Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.

Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage ΦKZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.

Self-Aggregated Nanoscale Metal-Organic Framework for Targeted Pulmonary Decorporation of Uranium.

The limited availability of effective agents for removing actinides from the lungs significantly restricts the effectiveness of medical treatments for nuclear emergencies. Inhalation is the primary route of internal contamination in 44.3% of actinide-related accidents, leading to the accumulation of radionuclides in the lungs and resulting in infections and potential tumor formation (tumorigenesis). This study focuses on the synthesis of a nanometal-organic framework (nMOF) material called ZIF-71-COOH, which is achieved by post-synthetic carboxyl functionalization of ZIF-71. The material demonstrates high and selective adsorption of uranyl, while also exhibiting increased particle size (≈2100 nm) when it aggregates in the blood, enabling passive targeting of the lungs through mechanical filtration. This unique property facilitates the rapid enrichment and selective recognition of uranyl, making nano ZIF-71-COOH highly effective in removing uranyl from the lungs. The findings of this study highlight the potential of self-aggregated nMOFs as a promising drug delivery system for targeted uranium decorporation in the lungs.

A Radioluminescent Metal-Organic Framework for Monitoring 225Ac in Vivo.

225Ac is considered as one of the most promising radioisotopes for alpha-therapy because its emitted high-energy α-particles can efficiently damage tumor cells. However, it also represents a significant threat to healthy tissues owing to extremely high radiotoxicity if targeted therapy fails. This calls for a pressing requirement of monitoring the biodistribution of 225Ac in vivo during the treatment of tumors. However, the lack of imageable photons or positrons from therapeutic doses of 225Ac makes this task currently quite challenging. We report here a nanoscale luminescent europium-organic framework (EuMOF) that allows for fast, simple, and efficient labeling of 225Ac in its crystal structure with sufficient 225Ac-retention stability based on similar coordination behaviors between Ac3+ and Eu3+. After labeling, the short distance between 225Ac and Eu3+ in the structure leads to exceedingly efficient energy transduction from225Ac-emitted α-particles to surrounding Eu3+ ions, which emits red luminescence through a scintillation process and produces sufficient photons for clearcut imaging. The in vivo intensity distribution of radioluminescence signal originating from the 225Ac-labeled EuMOF is consistent with the dose of 225Ac dispersed among the various organs determined by the radioanalytical measurement ex vivo, certifying the feasibility of in vivo directly monitoring 225Ac using optical imaging for the first time. In addition, 225Ac-labeled EuMOF displays notable efficiency in treating the tumor. These results provide a general design principle for fabricating 225Ac-labeled radiopharmaceuticals with imaging photons and propose a simple way to in vivo track radionuclides with no imaging photons, including but not limited to 225Ac.

Boosting Simultaneous Uranium Decorporation and Reactive Oxygen Species Scavenging Efficiency by Lacunary Polyoxometalates.

The chemical toxicity and the oxidative stress induced by the internal exposure of uranium is responsible for the long-term adverse effect of in vivo contamination of uranium. An agent with simultaneous removal capability of uranium and excess reactive oxygen species (ROS) is highly desired. Herein, the lacunary Keggin-type polyoxometalate (POM) is demonstrated to selectively bind with uranyl ions in the presence of excess essential divalent ions and exhibits a compelling ROS scavenging efficiency of 78.8%. In vivo uranium decorporation assays illustrate the uranium sequestration efficiencies of 74.0%, 49.4%, and 37.1% from kidneys by prophylactic, prompt, and delayed administration of lacunary POM solution, respectively. The superior ROS quenching and uranium removal performance in comparison with all reported bifunctional agents endow lacunary polyoxometalates as novel agents to effectively protect people from injuries caused by the internal exposure of actinides.

Bacteriophage genome engineering with CRISPR-Cas13a.

Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Both pursuits are currently limited by a lack of genetic engineering tools due to a proteinaceous 'phage nucleus' structure that protects from DNA-targeting CRISPR-Cas tools. To provide reverse-genetics tools for DNA jumbo phages from this family, we combined homologous recombination with an RNA-targeting CRISPR-Cas13a enzyme and used an anti-CRISPR gene (acrVIA1) as a selectable marker. We showed that this process can insert foreign genes, delete genes and add fluorescent tags to genes in the ФKZ genome. Fluorescent tagging of endogenous gp93 revealed that it is ejected with the phage DNA while deletion of the tubulin-like protein PhuZ surprisingly had only a modest impact on phage burst size. Editing of two other phages that resist DNA-targeting CRISPR-Cas systems was also achieved. RNA-targeting Cas13a holds great promise for becoming a universal genetic editing tool for intractable phages, enabling the systematic study of phage genes of unknown function.

Effective mitigation of gadolinium deposition using the bidentate hydroxypyridinone ligand Me-3,2-HOPO.

With the extensive usage of gadolinium-based contrast agents (GBCAs) in magnetic resonance imaging (MRI), gadolinium deposition has been observed in the brain, kidneys, liver, etc., and this is also closely related to the development of nephrogenic systemic fibrosis (NSF) in patients with renal dysfunction. Chelation, thereby promoting the elimination of deposited Gd(III), seems to be promising for alleviating these problems. Despite many ligands suitable for chelation therapy having been studied, the decorporation of transition metals (e.g. iron, copper, lead, etc.) and actinides (e.g. uranium, plutonium, etc.) has long been a primary concern, whereas the study of Gd(III) has been extremely limited. Due to their excellent metal binding abilities in vivo and therapeutic effects toward neurodegenerative diseases, bidentate hydroxypyridinone ligands are expected to be able to remove Gd(III) from the brain, kidneys, bones, and liver. Herein, the Gd(III) decorporation efficacy of a bidentate hydroxypyridinone ligand (Me-3,2-HOPO) has been evaluated. The complexation behavior between Me-3,2-HOPO and Gd(III) in solution and solid states was characterized with the assistance of potentiometric titration and X-ray diffraction techniques, respectively. Solution-based thermodynamic studies illustrate that the dominant species of complex between Gd(III) and Me-3,2-HOPO (HL) is GdL2+ (log ß120 = 11.8 (3)) at pH 7.4. The structure of the Gd-Me-3,2-HOPO crystal obtained from a room temperature reaction reveals the formation of a Gd(III) dimer that is chelated by four ligands as a result of metal ion hydration and ligand complexation. Cellular Gd(III) removal assays illustrate that Me-3,2-HOPO could effectively reduce final amounts of gadolinium by 77.6% and 66.1% from rat renal proximal tubular epithelial (NRK-52E) cells and alpha mouse liver 12 (AML-12) cells, respectively. Our current results suggest the potential of bidentate HOPO ligands as an effective approach to treat patients suffering from Gd(III) toxicity.

Hinokitiol, an Advanced Bidentate Ligand for Uranyl Decorporation.

Despite the critical role actinide decorporation agents play in the emergency treatment of people in nuclear accidents and other scenarios that may cause internal contamination of actinides, new ligands have seldom been reported in recent decades because the current inventory has been limited to only a handful of functional groups. Therefore, new functional groups are always being urgently sought for the introduction of advanced actinide decorporation agents. Herein, a tropolone derivative, 2-hydroxy-6-(propan-2-yl)cyclohepta-2,4,6-trien-1-one (Hinokitiol or Hino), is proposed to be a promising candidate for this purpose by virtue of its well-demonstrated high membrane permeability and high affinity for metal ions. The coordination stoichiometry of Hino with uranyl is demonstrated to be 3:1 both in an aqueous solution (pH 7.4) and in the solid state. The results of a liquid-liquid extraction experiment further show that Hino exhibits strong chelating ability and selectivity toward uranyl over biological essential metal ions (i.e., Mn2+, Zn2+, Co2+, and Ni2+) with an extraction efficiency of >90.0%. The in vivo uranyl removal efficacies of Hino in kidneys and bone of mice are demonstrated to be 67.0% and 32.3%, respectively. On the basis of the observations described above, it is highly possible that further modification of Hino will lead to a large family of multidentate agents with enhanced uranyl decorporation ability.

Interactions between Viral Regulatory Proteins Ensure an MOI-Independent Probability of Lysogeny during Infection by Bacteriophage P1.

