The structure of S. lividans acetoacetyl‐CoA synthetase shows a novel interaction between the C‐terminal extension and the N‐terminal domain

The adenosine monoposphate‐forming acyl‐CoA synthetase enzymes catalyze a two‐step reaction that involves the initial formation of an acyl adenylate that reacts in a second partial reaction to form a thioester between the acyl substrate and CoA. These enzymes utilize a Domain Alternation catalytic mechanism, whereby a ～110 residue C‐terminal domain rotates by 140° to form distinct catalytic conformations for the two partial reactions. The structure of an acetoacetyl‐CoA synthetase (AacS) is presented that illustrates a novel aspect of this C‐terminal domain. Specifically, several acetyl‐ and acetoacetyl‐CoA synthetases contain a 30‐residue extension on the C‐terminus compared to other members of this family. Whereas residues from this extension are disordered in prior structures, the AacS structure shows that residues from this extension may interact with key catalytic residues from the N‐terminal domain. Proteins 2015; 83:575–581. © 2014 Wiley Periodicals, Inc.     

The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes

The metabolism of microbial organisms and its diversity are partly the result of an adaptation process to the characteristics of the environments that they inhabit. In this work, we analyze the influence of lifestyle on the content of promiscuous enzymes in 761 nonredundant bacterial and archaeal genomes. Promiscuous enzymes were defined as those proteins whose catalytic activities are defined by two or more different Enzyme Commission (E.C.) numbers. The genomes analyzed were categorized into four lifestyles for their exhaustive comparisons: free‐living, extremophiles, pathogens, and intracellular. From these analyses we found that free‐living organisms have larger genomes and an enrichment of promiscuous enzymes. In contrast, intracellular organisms showed smaller genomes and the lesser proportion of promiscuous enzymes. On the basis of our data, we show that the proportion of promiscuous enzymes in an organism is mainly influenced by the lifestyle, where fluctuating environments promote its emergence. Finally, we evidenced that duplication processes occur preferentially in metabolism of free‐living and extremophiles species. Proteins 2015; 83:1625–1631. © 2015 Wiley Periodicals, Inc.     

Continuous removal of endocrine disruptors by versatile peroxidase using a two‐stage system

The oxidant Mn³⁺‐malonate, generated by the ligninolytic enzyme versatile peroxidase in a two‐stage system, was used for the continuous removal of endocrine disrupting compounds (EDCs) from synthetic and real wastewaters. One plasticizer (bisphenol‐A), one bactericide (triclosan) and three estrogenic compounds (estrone, 17β‐estradiol, and 17α‐ethinylestradiol) were removed from wastewater at degradation rates in the range of 28–58 µg/L·min, with low enzyme inactivation. First, the optimization of three main parameters affecting the generation of Mn³⁺‐malonate (hydraulic retention time as well as Na‐malonate and H₂O₂ feeding rates) was conducted following a response surface methodology (RSM). Under optimal conditions, the degradation of the EDCs was proven at high (1.3–8.8 mg/L) and environmental (1.2–6.1 µg/L) concentrations. Finally, when the two‐stage system was compared with a conventional enzymatic membrane reactor (EMR) using the same enzyme, a 14‐fold increase of the removal efficiency was observed. At the same time, operational problems found during EDCs removal in the EMR system (e.g., clogging of the membrane and enzyme inactivation) were avoided by physically separating the stages of complex formation and pollutant oxidation, allowing the system to be operated for a longer period (～8 h). This study demonstrates the feasibility of the two‐stage enzymatic system for removing EDCs both at high and environmental concentrations. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:908–916, 2015     

Trade‐off between thermal tolerance and insecticide resistance in Plutella xylostella

Fitness costs associated with resistance to insecticides have been well documented, usually at normal temperature conditions, in many insect species. In this study, using chlorpyrifos‐resistant homozygote (R_R) and chlorpyrifos‐susceptible homozygote (S_S) of resistance ace1 allele of Plutella xylostella (DBM), we confirmed firstly that high temperature experience in pupal stage influenced phenotype of wing venation in insecticide‐resistant and insecticide‐susceptible Plutella xylostella, and S_S DBM showed significantly higher thermal tolerance and lower damages of wing veins under heat stress than R_R DBM. As compared to S_S DBM, R_R DBM displayed significantly lower AChE sensitivity to chlorpyrifos, higher basal GSTs activity and P450 production at 25°C, but higher inhibitions on the enzyme activities and P450 production as well as reduced resistance to chlorpyrifos under heat stress. Furthermore, R_R DBM displayed significantly higher basal expressions of hsp69s, hsp72s, hsp20, hsp90, Apaf‐1, and caspase‐7 at 25°C, but lower induced expressions of hsps and higher induced expressions of Apaf‐1, caspase‐9, and caspase‐7 under heat stress. These results suggest that fitness costs of chlorpyrifos resistance in DBM may partly attribute to excess consumption of energy caused by over production of detoxification enzymes and hsps when the proteins are less demanded at conducive environments but reduced expressions when they are highly demanded by the insects to combat environmental stresses, or to excess expressions of apoptotic genes under heat stress, which results in higher apoptosis. The evolutionary and ecological implications of these findings at global warming are discussed.     

Utilization of the Soft Agar Colony Formation Assay to Identify Inhibitors of Tumorigenicity in Breast Cancer Cells

Given the inherent difficulties in investigating the mechanisms of tumor progression in vivo, cell-based assays such as the soft agar colony formation assay (hereafter called soft agar assay), which measures the ability of cells to proliferate in semi-solid matrices, remain a hallmark of cancer research. A key advantage of this technique over conventional 2D monolayer or 3D spheroid cell culture assays is the close mimicry of the 3D cellular environment to that seen in vivo. Importantly, the soft agar assay also provides an ideal tool to rigorously test the effects of novel compounds or treatment conditions on cell proliferation and migration. Additionally, this assay enables the quantitative assessment of cell transformation potential within the context of genetic perturbations. We recently identified peptidylarginine deiminase 2 (PADI2) as a potential breast cancer biomarker and therapeutic target. Here we highlight the utility of the soft agar assay for preclinical anti-cancer studies by testing the effects of the PADI inhibitor, BB-Cl-amidine (BB-CLA), on the tumorigenicity of human ductal carcinoma in situ (MCF10DCIS) cells.     

Multiple forms and specificity of coniferyl alcohol dehydrogenase from cambial regions of higher plants

Alcohol dehydrogenases of 89 species of plants, from the Bryophyta, Pteridophyta, Gymnosperms and Angiosperms were examined by starch gel electrophoresis for their substrate and coenzyme specificities. High activities and multiple bands were observed with EtOH and NAD in most species. The same, but weaker banding patterns were also observed with benzyl alcohol and salicin. When coniferyl alcohol was used as substrate, activity was found only with NADP as coenzyme and the resulting bands were distinct from those obtained with the other substrates. Most plants tested had only one or occasionally a second coniferyl alcohol dehydrogenase band. Salix species were an exception, with multiple bands found in each of the species tested.     

Polysaccharide and protein degradation,germination, and virulence against mosquitoes in the entomopathogenic fungus Metarhizium anisopliae

From a genetically uniform wild-type strain of Metarhizium anisopliae pathogenic to mosquitoes, mutants were selected which were altered in the ability to degrade starch, gelatin, or milk. The mutants with enhanced starch degradation (dep), when grown on starch-containing media, proved hypervirulent toward the mosquito Culex pipiens pipiens in standard laboratory tests. Alterations in protein (gelatin or milk) degradation did not correlate with changes in virulence. The dep mutants appear to belong to the same class as mutants selected previously as hypervirulent and characterized by early spore germination. The relationship among polysaccharide degradation, early germination, and virulence is discussed.     

Hymenolepis diminuta: Action of worm RNase against RNA

Hymenolepis diminuta possesses a tegumental ribonuclease (RNase) which hydrolyzes rat liver and degraded yeast RNA. Polyacrylamide gel electrophoresis and gel chromatography of rat liver RNA after incubation with intact worms demonstrated significant hydrolysis of the high molecular weight RNA fractions (28 S and 18 S), with the appearance of fractions of intermediate molecular weight (i.e., between 18 S and 4 S), as well as ethanol-soluble fractions. Hydrolysis of degraded yeast RNA (with a molecular weight of approximately 25,000) yielded a single ethanol-precipitable hydrolysis product, as well as ethanol-soluble hydrolysis products.     

The Importance of Amine-degrading Enzymes on the Biogenic Amine Degradation in Fermented Foods: A review

Biogenic amines (BAs) are a class of harmful compounds often be found in high protein foods, especially naturally fermented foods. BAs derive from free amino acid decarboxylation through microbial activities and can cause toxic effects (headache, heart palpitations, vomiting) on humans, depending on individual sensitivity. Indigenous amine-degrading strains or strains producing amine-degrading enzymes (ADEs) have drawn great attention since they play an important role in affecting BA accumulation, and enzymes/genes involved in the biosynthetic mechanisms. They also help maintain the sensory quality of the final products. Besides, due to ADEs’ harmless catalytic products, they can be further utilized in fermented foods and beverages to reduce BAs. This review describes in detail the mechanisms of BAs formation, as well as the diversity of ADEs able to degrade BAs in a model or real food systems. A deeper knowledge of this issue is crucial because ADEs’ activities are often associated with strains rather than species or genera. Moreover, this information can help to improve the selection and characterization of strains for further applications as starters or bioprotective cultures, to obtain high-quality foods with reduced BAs contents.