FRUIT,a Scar-Free System for Targeted Chromosomal Mutagenesis,Epitope Tagging,and Promoter Replacement in Escherichia coli and Salmonella enterica

Recombineering is a widely-used approach to delete genes, introduce insertions and point mutations, and introduce epitope tags into bacterial chromosomes. Many recombineering methods have been described, for a wide range of bacterial species. These methods are often limited by (i) low efficiency, and/or (ii) introduction of “scar” DNA into the chromosome. Here, we describe a rapid, efficient, PCR-based recombineering method, FRUIT, that can be used to introduce scar-free point mutations, deletions, epitope tags, and promoters into the genomes of enteric bacteria. The efficiency of FRUIT is far higher than that of the most widely-used recombineering method for Escherichia coli. We have used FRUIT to introduce point mutations and epitope tags into the chromosomes of E. coli K-12, Enterotoxigenic E. coli, and Salmonella enterica. We have also used FRUIT to introduce constitutive and inducible promoters into the chromosome of E. coli K-12. Thus, FRUIT is a versatile, efficient recombineering approach that can be applied in multiple species of enteric bacteria.     

Chemotography for multi-target SAR analysis in the context of biological pathways

The increasing amount of chemogenomics data, that is, activity measurements of many compounds across a variety of biological targets, allows for better understanding of pharmacology in a broad biological context. Rather than assessing activity at individual biological targets, today understanding of compound interaction with complex biological systems and molecular pathways is often sought in phenotypic screens. This perspective poses novel challenges to structure-activity relationship (SAR) assessment. Today, the bottleneck of drug discovery lies in the understanding of SAR of rich datasets that go beyond single targets in the context of biological pathways, potential off-targets, and complex selectivity profiles. To aid in the understanding and interpretation of such complex SAR, we introduce Chemotography (chemotype chromatography), which encodes chemical space using a color spectrum by combining clustering and multidimensional scaling. Rich biological data in our approach were visualized using spatial dimensions traditionally reserved for chemical space. This allowed us to analyze SAR in the context of target hierarchies and phylogenetic trees, two-target activity scatter plots, and biological pathways. Chemotography, in combination with the Kyoto Encyclopedia of Genes and Genomes (KEGG), also allowed us to extract pathway-relevant SAR from the ChEMBL database. We identified chemotypes showing polypharmacology and selectivity-conferring scaffolds, even in cases where individual compounds have not been tested against all relevant targets. In addition, we analyzed SAR in ChEMBL across the entire Kinome, going beyond individual compounds. Our method combines the strengths of chemical space visualization for SAR analysis and graphical representation of complex biological data. Chemotography is a new paradigm for chemogenomic data visualization and its versatile applications presented here may allow for improved assessment of SAR in biological context, such as phenotypic assay hit lists.     

Iron and proteins for iron storage and detoxification

Iron is required by most organisms, but is potentially toxic due to the low solubility of the stable oxidation state, Fe(III), and to the tendency to potentiate the production of reactive oxygen species, ROS. The reactivity of iron is counteracted by bacteria with the same strategies employed by the host, namely by sequestering the metal into ferritin, the ubiquitous iron storage protein. Ferritins are highly conserved, hollow spheres constructed from 24 subunits that are endowed with ferroxidase activity and can harbour up to 4500 iron atoms as oxy-hydroxide micelles. The release of the metal upon reduction can alter the microorganism-host iron balance and hence permit bacteria to overcome iron limitation. In bacteria, the relevance of the Dps (DNA-binding proteins from starved cells) family in iron storage-detoxification has been recognized recently. The seminal studies on the protein from Listeria innocua demonstrated that Dps proteins have ferritin-like activity and most importantly have the capacity to attenuate the production of ROS. This latter function allows bacterial pathogens that lack catalase, e.g. Porphyromonas gingivalis, to survive in an aerobic environment and resist to peroxide stress.     

Compartment-Specific Biosensors Reveal a Complementary Subcellular Distribution of Bioactive Furin and PC7

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Delineating boreal plains bog margin ecotones across hydrogeological settings for wildfire risk management

Canada’s Boreal Plains peatland vegetation species assemblages are characterized by their functional ecosystem roles and feedbacks, which are important for carbon and water storage in a sub-humid climate. The vegetation communities at the peatland-upland interface, or the peatland margin ecotone, have not been extensively delineated or characterized as a distinct ecotone. Because these ecotones constitute a smouldering “hotspot” during wildfire, with carbon loss from these margins accounting for 50–90% of total peatland carbon loss, their delineation is critical. Post-fire, areas of severe peat smouldering have previously been shown to undergo shifts in vegetation community composition, resulting in a loss of key peatland ecohydrological functions. The aim of this study was to delineate Boreal Plains peatland margin ecotones and assess their prevalence across the landscape. Using split moving window analysis on vegetation transect data from a chronosequence of study sites, the margin ecotones were delineated at sites having different times since fire. No significant differences were identified in margin width over time or margin peat depths across hydrogeological settings. However, with peat depths of up to 2.46 m in small peatlands characteristic of moraine and glaciofluvial deposits, vulnerable margin peat has been demonstrated to represent a significant carbon store. Fire managers employing peatland fuel treatments for wildfire abatement and community protection should consider these confined peatlands more carefully to mitigate catastrophic carbon losses. Further, we suggest that a greater understanding is needed of the roles of peatland margin ecotones in sustaining peatland autogenic feedback mechanisms that promote paludification and recovery following wildfire.     

Mechanisms for Intracellular Calcium Regulation in Heart : I. Stopped-Flow Measurements of Ca++ Uptake by Cardiac Mitochondria

Initial velocities of energy-dependent Ca⁺⁺ uptake were measured by stopped-flow and dual-wavelength techniques in mitochondria isolated from hearts of rats, guinea pigs, squirrels, pigeons, and frogs. The rate of Ca⁺⁺ uptake by rat heart mitochondria was 0.05 nmol/mg/s at 5 µM Ca⁺⁺ and increased sigmoidally to 8 nmol/mg/s at 200 µM Ca⁺⁺. A Hill plot of the data yields a straight line with slope n of 2, indicating a cooperativity for Ca⁺⁺ transport in cardiac mitochondria. Comparable rates of Ca⁺⁺ uptake and sigmoidal plots were obtained with mitochondria from other mammalian hearts. On the other hand, the rates of Ca⁺⁺ uptake by frog heart mitochondria were higher at any Ca⁺⁺ concentrations. The half-maximal rate of Ca⁺⁺ transport was observed at 30, 60, 72, 87, 92 µM Ca⁺⁺ for cardiac mitochondria from frog, squirrel, pigeon, guinea pig, and rat, respectively. The sigmoidicity and the high apparent K_m render mitochondrial Ca⁺⁺ uptake slow below 10 µM. At these concentrations the rate of Ca⁺⁺ uptake by cardiac mitochondria in vitro and the amount of mitochondria present in the heart are not consistent with the amount of Ca⁺⁺ to be sequestered in vivo during heart relaxation. Therefore, it appears that, at least in mammalian hearts, the energy-linked transport of Ca⁺⁺ by mitochondria is inadequate for regulating the beat-to-beat Ca⁺⁺ cycle. The results obtained and the proposed cooperativity for mitochondrial Ca⁺⁺ uptake are discussed in terms of physiological regulation of intracellular Ca⁺⁺ homeostasis in cardiac cells.