection of resistant alleles at low frequencies, and cross‐resistance studies will aid the implementation of anti‐resistance strategies to prolong the cost‐effectiveness and lifetime of SDHI fungicides.     

HIV-1 Nef binds PACS-2 to assemble a multikinase cascade that triggers major histocompatibility complex class I (MHC-I) down-regulation: analysis using short interfering RNA and knock-out mice

Human immunodeficiency virus, type 1, negative factor (Nef) initiates down-regulation of cell-surface major histocompatibility complex-I (MHC-I) by assembling an Src family kinase (SFK)-ZAP70/Syk-phosphoinositide 3-kinase (PI3K) cascade through the sequential actions of two sites, Nef EEEE(65) and PXXP(75). The internalized MHC-I molecules are then sequestered in endosomal compartments by a process requiring Nef Met(20). How Nef assembles the multikinase cascade to trigger the MHC-I down-regulation pathway is unknown. Here we report that EEEE(65)-dependent binding to the sorting protein PACS-2 targets Nef to the paranuclear region, enabling PXXP(75) to bind and activate a trans-Golgi network (TGN)-localized SFK. This SFK then phosphorylates ZAP-70 to recruit class I PI3K by interaction with the p85 C-terminal Src homology 2 domain. Using splenocytes and embryonic fibroblasts from PACS-2(-/-) mice, we confirm genetically that Nef requires PACS-2 to localize to the paranuclear region and assemble the multikinase cascade. Moreover, genetic loss of PACS-2 or inhibition of class I PI3K prevents Nef-mediated MHC-I down-regulation, demonstrating that short interfering RNA knockdown of PACS-2 phenocopies the gene knock-out. This PACS-2-dependent targeting pathway is not restricted to Nef, because PACS-2 is also required for trafficking of an endocytosed cation-independent mannose 6-phosphate receptor reporter from early endosomes to the TGN. Together, these results demonstrate PACS-2 is required for Nef action and sorting of itinerant membrane cargo in the TGN/endosomal system.