Identification and characterization of thousands of bacteriophage satellites across bacteria

Bacteriophage-bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacteria. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown. We developed SatelliteFinder to identify satellites in bacterial genomes, detecting the four best described families: P4-like, phage inducible chromosomal islands (PICI), capsid-forming PICI, and PICI-like elements (PLE). We vastly expanded the number of described elements to ∼5000, finding bacterial genomes with up to three different families of satellites. Most satellites were found in Proteobacteria and Firmicutes, but some are in novel taxa such as Actinobacteria. We characterized the gene repertoires of satellites, which are variable in size and composition, and their genomic organization, which is very conserved. Phylogenies of core genes in PICI and cfPICI indicate independent evolution of their hijacking modules. There are few other homologous core genes between other families of satellites, and even fewer homologous to phages. Hence, phage satellites are ancient, diverse, and probably evolved multiple times independently. Given the many bacteria infected by phages that still lack known satellites, and the recent proposals for novel families, we speculate that we are at the beginning of the discovery of massive numbers and types of satellites

Dual cobalt – copper light-driven catalytic reduction of aldehydes and aromatic ketones in aqueous media

We present an efficient, general, fast, and robust light-driven methodology based on earth-abundant elements to reduce aryl ketones, and both aryl and aliphatic aldehydes (up to 1400 TON). The catalytic system consists of a robust and well-defined aminopyridyl cobalt complex active for photocatalytic water reduction and the [Cu(bathocuproine)(Xantphos)](PF6) photoredox catalyst. The dual cobalt–copper system uses visible light as the driving-force and H2O and an electron donor (Et3N or iPr2EtN) as the hydride source. The catalytic system operates in aqueous mixtures (80–60% water) with high selectivity towards the reduction of organic substrates (>2000) vs. water reduction, and tolerates O2. High selectivity towards the hydrogenation of aryl ketones is observed in the presence of terminal olefins, aliphatic ketones, and alkynes. Remarkably, the catalytic system also shows unique selectivity for the reduction of acetophenone in the presence of aliphatic aldehydes. The catalytic system provides a simple and convenient method to obtain α,β-deuterated alcohols. Both the observed reactivity and the DFT modelling support a common cobalt hydride intermediate. The DFT modelled energy profile for the [Co–H] nucleophilic attack to acetophenone and water rationalises the competence of [CoII–H] to reduce acetophenone in the presence of water. Mechanistic studies suggest alternative mechanisms depending on the redox potential of the substrate. These results show the potential of the water reduction catalyst [Co(OTf)(Py2Tstacn)](OTf) (1), (Py2Tstacn = 1,4-di(picolyl)-7-(p-toluenesulfonyl)-1,4,7-triazacyclononane, OTf = trifluoromethanesulfonate anion) to develop light-driven selective organic transformations and fine solar chemicals

An Iron Bis(carbene) Catalyst for Low Overpotential CO2 Electroreduction to CO: Mechanistic Insights from Kinetic Zone Diagrams, Spectroscopy, and Theory

A common challenge in molecular electrocatalysis is the relationship between maximum activity and the overpotential required to reach that rate, with faster catalysts incurring higher overpotentials. This work follows a strategy based on independent tuning of ligands in the primary coordination sphere to discover a previously unreported iron catalyst for CO2 reduction with higher activity than similar complexes while maintaining the same overpotential. Iron complexes bearing a bis-N-heterocyclic carbene ligand (methylenebis(N-methylimidazol-2-ylidene), bis-mim) and a redox active 2,2′:6′,2″-terpyridine (tpy) ligand were synthesized and found to catalyze the selective reduction of CO2 to CO at low overpotential with water as the proton source. Mechanistic studies based on kinetic zone diagrams, spectroscopy, and computation enable comparisons with a previously studied pyridyl–carbene analogue. Changing the bidentate ligand donor ability accelerates catalysis at the same overpotential and changes the nature of the turnover-limiting step of the reaction.The synthesis, voltammetry, and spectroelectrochemistry were supported as part of the Alliance for Molecular PhotoElectrode Design for Solar Fuels (AMPED), an Energy Frontier Research Center (EFRC) funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001011 (E.A.A and A.J.M.M). Jordi Benet assisted with crystallographic data collection. Brandie M. Ehrmann assisted with mass spectrometry. The mass spectrometry work was supported by the National Science Foundation under grant no. (CHE-1726291). Computational studies, flow electrolyses, and X-ray diffraction studies were supported by the European Commission for the ERC-CoG-2015-648304 project and the Spanish Ministry of Science for the project PID2019-110050RB-I00 (J.Ll.-F). S.G. thanks the EU for Horizon 2020 Marie Skłodowska-Curie Fellowship (grant no. 794119, Fe-RedOx-Cat)

