Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage–host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage–host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages’ host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

This study presents the BASEL collection of phages that infect the model bacterium Escherichia coli; this resource for the community is representative of natural E. coli phage diversity and has been extensively characterized phenotypically and genomically.     

Electrochemical Potential Gradients of H+, K+, Ca2+, and Cl- across the Tonoplast of the Green Alga Eremosphaera Viridis

Using ion-selective microelectrodes, we measured the activity of H+, K+, Ca2+, and Cl- and the electrical potential both in the vacuole and in the cytoplasm of the unicellular green alga Eremosphaera viridis to obtain comparable values of the named parameters from the same object under identical conditions. The cytosol had a pH of 7.3, and activities of the other ions were 130 mM K+, 160 nM Ca2+, and 2.2 mM Cl-. We observed only small and transient light-dependent changes of the cytosolic Ca2+ activity. The vacuolar K+ activity did not differ significantly from the cytosolic one. The Ca2+ activity inside the vacuole was approximately 200 [mu]M, the pH was 5.0, and the Cl- activity was 6.2 mM. The concentrations of K+, Ca2+, and Cl- in cell extracts were measured by induction-coupled plasma spectroscopy and anion chromatography. This confirmed the vacuolar activities for K+ and Cl- obtained with ion-selective microelectrodes and indicated that approximately 60% of the vacuolar Ca2+ was buffered. The tonoplast potential was vanishingly low ([less than or equal to][plus or minus]2 mV). There was no detectable electrochemical potential gradient for K+ across the tonoplast, but there was, however, an obvious electrochemical potential gradient for Cl- (-26 mV), indicating an active accumulation of Cl- inside the vacuole.     

Pyrene fluorescence fine structure as a polarity probe of hydrophobic regions: Behavior in model solvents

The vibrational fine structure superimposed on pyrene monomer fluorescence is solvent dependent at room temperature. The fine structure pattern of pyrene monomer fluorescence was found to be independent of excitation conditions or collisional quenching, but highly dependent on solvent polarity. Variation in pyrene fluorescence fine structure was investigated in alkane and alkanol solvents and solvent mixtures. Although changes in the fine structure pattern were detected across the monomer fluorescence spectrum, the greatest difference occurred at the 373- and 384-nm peaks. In nonpolar environments, the 384-nm peak dominated the pyrene spectrum, whereas at higher polarity, the 373-nm peak was the most intense. By expressing the relative emission intensities at 373- and 384-nm peaks as a ratio, a sensitive parameter of solvent polarity was obtained. The $\text{373}\text{384}$ peak ratio results yielded a curvilinear relationship as a function of dielectric constant. This effect can be applied to monitor changes in polarity of pyrene microenvironments in proteins and membranes.     

Growth-modulating tripeptide (glycylhistidyllysine): association with copper and iron in plasma, and stimulation of adhesiveness and growth of hepatoma cells in culture by tripeptide-metal ion complexes

The tripeptide H-Gly-His-Lys-OH (GHL) is a human plasma constituent which has been previously shown to modulate the growth and viability of a variety of cell types and organisms. Experimental observations presented herein indicate that GHL is complexed with the transition metal ions Cu++ and Fe++ in vivo and may exert its biological effects as a peptide-metal chelate. At physiological pH in vitro, GHL associates with ionic copper, cobalt, iron, molybdenum, manganese, nickel, and zinc, but has no affinity for calcium, manganese, potassium, and sodium. GHL acts synergistically with copper, iron, cobalt, and zinc to alter patterns of cell growth in monolayer cultures of a tumorigenic hepatoma cell line (HTC4). These transition metals induce cellular flattening and adhesion to support surfaces, and inhibit DNA synthesis and lactic acid production when growth is limited by reduction of serum concentrations in medium. These inhibitory effects are neutralized, and intercellular adhesion and growth are stimulated by GHL in medium at nanomolar concentrations. Cu and Fe are the most active metals when combined with GHL. The results suggest that the inability of HTC4 cultures to replicate without adequate concentrations of serum in medium may reflect deficiency of GHL and transition metals, which appear to form complexes prior to interaction with cells. Chelation of transition metals with GHL and, potentially, with other growth-modulating peptide factors in plasma or medium, may provide a mechanism for expression and regulation of biological activities influenced by transition metals and polypeptide growth factors. The observed effects of GHL-metal complexes, including stimulation of cellular adhesiveness to substratum (flattening) and intercellular attachment (monolayer formation), appear to satisfy requirements for growth of hepatoma cells in monolayer culture.     

