Topological Behavior of Plasmid DNA

From non-affinity to high-affinity: Rapid preparation of nanobodies utilizing high-precision alphafold and structural-interaction analysis for detection of enrofloxacin in marine fish

Traditional antibody preparation methods rely on animal immunization and experimental screening, often requiring 3-6 months, which cannot meet the urgent demands for antibodies in environmental emergencies or contamination events. Herein, a rapid antibody preparation method was proposed to transform anti-macromolecule nanobodies into high-affinity anti-small molecule (enrofloxacin) nanobodies, based on the high-precision predictive capabilities of AlphaFold, integrated with structural and interaction analysis. The high-precision prediction capability of AlphaFold ensured the accuracy of nanobody structural analysis and targeted modification. Binding structure design enabled the antigen and antibody to adopt an optimal binding conformation. Interaction analysis provided guidance for targeted modifications and served as a tool for evaluating the results. Molecular docking results revealed that the template nanobodies, which initially couldn't dock with enrofloxacin, formed 3-5 noncovalent bonds after modification. Bio-layer interferometry (BLI) assays demonstrated that the equilibrium dissociation constant (KD) of the modified nanobodies ranged from 5.56 ± 0.34 nM to 94.73 ± 4.35 nM, with half-maximal inhibitory concentration (IC50) between 231.9 and 3293.6 ng/mL. Based on the modified nanobodies and BLI platform, the detection of enrofloxacin in marine fish was achieved with a limit of detection (LOD) as low as 59.97 μg/kg. In summary, this study provided a novel perspective for the rapid nanobody preparation, showing significant potential in food safety and environmental monitoring.

Generation of topologically defined linear and cyclic DNA bottle brush polymers via a graft-to approach

Herein, we report a graft-to approach for synthesizing linear and circular double-stranded DNA (dsDNA) bottlebrush polymers (BBPs). Using a bioreactor, plasmid DNA (pDNA) serves as an inexpensive and abundant source of circular, biodegradable, and unimolecular polymers. pDNA is easily converted to the linear isoform through enzymatic restriction, providing access to polymeric backbones with distinct topological states. DNA is grafted with polyethylene glycol monomethyl ether chloroethylamines (mPEGCEA) to yield DNA BBPs. Importantly this PEGylation occurs rapidly under ambient conditions in aqueous buffer. By varying the molecular weight of mPEGCEA (M w = 750, 2000, 5000 Da) and the concentration relative to μmol of nucleotides, different brush arm densities and lengths were achieved with both linear and macrocyclic DNA backbones. Analysis of the DNA BBPs was achieved through agarose gel electrophoresis, which showed graft densities of up to ~68% and ~74% for linear and ring DNA respectively. The grafting process does not alter base pairing or circularity as determined using atomic force microscopy. Shear rheology was used to compare the mechanical response of 1% wt/wt solutions of the ring and linear DNA BBPs to their un-alkylated forms. Linear DNA BBPs exhibited a lower shear modulus versus linear DNA, which is expected due to the increased persistence length and decreased ability to interpenetrate associated with the attachment of polymer arms. However, the circular DNA BBPs exhibited a universally higher shear modulus versus the un-alkylated sample suggesting an increase in interchain interaction via addition of polymer arms. Finally, the increased steric encumbrance of the DNA BBPs slows enzymatic degradation, potentially providing a general method to increase stability of DNA constructs towards nuclease.

Quality assessment strategy development and analytical method selection of GMP grade biological drugs for gene and cell therapy

Biological drugs with gene and cell therapy potentials, including natural or rationally created biomacromolecules, recombinant proteins/enzymes, gene-carrying DNA/RNA fragments, oncolytic viruses, plasmid and viral vectors or other gene delivering vehicles with specific therapeutic genes and gene manipulation tools, and genetically modified and reprogrammed human cells comprise a large fraction of drug development candidates in modern precision and regeneration medicine. These drugs have displayed unique capabilities in treating patients with previously incurable diseases. However, most of the drug preparations have complex multimolecular structures and require specific biomanufacturing systems and many other additional biological active materials for drug synthesis, cell expansion, and production enhancement. Thus, the final products would have to be subjected to sequential extensive purification processes to exclude impurities and to concentrate the drug products after manufacturing. The quality evaluation for each drug product is an individualized process and must be specifically designed and performed according to the characteristics of the drug and its manufacturing and purification methods. Some of the Quality Control (QC) assays may be very costly and time-consuming, frequently with inconsistent test results from batch-to-batch. This review focuses on QC assessment strategy development for common gene and cell therapy drugs which use prokaryotic or eukaryotic cells for manufacturing or cell factories for in vitro expansions, especially for drug identification and concentration determination, impurity detection and quantification, drug potency, stability, and safety evaluations; and discusses some key issues for drug quality assessments in different categories and emphasizes the importance of individualized QC strategy design.

PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools

Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They contain diverse functional elements and are capable of horizontal gene transfer among hosts. While existing plasmid databases have archived plasmid sequences isolated from individual microorganisms or natural environments, there is a need for a comprehensive, standardized, and annotated plasmid database to address the vast accumulation of plasmid sequences. Here, we propose PlasmidScope (https://plasmid.deepomics.org/), a plasmid database offering comprehensive annotations, automated online analysis, and interactive visualization. PlasmidScope harbors a substantial collection of 852 600 plasmids curated from 10 repositories. Along with consolidated background information, PlasmidScope utilizes 12 state-of-the-art tools and provides comprehensive annotations for the curated plasmids, covering genome completeness, topological structure, mobility, host source, tRNA, tmRNA, signal peptides, transmembrane proteins and CRISPR/Cas systems. PlasmidScope offers diverse functional annotations for its 25 231 059 predicted genes from 9 databases as well as corresponding protein structures predicted by ESMFold. In addition, PlasmidScope integrates online analytical modules and interactive visualization, empowering researchers to delve into the complexities of plasmids.

Rapid transformation of nanobodies affinity based on AlphaFold2's high-accuracy predictions and interaction analysis for enrofloxacin detection in coastal fish

High-affinity antibodies are crucial in biosensors, disease diagnostics, therapeutic drug development, and immunological analysis, making the enhancement of antibody affinity a key research focus within the field. Computer-aided design is recognized as a time-saving and labor-efficient method for nanobodies in vitro affinity maturation. Compared to experimental mutagenesis techniques, it is advantageous due to the elimination of the need for laborious library construction and screening processes. However, these approaches are constrained by structural prediction since inaccuracy in structure could readily result in maturation failures. Herein, a novel nanobodies modification method for in vitro affinity maturation, utilizing the high accuracy prediction of AlphaFold2, was employed to rapidly transform a low affinity nanobody against enrofloxacin (ENR) into one with high affinity. The molecular docking results revealed a 1.5- to 2.5-fold increase in the number of noncovalent interactions of modified nanobodies, accompanied by a reduction in binding free energy ranging from 14.1 to 62.6%. The evaluation results from ELISA and BLI indicated that the affinity of the modified nanobodies had been enhanced by 6.2-91.6 times compared to the template nanobody. Furthermore, the modified nanobodies were employed for the detection of ENR-spiked coastal fish samples. In summary, this research proposed a nanobodies modification method from a new perspective, endowing its great application potential in biosensors, food safety, and environmental monitoring.

Spatio-temporal organization of the E. coli chromosome from base to cellular length scales

Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.

Reentrant DNA shells tune polyphosphate condensate size

The inorganic biopolymer polyphosphate (polyP) occurs in all domains of life and affects myriad cellular processes. A longstanding observation is polyP's frequent proximity to chromatin, and, in many bacteria, its occurrence as magnesium (Mg2+)-enriched condensates embedded in the nucleoid region, particularly in response to stress. The physical basis of the interaction between polyP, DNA and Mg2+, and the resulting effects on the organization of the nucleoid and polyP condensates, remain poorly understood. Here, using a minimal system of polyP, Mg2+, and DNA, we find that DNA can form shells around polyP-Mg2+ condensates. These shells show reentrant behavior, that is, they form within a window of Mg2+ concentrations, representing a tunable architecture with potential relevance in other multicomponent condensates. This surface association tunes condensate size and DNA morphology in a manner dependent on DNA length and concentration, even at DNA concentrations orders of magnitude lower than found in the cell. Our work also highlights the remarkable capacity of two primordial inorganic species to organize DNA.