Phage P1 is a temperate phage which makes the lytic or lysogenic decision upon infecting bacteria. During the lytic cycle, progeny phages are produced and the cell lyses, and in the lysogenic cycle, P1 DNA exists as a low-copy-number plasmid and replicates autonomously. Previous studies at the bulk level showed that P1 lysogenization was independent of multiplicity of infection (MOI; the number of phages infecting a cell), whereas lysogenization probability of the paradigmatic phage λ increases with MOI. However, the mechanism underlying the P1 behavior is unclear. In this work, using a fluorescent reporter system, we demonstrated this P1 MOI-independent lysogenic response at the single-cell level. We further observed that the activity of the major repressor of lytic functions (C1) is a determining factor for the final cell fate. Specifically, the repression activity of P1, which arises from a combination of C1, the anti-repressor Coi, and the corepressor Lxc, remains constant for different MOI, which results in the MOI-independent lysogenic response. Additionally, by increasing the distance between phages that infect a single cell, we were able to engineer a λ-like, MOI-dependent lysogenization upon P1 infection. This suggests that the large separation of coinfecting phages attenuates the effective communication between them, allowing them to make decisions independently of each other. Our work establishes a highly quantitative framework to describe P1 lysogeny establishment. This system plays an important role in disseminating antibiotic resistance by P1-like plasmids and provides an alternative to the lifestyle of phage λ. IMPORTANCE Phage P1 has been shown potentially to play an important role in disseminating antibiotic resistance among bacteria during lysogenization, as evidenced by the prevalence of P1 phage-like elements in animal and human pathogens. In contrast to phage λ, a cell fate decision-making paradigm, P1 lysogenization was shown to be independent of MOI. In this work, we built a simple genetic model to elucidate this MOI independency based on the gene-regulatory circuitry of P1. We also proposed that the effective communication between coinfecting phages contributes to the lysis-lysogeny decision-making of P1 and highlighted the significance of spatial organization in the process of cell fate determination in a single-cell environment. Finally, our work provides new insights into different strategies acquired by viruses to interact with their bacterial hosts in different scenarios for their optimal survival.

In Vivo Uranium Sequestration using a Nanoscale Metal-Organic Framework.

An agent for actinide sequestration with fast uranium uptake kinetics and efficient in vivo uranium removal using a nanoscale metal-organic framework (nano-MOF) is proposed. UiO-66 nanoparticles post-synthetically functionalized with carboxyl groups, UiO-66-(COOH)4 -180, exhibit the fastest uranium uptake kinetics reported with more than 65 % of uranyl in fetal bovine serum (FBS) removed within 5 min. Moreover, the in vivo bio-distribution studies show that the material partially accumulates in kidneys and femurs where uranium mainly deposits facilitating the in vivo sequestration of uranium. The results of the in vivo uranium decorporation assays with mice show that UiO-66-(COOH)4 -180 could successfully reduce the amounts of uranyl deposited in kidneys and femurs by up to 55.4 % and 36.5 %, respectively, and is significantly more efficient than the commercial actinide decorporation agent, ZnNa3 -DTPA.

Intracellular Organization by Jumbo Bacteriophages.

Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.

Emerging heterogeneous compartments by viruses in single bacterial cells.

Spatial organization of biological processes allows for variability in molecular outcomes and coordinated development. Here, we investigate how organization underpins phage lambda development and decision-making by characterizing viral components and processes in subcellular space. We use live-cell and in situ fluorescence imaging at the single-molecule level to examine lambda DNA replication, transcription, virion assembly, and resource recruitment in single-cell infections, uniting key processes of the infection cycle into a coherent model of phage development encompassing space and time. We find that different viral DNAs establish separate subcellular compartments within cells, which sustains heterogeneous viral development in single cells. These individual phage compartments are physically separated by the E. coli nucleoid. Our results provide mechanistic details describing how separate viruses develop heterogeneously to resemble single-cell phenotypes.

Detection of proteins associated with the pyroptosis signaling pathway in breast cancer tissues and their significance.