A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature

Phage satellites are genetic elements that couple their life cycle to that of helper phages they parasitize, interfering with phage packaging through the production of small capsids, where only satellites are packaged. So far, in all analyzed systems, the satellite-sized capsids are composed of phage proteins. Here, we report that a family of phage-inducible chromosomal islands (PICIs), a type of satellites, encodes all the proteins required for both the production of small-sized capsids and the exclusive packaging of the PICIs into these capsids. Therefore, this new family, named capsid-forming PICIs (cf-PICIs), only requires phage tails to generate PICI particles. Remarkably, the representative cf-PICIs are produced with no cost from their helper phages, suggesting that the relationship between these elements is not parasitic. Finally, our phylogenomic studies indicate that cf-PICIs are present both in gram-positive and gram-negative bacteria and have evolved at least three times independently to spread in nature

Characterization of an 241AmBe neutron irradiation facility by different spectrometric techniques

An automated panoramic irradiator with a 3 Ci 241Am-Be neutron source is installed in a bunker-type large room at the Universidad Politécnica de Madrid (UPM). It was recently modified and a neutron spectrometry campaign was organized to characterize the neutron fields in different measurement points along the irradiation bench. Four research groups working with different Bonner Sphere Spectrometers (BSS) and using different spectral unfolding codes took part to this exercise. INFN-LNF used a BSS formed by 9 spheres plus bare detector, with cylindrical, almost point like, 6LiI(Eu) scintillator (4 mm x 4 mm, from Ludlum); UAZ-UPM employed a similar system but with only 6 spheres plus bare detector; UAB worked with a 3He filled proportional counter at 8kPa filling pressure, cylindrical 9 mm x 10 mm (05NH1 from Eurisys) with 11 spheres configuration; and CIEMAT used 12 spheres with an spherical 3He SP9 counter (Centronic Ltd., UK) with very high sensitivity due to the large diameter (3.2 cm) and the filling pressure of the order of 228 kPa. Each group applied a different spectral unfolding method: INFN and UAB worked with FRUIT ver. 3.0 with their own response matrixes; UAZ-UPM used the BUNKIUT unfolding code with the response matrix UTA4 and CIEMAT employed the GRAVEL-MAXED-IQU package with their own response matrix. The paper shows the main results obtained in terms of neutron spectra at fixed distances from the source as well as total neutron fluence rate and ambient dose equivalent rate H*(10) determined from the spectra. The latter are compared with the readings of a common active survey-meter (LB 6411). The small differences in the results of the various groups are discussed

Tentativas de suicidio en el municipio de Valencia.

Se obtuvo información sobre las tentativas de suicidio registradas en los libros de urgencias de los hospitales de Valencia ejecutados por residentes de este municipio mayores de 14 años, desde 1982 a 1985. Su análisis mostró que las tasas, la edad, el sexo y el método empleado fueron similares a lo descrito en otros países europeos. Sin embargo, la proporción de personas remitidas a su casa sin mediar ingreso fue comparativamente muy elevad

Tentativas de suicidio en el municipio de Valencia.

Se obtuvo información sobre las tentativas de suicidio registradas en los libros de urgencias de los hospitales de Valencia ejecutados por residentes de este municipio mayores de 14 años, desde 1982 a 1985. Su análisis mostró que las tasas, la edad, el sexo y el método empleado fueron similares a lo descrito en otros países europeos. Sin embargo, la proporción de personas remitidas a su casa sin mediar ingreso fue comparativamente muy elevad

Bacteriophages benefit from generalized transduction

Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival