Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system.

Bacteriophage exclusion ('BREX') phage restriction systems are found in a wide range of bacteria. Various BREX systems encode unique combinations of proteins that usually include a site-specific methyltransferase; none appear to contain a nuclease. Here we describe the identification and characterization of a Type I BREX system from Acinetobacter and the effect of deleting each BREX ORF on growth, methylation, and restriction. We identified a previously uncharacterized gene in the BREX operon that is dispensable for methylation but involved in restriction. Biochemical and crystallographic analyses of this factor, which we term BrxR ('BREX Regulator'), demonstrate that it forms a homodimer and specifically binds a DNA target site upstream of its transcription start site. Deletion of the BrxR gene causes cell toxicity, reduces restriction, and significantly increases the expression of BrxC. In contrast, the introduction of a premature stop codon into the BrxR gene, or a point mutation blocking its DNA binding ability, has little effect on restriction, implying that the BrxR coding sequence and BrxR protein play independent functional roles. We speculate that elements within the BrxR coding sequence are involved in cis regulation of anti-phage activity, while the BrxR protein itself plays an additional regulatory role, perhaps during horizontal transfer.

The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity.

To overcome CRISPR-Cas defense systems, many phages and mobile genetic elements (MGEs) encode CRISPR-Cas inhibitors called anti-CRISPRs (Acrs). Nearly all characterized Acrs directly bind Cas proteins to inactivate CRISPR immunity. Here, using functional metagenomic selection, we describe AcrIIA22, an unconventional Acr found in hypervariable genomic regions of clostridial bacteria and their prophages from human gut microbiomes. AcrIIA22 does not bind strongly to SpyCas9 but nonetheless potently inhibits its activity against plasmids. To gain insight into its mechanism, we obtained an X-ray crystal structure of AcrIIA22, which revealed homology to PC4-like nucleic acid-binding proteins. Based on mutational analyses and functional assays, we deduced that acrIIA22 encodes a DNA nickase that relieves torsional stress in supercoiled plasmids. This may render them less susceptible to SpyCas9, which uses free energy from negative supercoils to form stable R-loops. Modifying DNA topology may provide an additional route to CRISPR-Cas resistance in phages and MGEs.

Multi-stressor Effects of Ultraviolet Light, Temperature, and Salinity on Louisiana Sweet Crude Oil Toxicity in Larval Estuarine Organisms.

When oil is spilled into the environment its toxicity is affected by abiotic conditions. The cumulative and interactive stressors of chemical contaminants and environmental factors are especially relevant in estuaries where tidal fluctuations cause wide variability in salinity, temperature, and ultraviolet (UV) light penetration, which is an important modifying factor for polycyclic aromatic hydrocarbon (PAH) toxicity. Characterizing the interactions of multiple stressors on oil toxicity will improve prediction of environmental impacts under various spill scenarios. This study examined changes in crude oil toxicity with temperature, salinity, and UV light. Oil exposures included high-energy, water-accommodated fractions (HEWAFs) and thin oil sheens. Larval (24-48 h post hatch) estuarine species representing different trophic levels and habitats were evaluated. Mean 96 h LC50 values for oil prepared as a HEWAF and tested under standard conditions (20 ppt, 25 °C, No-UV) were 62.5 µg/L tPAH50 (mud snails), 198.5 µg/L (grass shrimp), and 774.5 µg/L (sheepshead minnows). Thin oil sheen 96 h LC50 values were 5.3 µg/L tPAH50 (mud snails), 14.7 µg/L (grass shrimp), and 22.0 µg/L (sheepshead minnows) under standard conditions. UV light significantly increased the toxicity of oil in all species tested. Oil toxicity also was greater under elevated temperature and lower salinity. Multi-stressor (oil combined with either increased temperature, decreased salinity, or both) LC50 values were reduced to 3 µg/L tPAH50 for HEWAFs and < 1.0 µg/L tPAH50 for thin oil sheens. Environmental conditions at the time of an oil spill will significantly influence oil toxicity and organismal response and should be taken into consideration in toxicity testing and oil spill damage assessments.