OBJECTIVE: To study the expression of pyroptosis signaling pathway related proteins in breast cancer tissues and paracancer tissues, analyze their relationship with breast cancer clinicopathologic features, and explore their relationship to prognosis. METHODS: Immunohistochemistry ElivisionTM plus was used to detect the expression of caspase-1, IL-1ß and Gasdermin-D (GSDMD) in 108 cases of breast cancer and 23 cases of benign lesions adjacent to breast cancer. RESULTS: Using 108 cases of breast cancer and 23 cases of para-cancerous benign tissues, the pyroptosis signaling pathway effector proteins caspase-1, IL-1ß, and GSDMD were positively correlated with each other. The higher the expression level, the lower the histophologic grade of breast cancer, the smaller the tumor size, the lower the clinical stage, the lower the possibility of lymph node metastasis, the lower the risk of death, and the better the prognosis. CONCLUSIONS: Pyroptosis signaling pathway effectors caspase-1, IL-1ß and GSDMD expression may play an important role in the invasion, metastasis, and prognosis of breast cancer.

A unique uranyl framework containing uranyl pentamers as secondary building units: synthesis, structure, and spectroscopic properties.

Two three-dimensional uranyl framework compounds consisting of 1,2,4-benzenetricarboxylic ligands and uranyl units have been synthesized under mild solvothermal conditions. Compound 1 adopts an open framework structure built from uranyl pentamers, which is a rare topology for uranyl structures. Compound 2 is constructed from UO8 and UO7 bipyramids that are connected by the ligand to form a three-dimensional framework. As a consequence, compound 1 exhibits an unusual photoluminescence spectrum of one broad peak at 545 nm with a significant red shift compared to the typical uranyl emissive peaks as shown in the spectra of uranyl nitrate and compound 2. In addition, since compound 1 crystallizes in the noncentrosymmetric space group Cc, its secondary-harmonic generation property was measured under 1064 nm laser radiation, showing a moderate SHG signal response of 0.91 × KDP.

Biochemical characteristics and synergistic effect of two novel alginate lyases from Photobacterium sp. FC615.

BACKGROUND: Macroalgae and microalgae, as feedstocks for third-generation biofuel, possess competitive strengths in terms of cost, technology and economics. The most important compound in brown macroalgae is alginate, and the synergistic effect of endolytic and exolytic alginate lyases plays a crucial role in the saccharification process of transforming alginate into biofuel. However, there are few studies on the synergistic effect of endolytic and exolytic alginate lyases, especially those from the same bacterial strain. RESULTS: In this study, the endolytic alginate lyase AlyPB1 and exolytic alginate lyase AlyPB2 were identified from the marine bacterium Photobacterium sp. FC615. These two enzymes showed quite different and novel enzymatic properties whereas behaved a strong synergistic effect on the saccharification of alginate. Compared to that when AlyPB2 was used alone, the conversion rate of alginate polysaccharides to unsaturated monosaccharides when AlyPB1 and AlyPB2 acted on alginate together was dramatically increased approximately sevenfold. Furthermore, we found that AlyPB1 and AlyPB2 acted the synergistic effect basing on the complementarity of their substrate degradation patterns, particularly due to their M-/G-preference and substrate-size dependence. In addition, a novel method for sequencing alginate oligosaccharides was developed for the first time by combining the 1H NMR spectroscopy and the enzymatic digestion with the exo-lyase AlyPB2, and this method is much simpler than traditional methods based on one- and two-dimensional NMR spectroscopy. Using this strategy, the sequences of the final tetrasaccharide and pentasaccharide product fractions produced by AlyPB1 were easily determined: the tetrasaccharide fractions contained two structures, ΔGMM and ΔMMM, at a molar ratio of 1:3.2, and the pentasaccharide fractions contained four structures, ΔMMMM, ΔMGMM, ΔGMMM, and ΔGGMM, at a molar ratio of ~ 1:1.5:3.5:5.25. CONCLUSIONS: The identification of these two novel alginate lyases provides not only excellent candidate tool-type enzymes for oligosaccharide preparation but also a good model for studying the synergistic digestion and saccharification of alginate in biofuel production. The novel method for oligosaccharide sequencing described in this study will offer a very useful approach for structural and functional studies on alginate.

Comparative Study of Two Chondroitin Sulfate/Dermatan Sulfate 4-O-Sulfatases With High Identity.