Die Plastiden derCleome-Epidermis

Zusammenfassung In den Epidermiszellen der Blattunterseite vonCleome spinosa befinden sich fast farblose Plastiden, die tagsüber mit Stärke vollgepfropft sind und dabei beträchtliche Größe erreichen. Bei Verdunkelung und Vergilbung verschwindet diese Stärke, sie kann aber bei Angebot von Traubenzucker auch im Dunkeln gebildet werden. Für solche Plastiden der Epidermis wird zum Unterschied zu den inaktiven Intermediärplastiden die Bezeichnung aktive Intermediärplastiden oder Amylointermediärplastiden vorgeschlagen, diese Plastiden der Epidermis bilden die Stärke nicht durch Photosynthese, sondern aus zugeleitetem Zucker.     

Tests of the Double-Strand-Break Repair Model for Red-Mediated Recombination of Phage λ and Plasmid λdv

The double-strand-break repair (DSBR) model was formulated to account for various aspects of yeast mitotic and meiotic recombination. In this study three features of the DSBR model are tested for Red-mediated recombination between phage lambda and lambda dv, a plasmid that is perfectly homologous to about 10% of lambda. The results support the applicability of the DSBR model to lambda's Red system: (1) Creating a double-strand-break (DSB) within the region of homology shared by phage and plasmid increases their genetic interaction by about 20-fold. A DSB outside the region of shared homology has no such effect. (2) Both patches, i.e., simple marker rescue, and splices, i.e., co-integration of the phage and plasmid, are stimulated by a DSB in the region of shared homology. (3) Co-integrants harbor a duplication of the region of shared homology. Among co-integrants that were formed by the creation of a DSB, there is a preferential loss of whichever allele was in cis to a utilized cut site. The DSBR model as originally formulated involves the isomerization and cleavage of Holliday junctions to resolve the canonical intermediate. We propose as an alternative mechanism that a topoisomerase can resolve the canonical DSBR intermediate.     

Perinatal developmental changes in hepatic UDP-glucuronyltransferase.

Postnatal developmental changes in hapatic microsomal UDP-glucuronyltransferase were studied in the rat. The previously reported postnatal decline in the capacity of microsomal fractions to glucuronidate p-nitrophenol was found to be observable in unperturbed preparations only at non-saturating concentrations of the substrate UDP-glucuronic acid. At saturating concentrations of UDP-glucuronic acid, activity is identical in newborns and adults. Kinetic analysis revealed that the enzyme from liver of newborns has a much higher affinity for UDP-glucuronic acid than does the enzyme in adults, but the same activity at Vmax. On the other hand, the enzyme from adult liver microsomal fractions can be activated by the physiological allosteric effector UDP-N-acetylglucosamine, whereas the enzyme from newborns is largely unaffected by it. Thus it appears that the number of enzyme active sites is not changing; rather, the enzyme is maturing to a more highly regulable form. There were also differences between the enzymes in newborns and adults in their response to perturbation of the membrane-lipid environment by detergent and phospholipase A. Possible interpretations of these differences are discussed.     

The role of the jasmonate response in plant susceptibility to diverse pathogens with a range of lifestyles

Plants defend themselves against attack from insects and pathogens with various resistance strategies. The jasmonate and salicylate signaling pathways are two induced responses that protect plants against these attackers. Knowledge of the range of organisms that are affected by each response is important for understanding how plants coordinate their defenses against multiple attackers and the generality of effect of different resistance mechanisms. The jasmonate response is known to protect plants against a wide range of insect herbivores; in this study, we examined the role of the jasmonate response in susceptibility to eight pathogens with diverse lifestyles in the laboratory and field. Recent biochemical models suggest that the lifestyle of the pathogen (necrotroph versus biotroph) should predict whether the jasmonate response will be involved in resistance. We tested this by examining the susceptibility of wild-type (cv Castlemart with no known genes for resistance to the pathogens used) and jasmonate-deficient mutant tomato (Lycopersicon esculentum) plants (def1) and by employing rescue treatments of the mutant. Plant susceptibility to five of the eight pathogens we examined was reduced by the jasmonate response, including two bacteria (Pseudomonas syringae and Xanthomonas campestris), two fungi (Verticillium dahliae and Fusarium oxysporum f. sp. lycopersici), and an oomycete (Phytophthora infestans). Susceptibility to three fungi was unaffected (Cladosporium fulvum, Oidium neolycopersici, and Septoria lycopersici). Our results indicate that the jasmonate response reduces damage by a wide range of pathogens from different lifestyles, a result that contrasts with the emerging picture of diseases on Arabidopsis. Thus, the generality of jasmonate-based resistance of tomato challenges the view that ecologically distinct plant parasites are resisted via different mechanisms.