Mechanism of a GatCAB amidotransferase: aspartyl-tRNA synthetase increases its affinity for Asp-tRNA(Asn) and novel aminoacyl-tRNA analogues are competitive inhibitors

The trimeric GatCAB aminoacyl-tRNA amidotransferases catalyze the amidation of Asp-tRNAAsn and/or Glu-tRNAGln to Asn-tRNAAsn and/or Gln-tRNAGln, respectively, in bacteria and archaea lacking an asparaginyl-tRNA synthetase and/or a glutaminyl-tRNA synthetase. The two misacylated tRNA substrates of these amidotransferases are formed by the action of nondiscriminating aspartyl-tRNA synthetases and glutamyl-tRNA synthetases. We report here that the presence of a physiological concentration of a nondiscriminating aspartyl-tRNA synthetase in the transamidation assay decreases the Km of GatCAB for Asp-tRNAAsn. These conditions, which were practical for the testing of potential inhibitors of GatCAB, also allowed us to discover and characterize two novel inhibitors, aspartycin and glutamycin. These analogues of the 3'-ends of Asp-tRNA and Glu-tRNA, respectively, are competitive inhibitors of the transamidase activity of Helicobacter pylori GatCAB with respect to Asp-tRNAAsn, with Ki values of 134 microM and 105 microM, respectively. Although the 3' end of aspartycin is similar to the 3' end of Asp-tRNAAsn, this analogue was neither phosphorylated nor transamidated by GatCAB. These novel inhibitors could be used as lead compounds for designing new types of antibiotics targeting GatCABs, since the indirect pathway for Asn-tRNAAsn or Gln-tRNAGln synthesis catalyzed by these enzymes is not present in eukaryotes and is essential for the survival of the above-mentioned bacteria.     

Tolerable amounts of amino acids for human supplementation: summary and lessons from published peer-reviewed studies

Amino acid supplementation may be indicated to correct for insufficient amino acid intake in healthy individuals, and in specific physiological or pathophysiological situations. However, there is a concern to not supplement beyond the tolerable upper intake level (UL) by determining parameters of no-observed-adverse-effect level (NOAEL) or lowest-observed-adverse-effect level (LOAEL) for each amino acid. Since the NOAEL and LOAEL values are at least one order of magnitude different when comparing the values obtained in rats and humans, the aim of this review is to evaluate to what extent the amino acid UL measured in the rat model, when referenced to the dietary usual consumption (UC) and dietary requirement (RQ) for indispensable amino acids, may be used as an approximation of the UL in humans. This review then compares the ratios of the NOAEL or LOAEL over UC and RQ in the rat model with the same ratios calculated in humans for the nine amino acids (arginine, serine, glycine, histidine, leucine, lysine, methionine, phenylalanine, and tryptophan) for which this comparison can be done. From the calculations made, it appears that for these 9 amino acids, the calculated ratios for rats and humans, although rather different for several amino acids, remains for all of them in the same order of magnitude. For tryptophan, tyrosine, and valine, the ratios calculated in rats are markedly different according to the sex of animals, raising the view that it may be also the case in humans.

     

Optimization of Operating Parameters for the Selective Flotation of Heavy Metals from Contaminated Fine Sediment Using Response Surface Model

In this study, the effect of different flotation operating variables, such as pH, pulp density, collector concentration, impeller speed, frother concentration, and air flow rate, on selective flotation of heavy metals, especially Cu, from fine dredged sediment has been evaluated. Parameter optimization was done using the single parameter at a time method and response surface method (RSM) using Box-Behnken design and was assessed in terms of metal removal, metal recovery, metal concentration factor, and mass recovery. Among the operating variables studied, pulp pH, collector concentration, pulp density, and impeller speed were found to have significant effect on metal flotation selectivity. A validation study of the response surface model showed its aptness to predict the optimum values of operating parameters and their interactions on flotation responses which evaluate flotation performance. Flotation experiments under optimum operating parameters showed good flotation selectivity for Cu (3.3 ± 0.2) with a mass recovery of (mass of sediment in the froth) 14.1 ± 1 and Cu removal of 37.4 ± 3.6%.     

A Thirteen-Gene Expression Signature Predicts Survival of Patients with Pancreatic Cancer and Identifies New Genes of Interest

Background

Currently, prognostication for pancreatic ductal adenocarcinoma (PDAC) is based upon a coarse clinical staging system. Thus, more accurate prognostic tests are needed for PDAC patients to aid treatment decisions.

Methods and Findings

Affymetrix gene expression profiling was carried out on 15 human PDAC tumors and from the data we identified a 13-gene expression signature (risk score) that correlated with patient survival. The gene expression risk score was then independently validated using published gene expression data and survival data for an additional 101 patients with pancreatic cancer. Patients with high-risk scores had significantly higher risk of death compared to patients with low-risk scores (HR 2.27, p = 0.002). When the 13-gene score was combined with lymph node status the risk-score further discriminated the length of patient survival time (p<0.001). Patients with a high-risk score had poor survival independent of nodal status; however, nodal status increased predictability for survival in patients with a low-risk gene signature score (low-risk N1 vs. low-risk N0: HR = 2.0, p = 0.002). While AJCC stage correlated with patient survival (p = 0.03), the 13-gene score was superior at predicting survival. Of the 13 genes comprising the predictive model, four have been shown to be important in PDAC, six are unreported in PDAC but important in other cancers, and three are unreported in any cancer.

Conclusions

We identified a 13-gene expression signature that predicts survival of PDAC patients and could prove useful for making treatment decisions. This risk score should be evaluated prospectively in clinical trials for prognostication and for predicting response to chemotherapy. Investigation of new genes identified in our model may lead to novel therapeutic targets.     

Fate and Persistence of Particulate and Dissolved Microcystin-LA from Microcystis Blooms

Few studies have estimated fate and persistence of the hepatotoxic microcystins (MCs) in situ, making ecological and human health risk assessments challenging. We determined fate and persistence of MC congeners during 2 years of Microcystis blooms in a small, shallow, closed-basin lake in Ontario, Canada. In situ half-lives were compared to estimates obtained in vitro under controlled temperature and light. The blooms produced elevated microcystin-LA (MC-LA) (maximum ～4.2 mg L^?1) with minor concentrations of MC-LR, -RR, and -YR. Dissolved MC-LA declined more slowly and persisted longer than particulate MC-LA with in situ half-lives (total 1.5–8.5 days) shorter than in vitro (total 6.8–60.0 days). Half-lives in 2010 were two to eight times shorter compared to 2009, likely due to differences in bloom phenology and species/strain composition. In vitro, higher temperature (4°C → 25°C in dark), and irradiance (dark → 45 → 260 μE m^?2s^?1 at 25°C) accelerated particulate and dissolved MC-LA decline, respectively. MC-RR accumulated in surface sediments while MC-LA was near detection despite elevated surface water concentrations. MC-LA appears to persist longer in surface waters than the equally toxic MC-LR, requiring almost the entire recreational season (9.5 weeks) to reach guideline concentrations (20 μg L^?1).     

Traf7, a MyoD1 transcriptional target, regulates nuclear factor-κB activity during myogenesis

We have identified the E3 ligase Traf7 as a direct MyoD1 target and show that cell cycle exit-an early event in muscle differentiation-is linked to decreased Traf7 expression. Depletion of Traf7 accelerates myogenesis, in part through downregulation of nuclear factor-κB (NF-κB) activity. We used a proteomic screen to identify NEMO, the NF-κB essential modulator, as a Traf7-interacting protein. Finally, we show that ubiquitylation of NF-κB essential modulator is regulated exclusively by Traf7 activity in myoblasts. Our results suggest a new mechanism by which MyoD1 function is coupled to NF-κB activity through Traf7, regulating the balance between cell cycle progression and differentiation during myogenesis.     

Activity-based protein profiling of the hepatitis C virus replication in Huh-7 hepatoma cells using a non-directed active site probe

Background  

Hepatitis C virus (HCV) poses a growing threat to global health as it often leads to serious liver diseases and is one of the primary causes for liver transplantation. Currently, no vaccines are available to prevent HCV infection and clinical treatments have limited success. Since HCV has a small proteome, it relies on many host cell proteins to complete its life cycle. In this study, we used a non-directed phenyl sulfonate ester probe (PS4≡) to selectively target a broad range of enzyme families that show differential activity during HCV replication in Huh-7 cells.     

Characterization of ecdysteroids in Drosophila melanogaster by enzyme immunoassay and nano-liquid chromatography–tandem mass spectrometry

Ecdysteroids are polyhydroxylated steroids that function as molting hormones in insects. 20-Hydroxyecdysone (a 27C-ecdysteroid) is classically considered as the major steroid hormone of Drosophila melanogaster, but this insect also contains 28C-ecdysteroids. This arises from both the use of several dietary sterols as precursors for the synthesis of its steroid hormones, and its inability to dealkylate the 28C-phytosterols to produce cholesterol. The nature of Drosophila ecdysteroids has been re-investigated using both high-performance liquid chromatography coupled to enzyme immunoassay and a particularly sensitive nano-liquid chromatography–mass spectrometry methodology, while taking advantage of recently available ecdysteroid standards isolated from plants. In vitro incubations of the larval steroidogenic organ, the ring-gland, reveals the synthesis of ecdysone, 20-deoxy-makisterone A and a third less polar compound identified as the 24-epimer of the latter, while wandering larvae contain the three corresponding 20-hydroxylated ecdysteroids. This pattern results from the simultaneous use of higher plant sterols (from maize) and fungal sterols (from yeast). The physiological relevance of all these ecdysteroids, which display different affinities to the ecdysteroid receptors, is still a matter of debate.     

Molting cycle-dependent expression of CYP4C15, a cytochrome P450 enzyme putatively involved in ecdysteroidogenesis in the crayfish, Orconectes limosus.

A cytochrome P450 enzyme cDNA (CYP4C15) has been previously cloned from a cDNA library of crayfish steroidogenic glands (Y-organs). The conceptual translation of the CYP4C15 cDNA sequence was analyzed for regions of putative high antigenicity and a mixture of two synthetic peptides was chosen for the production of a specific polyclonal antibody. Western blot analysis on Y-organ subcellular fractions indicated an endoplasmic reticulum location of CYP4C15, in agreement with the structural feature of the predicted protein, i.e. the presence of a hydrophobic N-terminal segment.The protein is only expressed in Y-organs, thus showing a similar distribution to the corresponding mRNA. From this tissue specific expression, it has been postulated that CYP4C15 would play a role in ecdysteroid biosynthesis rather than detoxification and the variations of its expression during a molt cycle were carefully examined. CYP4C15 is not detectable in intermolt animals, expression levels are maximal during early premolt and decrease during late premolt. The results are discussed in relation to the variations of hemolymphatic ecdysteroid titers and steroidogenic capacities of the Y-organs during the molt cycle.