Chondroitin sulfate/dermatan sulfate (CS/DS) sulfatases are potential tools for structural and functional studies of CD/DS chains. In our previous study, a CS/DS 4-O-endosulfatase (endoVB4SF) was identified from a marine bacterium (Wang et al., 2015). Herein, another CS/DS 4-O-sulfatase (exoPB4SF) was identified from a Photobacterium sp. ExoPB4SF shares an 83% identity with endoVB4SF but showed strict exolytic activity. Comparative studies were performed for both enzymes on the basis of biochemical features, substrate-degrading patterns and three-dimensional structures. exoPB4SF exhibited a wider temperature and pH adaptability and better thermostability than endoVB4SF. Furthermore, exoPB4SF is a strict exolytic sulfatase that only releases the sulfate group from the GalNAc residue located at the reducing end, whereas endoVB4SF preferentially removed sulfate esters from the reducing end toward the non-reducing end though its directional degradation property was not strict. In addition, the structure of endoVB4SF was determined by X-ray crystallography at 1.95 Å. It adopts a globular conformation with two monomers per asymmetric unit. The exoPB4SF structure was constructed by homology modeling. Molecular docking results showed that although the residues around the catalytic center are conserved, the residues at the active site of endoVB4SF adopted a more favorable conformation for the binding of long CS/DS chains than those of exoPB4SF, which may explain why the two highly homogenous sulfatases possessed different action patterns. The results of this study provide insight into the structure-function relationship of CS/DS endo- and exosulfatases for the first time.

Identification and Signature Sequences of Bacterial Δ4,5Hexuronate-2-O-Sulfatases.

Glycosaminoglycan (GAG) sulfatases, which catalyze the hydrolysis of sulfate esters from GAGs, belong to a large and conserved sulfatase family. Bacterial GAG sulfatases are essential in the process of sulfur cycling and are useful for the structural analysis of GAGs. Only a few GAG-specific sulfatases have been studied in detail and reported to date. Herein, the GAG-degrading Photobacterium sp. FC615 was isolated from marine sediment, and a novel Δ4,5hexuronate-2-O-sulfatase (PB2SF) was identified from this bacterium. PB2SF specifically removed 2-O-sulfate from the unsaturated hexuronate residue located at the non-reducing end of GAG oligosaccharides produced by GAG lyases. A structural model of PB2SF was constructed through a homology-modeling method. Six conserved amino acids around the active site were chosen for further analysis using site-directed mutagenesis. N113A, K141A, K141H, H143A, H143K, H205A, and H205K mutants exhibited only feeble activity, while the H310A, H310K, and D52A mutants were totally inactive, indicating that these conserved residues, particularly Asp52 and His310, were essential in the catalytic mechanism. Furthermore, bioinformatic analysis revealed that GAG sulfatases with specific degradative properties clustered together in the neighbor-joining phylogenetic tree. Based on this finding, 60 Δ4,5hexuronate-2-O-sulfatases were predicted in the NCBI protein database, and one with relatively low identity to PB2SF was characterized to confirm our prediction. Moreover, the signature sequences of bacterial Δ4,5hexuronate-2-O-sulfatases were identified. With the reported signature motifs, the sulfatase sequence of the Δ4,5hexuronate-2-O-sulfatase family could be simply identified before cloning. Taken together, the results of this study should aid in the identification and further application of novel GAG sulfatases.

3-Hydroxy-2-Pyrrolidinone as a Potential Bidentate Ligand for in Vivo Chelation of Uranyl with Low Cytotoxicity and Moderate Decorporation Efficacy: A Solution Thermodynamics, Structural Chemistry, and in Vivo Uranyl Removal Survey.

Uranium poses a threat for severe renal and bone damage in vivo. With the rapid development of nuclear industry, it is more urgent than ever to search for potential in vivo uranium chelators. In this work, 3-hydroxy-2-pyrrolidinone (HPD) is investigated as a new potential uranium decorporation ligand. The potentiometric titration measurements were carried out, and the stability constants were determined to be log ß110 = 10.5(7), log ß120 = 20.7(9), and log ß130 = 28.2(4). The species distribution diagram shows that nearly all uranyl is complexed by HPD at pH 7.4 under the defined condition. A single crystal of uranyl and HPD complexes, [(UO2)3O(H2O)3(C4H6NO2)3]·NO3·12H2O (uranyl-HPD), was obtained via an evaporation method. The overall structure of uranyl-HPD is a trimer that consists of three uranyl units and three HPD ligands. The uranyl unit is equatorially coordinated by three oxygen atoms from two HPD agents, one coordinated water molecule, and one µ3-O atom that is shared by three uranyl units. The results of the cytotoxicity assay indicate that the ligand is less toxic than the chelators used clinically (i.e., DTPA-ZnNa3 and 3-hydroxy-1,2-dimethyl-4(1 H)-pyridone (DFP)). The results of the uranium removal assay using the NRK-52E cell show that it could reduce as much as 58% of the uranium content at the cellular level. Furthermore, the in vivo uranium decorporation assays demonstrate that HPD can remove 52% of uranium deposited in the kidney but shows poor uranium removal efficacy in the bone.

The role of side tail fibers during the infection cycle of phage lambda.

Bacteriophage λ has served as an important model for molecular biology and different cellular processes over the past few decades. In 1992, the phage strain used in most laboratories around the world, thought of as λ wild type, was discovered to carry a mutation in the stf gene which encodes four side tail fibers. Up to now, the role of the side tail fibers during the infection cycle, especially at the single-cell level, remains largely unknown. Here we utilized fluorescent reporter systems to characterize the effect of the side tail fibers on phage infection. We found that the side tail fibers interfere with phage DNA ejection process, most likely through the binding with their receptors, OmpC, leading to a more frequent failed infection. However, the side tail fibers do not seem to affect the lysis-lysogeny decision-making or lysis time.

Coupling of DNA Replication and Negative Feedback Controls Gene Expression for Cell-Fate Decisions.

Cellular decision-making arises from the expression of genes along a regulatory cascade, which leads to a choice between distinct phenotypic states. DNA dosage variations, often introduced by replication, can significantly affect gene expression to ultimately bias decision outcomes. The bacteriophage lambda system has long served as a paradigm for cell-fate determination, yet the effect of DNA replication remains largely unknown. Here, through single-cell studies and mathematical modeling we show that DNA replication drastically boosts cI expression to allow lysogenic commitment by providing more templates. Conversely, expression of CII, the upstream regulator of cI, is surprisingly robust to DNA replication due to the negative autoregulation of the Cro repressor. Our study exemplifies how living organisms can not only utilize DNA replication for gene expression control but also implement mechanisms such as negative feedback to allow the expression of certain genes to be robust to dosage changes resulting from DNA replication.

Visualization of phage DNA degradation by a type I CRISPR-Cas system at the single-cell level.

BACKGROUND: The CRISPR-Cas system is a widespread prokaryotic defense system which targets and cleaves invasive nucleic acids, such as plasmids or viruses. So far, a great number of studies have focused on the components and mechanisms of this system, however, a direct visualization of CRISPR-Cas degrading invading DNA in real-time has not yet been studied at the single-cell level. METHODS: In this study, we fluorescently label phage lambda DNA in vivo, and track the labeled DNA over time to characterize DNA degradation at the single-cell level. RESULTS: At the bulk level, the lysogenization frequency of cells harboring CRISPR plasmids decreases significantly compared to cells with a non-CRISPR control. At the single-cell level, host cells with CRISPR activity are unperturbed by phage infection, maintaining normal growth like uninfected cells, where the efficiency of our anti-lambda CRISPR system is around 26%. During the course of time-lapse movies, the average fluorescence of invasive phage DNA in cells with CRISPR activity, decays more rapidly compared to cells without, and phage DNA is fully degraded by around 44 minutes on average. Moreover, the degradation appears to be independent of cell size or the phage DNA ejection site suggesting that Cas proteins are dispersed in sufficient quantities throughout the cell. CONCLUSIONS: With the CRISPR-Cas visualization system we developed, we are able to examine and characterize how a CRISPR system degrades invading phage DNA at the single-cell level. This work provides direct evidence and improves the current understanding on how CRISPR breaks down invading DNA.