Torsional Mechanics of Circular DNA

Circular DNA found in the cell is actively regulated to an underwound state, with their superhelical density close to σ ~ - 0 . 06 . While this underwound state is essential to life, how it impacts the torsional mechanical properties of DNA is not fully understood. In this work, we performed simulations to understand the torsional mechanics of circular DNA and validated our results with single-molecule measurements and analytical theory. We found that the torque generated at σ ~ - 0 . 06 is near but slightly below that required to melt DNA, significantly decreasing the energy barrier for proteins that interact with melted DNA. Furthermore, supercoiled circular DNA experiences force (tension) and torque that are equally distributed through the DNA contour. We have also extended a previous analytical framework to show how the plectonemic twist persistence length depends on the intrinsic bending persistence length and twist persistence length. Our work establishes a framework for understanding DNA supercoiling and torsional dynamics of circular DNA.

Ratiometric nonfluorescent CRISPR assay utilizing Cas12a-induced plasmid supercoil relaxation

Most CRISPR-based biosensors rely on labeled reporter molecules and expensive equipment for signal readout. A recent approach quantifies analyte concentration by sizing λ DNA reporters via gel electrophoresis, providing a simple solution for label-free detection. Here, we report an alternative strategy for label-free CRISPR-Cas12a, which relies on Cas12a trans-nicking induced supercoil relaxation of dsDNA plasmid reporters to generate a robust and ratiometric readout. The ratiometric CRISPR (rCRISPR) measures the relative percentage of supercoiled plasmid DNA to the relaxed circular DNA by gel electrophoresis for more accurate target concentration quantification. This simple method is two orders of magnitude more sensitive than the typical fluorescent reporter. This self-referenced strategy solves the potential application limitations of previously demonstrated DNA sizing-based CRISPR-Dx without compromising the sensitivity. Finally, we demonstrated the applicability of rCRISPR for detecting various model DNA targets such as HPV 16 and real AAV samples, highlighting its feasibility for point-of-care CRISPR-Dx applications.

A Ru(II)-Strained Complex with 2,9-Diphenyl-1,10-phenanthroline Ligand Induces Selective Photoactivatable Chemotherapeutic Activity on Human Alveolar Carcinoma Cells via Apoptosis

[Ru(bipy)2(dpphen)]Cl2 (where bipy = 2,2'-bipyridine and dpphen = 2,9-diphenyl-1,10-phenanthroline) (complex 1) is a sterically strained compound that exhibits promising in vitro photocytotoxicity on an array of cell lines. Since lung adenocarcinoma cancer remains the most common lung cancer and the leading cause of cancer deaths, the current study aims to evaluate the plausible effect and uptake of complex 1 on human alveolar carcinoma cells (A549) and mesenchymal stem cells (MSC), and assess its cytotoxicity in vitro while considering its effect on cell morphology, membrane integrity and DNA damage. MSC and A549 cells showed similar rates of complex 1 uptake with a plateau at 12 h. Upon photoactivation, complex 1 exhibited selective, potent anticancer activity against A549 cells with phototoxicity index (PI) values of 16, 25 and 39 at 24, 48 and 72 h, respectively. This effect was accompanied by a significant increase in A549-cell rounding and detachment, loss of membrane integrity and DNA damage. Flow cytometry experiments confirmed that A549 cells undergo apoptosis when treated with complex 1 followed by photoactivation. In conclusion, this present study suggests that complex 1 might be a promising candidate for photochemotherapy with photoproducts that possess selective anticancer effects in vitro. These results are encouraging to probe the potential activity of this complex in vivo.

Development of a Holistic In Vitro Cell-Free Approach to Determine the Redox Bioactivity of Agricultural Products

In recent years, there has been a strong consumer demand for food products that provide nutritional benefits to human health. Therefore, the assessment of the biological activity is considered as an important parameter for the promotion of high-quality food products. Herein, we introduce a novel methodology comprising a complete set of in vitro cell-free screening techniques for the evaluation of the bioactivity of various food products on the basis of their antioxidant capacity. These assays examine the free radical scavenging activities, the reducing properties, and the protective ability against oxidative damage to biomolecules. The adoption of the proposed battery of antioxidant assays is anticipated to contribute to the holistic characterization of the bioactivity of the food product under examination. Consumer motivations and expectations with respect to nutritious food products with bio-functional properties drive the global food market toward food certification. Therefore, the development and application of scientific methodologies that examine the quality characteristics of food products could increase consumers' trust and promote their beneficial properties for human health.

Synthetic lethal mutants in Escherichia coli define pathways necessary for survival with RNase H deficiency

Ribonucleotides frequently contaminate DNA and, if not removed, cause genomic instability. Consequently, all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids (RDHs). Escherichia coli lacking RNase HI (rnhA) and RNase HII (rnhB) enzymes, the ∆rnhA ∆rnhB double mutant, accumulates RDHs in its DNA. These RDHs can convert into RNA-containing DNA lesions (R-lesions) of unclear nature that compromise genomic stability. The ∆rnhAB double mutant has severe phenotypes, like growth inhibition, replication stress, sensitivity to ultraviolet radiation, SOS induction, increased chromosomal fragmentation, and defects in nucleoid organization. In this study, we found that RNase HI deficiency also alters wild-type levels of DNA supercoiling. Despite these severe chromosomal complications, ∆rnhAB double mutant survives, suggesting that dedicated pathways operate to avoid or repair R-lesions. To identify these pathways, we systematically searched for mutants synthetic lethal (colethal) with the rnhAB defect using an unbiased color screen and a candidate gene approach. We identified both novel and previously reported rnhAB-colethal and -coinhibited mutants, characterized them, and sorted them into avoidance or repair pathways. These mutants operate in various parts of nucleic acid metabolism, including replication fork progression, R-loop prevention and removal, nucleoid organization, tRNA modification, recombinational repair, and chromosome-dimer resolution, demonstrating the pleiotropic nature of RNase H deficiency. IMPORTANCE Ribonucleotides (rNs) are structurally very similar to deoxyribonucleotides. Consequently, rN contamination of DNA is common and pervasive across all domains of life. Failure to remove rNs from DNA has severe consequences, and all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids. RNase H deficiency leads to complications in bacteria, yeast, and mouse, and diseases like progressive external ophthalmoplegia (mitochondrial defects in RNASEH1) and Aicardi-Goutières syndrome (defects in RNASEH2) in humans. Escherichia coli ∆rnhAB mutant, deficient in RNases H, has severe chromosomal complications. Despite substantial problems, nearly half of the mutant population survives. We have identified novel and previously confirmed pathways in various parts of nucleic acid metabolism that ensure survival with RNase H deficiency.

Physical characteristics and stability profile of recombinant plasmid DNA within a film matrix

Plasmids are essential source material for production of biological drugs, vaccines and vectors for gene therapy. They are commonly formulated as frozen solutions. Considering the cost associated with maintenance of cold chain conditions during storage and transport, there is a significant need for alternative methods for stabilization of plasmids at ambient temperature. The objective of these studies was to identify a film-based formulation that preserved transfection efficiency of plasmids at 25 °C. A model plasmid, pAAVlacZ, was used for these studies. Transfection efficiency and agarose gel electrophoresis were utilized to assess bioactivity and changes in physical conformation of plasmid during storage. An amino acid, capable of sustaining a positive charge while supporting an alkaline environment within the film matrix, preserved transfection efficiency for 9 months at 25 °C. Addition of sugar and a plasticizer to the formulation preserved the plasmid in an amorphous state and improved handling properties of the film. The manner in which excipients were incorporated into bulk formulations and environmental humidity in which films were stored significantly impacted transfection efficiency of plasmid in the rehydrated solution. Taken together, these results suggest that plasmids can be stored for extended periods of time without refrigeration within a film matrix.

PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer

Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.

Comparative Genomics of a Polyvalent Escherichia-Salmonella Phage fp01 and In Silico Analysis of Its Receptor Binding Protein and Conserved Enterobacteriaceae Phage Receptor

The polyvalent bacteriophage fp01, isolated from wastewater in Valparaiso, Chile, was described to have lytic activity across bacterial species, including Escherichia coli and Salmonella enterica serovars. Due to its polyvalent nature, the bacteriophage fp01 has potential applications in the biomedical, food and agricultural industries. Also, fundamental aspects of polyvalent bacteriophage biology are unknown. In this study, we sequenced and described the complete genome of the polyvalent phage fp01 (MH745368.2) using long- (MinION, Nanopore) and short-reads (MiSeq, Illumina) sequencing. The bacteriophage fp01 genome has 109,515 bp, double-stranded DNA with an average G+C content of 39%, and 158 coding sequences (CDSs). Phage fp01 has genes with high similarity to Escherichia coli, Salmonella enterica, and Shigella sp. phages. Phylogenetic analyses indicated that the phage fp01 is a new Tequintavirus fp01 specie. Receptor binding protein gp108 was identified as potentially responsible for fp01 polyvalent characteristics, which binds to conserved amino acid regions of the FhuA receptor of Enterobacteriaceae.

A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex

CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.

Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics

Measurements of protein-mediated DNA looping reveal that in vivo conditions favor the formation of loops shorter than those that occur in vitro, yet the precise physical mechanisms underlying this shift remain unclear. To understand the extent to which in vivo supercoiling may explain these shifts, we develop a theoretical model based on coarse-grained molecular simulation and analytical transition state theory, enabling us to map out looping energetics and kinetics as a function of two key biophysical parameters: superhelical density and loop length. We show that loops on the scale of a persistence length respond to supercoiling over a much wider range of superhelical densities and to a larger extent than longer loops. This effect arises from a tendency for loops to be centered on the plectonemic end region, which bends progressively more tightly with superhelical density. This trend reveals a mechanism by which supercoiling favors shorter loop lengths. In addition, our model predicts a complex kinetic response to supercoiling for a given loop length, governed by a competition between an enhanced rate of looping due to torsional buckling and a reduction in looping rate due to chain straightening as the plectoneme tightens at higher superhelical densities. Together, these effects lead to a flattening of the kinetic response to supercoiling within the physiological range for all but the shortest loops. Using experimental estimates for in vivo superhelical densities, we discuss our model's ability to explain available looping data, highlighting both the importance of supercoiling as a regulatory force in genetics and the additional complexities of looping phenomena in vivo.

A new device-mediated miniprep method

Small-scale plasmid DNA preparation or miniprep is a fundamental technique in estimation cloning experiments and is widely used for DNA methylation analysis in epigenetic research. Current plasmid DNA minipreps use the alkali-SDS-based method in a three-solution format and require spin column-based purification steps. This procedure requires the vortexing or pipetting of pelleted bacteria by centrifugation and manual mixing of the solutions. Here, we describe a centrifuge/mixer-based instrument with the ability to perform centrifugation, vibration, and rotor oscillation in order to perform all steps of plasmid DNA isolation by device only. We found that by applying rotor oscillation-driven mixing of solutions added in the lysis and neutralization steps, homogeneous mixing was achieved within 5 s at a rotor oscillation amplitude of 45° and oscillation frequency of 400 ± 30 rpm, yielding the maximal quantity and quality of plasmid DNA. No increase in host chromosome presence purified by this approach occurs for high-copy-number plasmids compared to manually performed miniprep, and indeed, there is a significant decrease in the presence of the chromosomal fraction in low-copy-number plasmids. The supercoiled form of plasmid DNA purified at a rotor oscillation amplitude of 45° does not turn into an open circular (OC) isoform when the plasmid is stored for 1 year at plus four degrees, in contrast to the plasmid purified with rotor oscillation amplitudes of 270°, 180° and 90°. The programmed time-work-efficient protocol of plasmid miniprep installed in the device gives the extreme simplicity of plasmid minipreps speeding up and facilitating the isolation of plasmid DNAs.

New devise-mediated plasmid miniprep method (DM) performs all mixing steps without operator intervention.

The DM method produces plasmid DNAs free of the dCCC form and significantly reduces the contamination with genomic DNA in the low-copy-number plasmid.

DM miniprep plasmids are reliable templates for bisulfite PCR sequencing analysis.

Dioxin Disrupts Thyroid Hormone and Glucocorticoid Induction of klf9, a Master Regulator of Frog Metamorphosis

Frog metamorphosis, the development of an air-breathing froglet from an aquatic tadpole, is controlled by thyroid hormone (TH) and glucocorticoids (GC). Metamorphosis is susceptible to disruption by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AHR) agonist. Krüppel-like factor 9 (klf9), an immediate early gene in the endocrine-controlled cascade of expression changes governing metamorphosis, can be synergistically induced by both hormones. This process is mediated by an upstream enhancer cluster, the klf9 synergy module (KSM). klf9 is also an AHR target. We measured klf9 mRNA following exposures to triiodothyronine (T3), corticosterone (CORT), and TCDD in the Xenopus laevis cell line XLK-WG. klf9 was induced 6-fold by 50 nM T3, 4-fold by 100 nM CORT, and 3-fold by 175 nM TCDD. Cotreatments of CORT and TCDD or T3 and TCDD induced klf9 7- and 11-fold, respectively, whereas treatment with all 3 agents induced a 15-fold increase. Transactivation assays examined enhancers from the Xenopus tropicalis klf9 upstream region. KSM-containing segments mediated a strong T3 response and a larger T3/CORT response, whereas induction by TCDD was mediated by a region ∼1 kb farther upstream containing 5 AHR response elements (AHREs). This region also supported a CORT response in the absence of readily identifiable GC responsive elements, suggesting mediation by protein-protein interactions. A functional AHRE cluster is positionally conserved in the human genome, and klf9 was induced by TCDD and TH in HepG2 cells. These results indicate that AHR binding to upstream AHREs represents an early key event in TCDD's disruption of endocrine-regulated klf9 expression and metamorphosis.

DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions

The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by⁶⁰Co or¹³⁷Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.

Bacterial transcription during growth arrest

Bacteria in most natural environments spend substantial periods of time limited for essential nutrients and not actively dividing. While transcriptional activity under these conditions is substantially reduced compared to that occurring during active growth, observations from diverse organisms and experimental approaches have shown that new transcription still occurs and is important for survival. Much of our understanding of transcription regulation has come from measuring transcripts in exponentially growing cells, or from in vitro experiments focused on transcription from highly active promoters by the housekeeping RNA polymerase holoenzyme. The fact that transcription during growth arrest occurs at low levels and is highly heterogeneous has posed challenges for its study. However, new methods of measuring low levels of gene expression activity, even in single cells, offer exciting opportunities for directly investigating transcriptional activity and its regulation during growth arrest. Furthermore, much of the rich structural and biochemical data from decades of work on the bacterial transcriptional machinery is also relevant to growth arrest. In this review, the physiological changes likely affecting transcription during growth arrest are first considered. Next, possible adaptations to help facilitate ongoing transcription during growth arrest are discussed. Finally, new insights from several recently published datasets investigating mRNA transcripts in single bacterial cells at various growth phases will be explored. Keywords: Growth arrest, stationary phase, RNA polymerase, nucleoid condensation, population heterogeneity.

Actin-Related Protein 6 (Arp6) Influences Double-Strand Break Repair in Yeast

DNA double-strand breaks (DSBs) are the most deleterious form of DNA damage and are repaired through non-homologous end-joining (NHEJ) or homologous recombination (HR). Repair initiation, regulation and communication with signaling pathways require several histone-modifying and chromatin-remodeling complexes. In budding yeast, this involves three primary complexes: INO80-C, which is primarily associated with HR, SWR1-C, which promotes NHEJ, and RSC-C, which is involved in both pathways as well as the general DNA damage response. Here we identify ARP6 as a factor involved in DSB repair through an RSC-C-related pathway. The loss of ARP6 significantly reduces the NHEJ repair efficiency of linearized plasmids with cohesive ends, impairs the repair of chromosomal breaks, and sensitizes cells to DNA-damaging agents. Genetic interaction analysis indicates that ARP6, MRE11 and RSC-C function within the same pathway, and the overexpression of ARP6 rescues rsc2∆ and mre11∆ sensitivity to DNA-damaging agents. Double mutants of ARP6, and members of the INO80 and SWR1 complexes, cause a significant reduction in repair efficiency, suggesting that ARP6 functions independently of SWR1-C and INO80-C. These findings support a novel role for ARP6 in DSB repair that is independent of the SWR1 chromatin remodeling complex, through an apparent RSC-C and MRE11-associated DNA repair pathway.

Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides

In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.

Sequence and Nuclease Requirements for Breakage and Healing of a Structure-Forming (AT)n Sequence within Fragile Site FRA16D

Common fragile sites (CFSs) are genomic regions that display gaps and breaks in human metaphase chromosomes under replication stress and are often deleted in cancer cells. We studied an ∼300-bp subregion (Flex1) of human CFS FRA16D in yeast and found that it recapitulates characteristics of CFS fragility in human cells. Flex1 fragility is dependent on the ability of a variable-length AT repeat to form a cruciform structure that stalls replication. Fragility at Flex1 is initiated by structure-specific endonuclease Mus81-Mms4 acting together with the Slx1-4/Rad1-10 complex, whereas Yen1 protects Flex1 against breakage. Sae2 is required for healing of Flex1 after breakage. Our study shows that breakage within a CFS can be initiated by nuclease cleavage at forks stalled at DNA structures. Furthermore, our results suggest that CFSs are not just prone to breakage but also are impaired in their ability to heal, and this deleterious combination accounts for their fragility.

Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles

We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.

Controlling Heterogeneity and Increasing Titer from Riboswitch-Regulated Bacillus subtilis Spores for Time-Delayed Protein Expression Applications

Sporulated cells have potential as time-delayed expression chassis of proteins for applications such as "on-demand" biologics production, whole cell biosensors, or oral vaccines. However, the desired attributes of high expression rates and low product variances are difficult to maintain from germinated spores. In this work, we study the effect of an integrating vs theta-replicating plasmid in a wild-type Bacillus subtilis and two PolY mutants. The cells were engineered to produce a fluorescent reporter protein (RFP) under the control of a riboswitch activated by theophylline. This allowed for greater sensitivity to point mutations. The fluorescence and cell-growth curves were fit with a custom kinetic model, and a peak kinetic rate (LKP_max) was extracted for each clonal population (n = 30 for all cell, vector, and growth combinations). Plasmid-based expression yields higher (8.7×) expression rates because of an increased copy number of the expression cassette (10× over integrated). The variance of LKP_max values increased 2.1× after sporulation for the wild-type strain. This increase in variance from sporulation is very similar to what is observed with UV exposure. This effect can be partially mitigated by the use of PolY knockouts observed in suspended cell growths and adherent biofilms.

Dependence of DNA looping on Escherichia coli culture density

Repression of a promoter by entrapment within a tightly bent DNA loop is a common mechanism of gene regulation in bacteria. Besides the mechanical properties of the looped DNA and affinity of the protein that anchors the loop, cellular energetics and DNA negative supercoiling are likely factors determining the stability of the repression loop. E. coli cells undergo numerous highly regulated and dynamic transitions as resources are depleted during bacterial growth. We hypothesized that the probability of DNA looping depends on the growth status of the E. coli culture. We utilized a well-characterized repression loop model assembled from elements of the lac operon to measure loop length-dependent repression at three different culture densities. Remarkably, even with changes in supercoiling, there exists a dynamic compensation in which the contribution of DNA looping to gene repression remains essentially constant.

Application of Plasmid Engineering to Enhance Yield and Quality of Plasmid for Vaccine and Gene Therapy

There is an increased interest in plasmid DNA as therapeutics. This is evident in the number of ongoing clinical trials involving the use of plasmid DNA. In order to be an effective therapeutic, high yield and high level of supercoiling are required. From the bioprocessing point of view, the supercoiling level potentially has an impact on the ease of downstream processing. We approached meeting these requirements through plasmid engineering. A 7.2 kb plasmid was developed by the insertion of a bacteriophage Mu strong gyrase-binding sequence (Mu-SGS) to a 6.8 kb pSVβ-Gal and it was used to transform four different E. coli strains, and cultured in order to investigate the Mu-SGS effect and dependence on strain. There was an increase of over 20% in the total plasmid yield with pSVβ-Gal398 in two of the strains. The supercoiled topoisomer content was increased by 5% in both strains leading to a 27% increase in the overall yield. The extent of supercoiling was examined using superhelical density (σ) quantification with pSVβ-Gal398 maintaining a superhelical density of −0.022, and pSVβ-Gal −0.019, in both strains. This study has shown that plasmid modification with the Mu-phage SGS sequence has a beneficial effect on improving not only the yield of total plasmid but also the supercoiled topoisomer content of therapeutic plasmid DNA during bioprocessing.

Chromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures

Temperature shifts trigger genome-wide changes in Escherichia coli's gene expression. We studied if chromosome integration impacts on a gene's sensitivity to these shifts, by comparing the single-RNA production kinetics of a PLacO3O1 promoter, when chromosomally-integrated and when single-copy plasmid-borne. At suboptimal temperatures their induction range, fold change, and response to decreasing temperatures are similar. At critically low temperatures, the chromosome-integrated promoter becomes weaker and noisier. Dissection of its initiation kinetics reveals longer lasting states preceding open complex formation, suggesting enhanced supercoiling buildup. Measurements with Gyrase and Topoisomerase I inhibitors suggest hindrance to escape supercoiling buildup at low temperatures. Consistently, similar phenomena occur in energy-depleted cells by DNP at 30 °C. Transient, critically-low temperatures have no long-term consequences, as raising temperature quickly restores transcription rates. We conclude that the chromosomally-integrated PLacO3O1 has higher sensitivity to low temperatures, due to longer-lasting super-coiled states. A lesser active, chromosome-integrated native lac is shown to be insensitive to Gyrase overexpression, even at critically low temperatures, indicating that the rate of escaping positive supercoiling buildup is temperature and transcription rate dependent. A genome-wide analysis supports this, since cold-shock genes exhibit atypical supercoiling-sensitivities. This phenomenon might partially explain the temperature-sensitivity of some transcriptional programs of E. coli.

Plasmid Characteristics Modulate the Propensity of Gene Exchange in Bacterial Vesicles

Horizontal gene transfer is responsible for the exchange of many types of genetic elements, including plasmids. Properties of the exchanged genetic element are known to influence the efficiency of transfer via the mechanisms of conjugation, transduction, and transformation. Recently, an alternative general pathway of horizontal gene transfer has been identified, namely, gene exchange by extracellular vesicles. Although extracellular vesicles have been shown to facilitate the exchange of several types of plasmids, the influence of plasmid characteristics on genetic exchange within vesicles is unclear. Here, a set of different plasmids was constructed to systematically test the impact of plasmid properties, specifically, plasmid copy number, size, and origin of replication, on gene transfer in vesicles. The influence of each property on the production, packaging, and uptake of vesicles containing bacterial plasmids was quantified, revealing how plasmid properties modulate vesicle-mediated horizontal gene transfer. The loading of plasmids into vesicles correlates with the plasmid copy number and is influenced by characteristics that help set the number of plasmids within a cell, including size and origin of replication. Plasmid origin also has a separate impact on both vesicle loading and uptake, demonstrating that the origin of replication is a major determinant of the propensity of specific plasmids to transfer within extracellular vesicles.IMPORTANCE Extracellular vesicle formation and exchange are common within bacterial populations. Vesicles package multiple types of biomolecules, including genetic material. The exchange of extracellular vesicles containing genetic material facilitates interspecies DNA transfer and may be a promiscuous mechanism of horizontal gene transfer. Unlike other mechanisms of horizontal gene transfer, it is unclear whether characteristics of the exchanged DNA impact the likelihood of transfer in vesicles. Here, we systematically examine the influence of plasmid copy number, size, and origin of replication on the loading of DNA into vesicles and the uptake of DNA containing vesicles by recipient cells. These results reveal how each plasmid characteristic impacts gene transfer in vesicles and contribute to a greater understanding of the importance of vesicle-mediated gene exchange in the landscape of horizontal gene transfer.

Increase of positive supercoiling in a hyperthermophilic archaeon after UV irradiation

Diverse DNA repair mechanisms are essential to all living organisms. Some of the most widespread repair systems allow recovery of genome integrity in the face of UV radiation. Here, we show that the hyperthermophilic archaeon Thermococcus nautili possesses a remarkable ability to recovery from extreme chromosomal damage. Immediately following UV irradiation, chromosomal DNA of T. nautili is fragmented beyond recognition. However, the extensive UV-induced double-stranded breaks (DSB) are repaired over the course of several hours, allowing restoration of growth. DSBs also disrupted plasmid DNA in this species. Similar to the chromosome, plasmid integrity was restored during an outgrowth period. Intriguingly, the topology of recovered pTN1 plasmids differed from control strain by being more positively supercoiled. As reverse gyrase (RG) is the only enzyme capable of inducing positive supercoiling, our results suggest the activation of RG activity by UV-induced stress. We suggest simple UV stress could be used to study archaeal DNA repair and responses to DSB.

Type IA DNA Topoisomerases: A Universal Core and Multiple Activities

All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further retrieved in Archaea and Eukarya as well. This is representative of an extremely ancient origin, probably due to an inheritance from the RNA world. As remaining evidence, some current topoisomerases IA have retained a RNA topoisomerase activity. Despite the presence of this core region in all of these TopoIAs, some differences exist and are originated from variable regions, located essentially within both extremities, conferring on them their specificities. During the last 2 decades the evidence of multiple activities and dedicated roles highlighted the importance of the topoisomerases IA. It is now obvious that topoisomerases IA are key enzymes involved in the maintenance of the genome stability. The discovery of these new activities was done thanks to the use of more accurate assays, based on new sophisticated DNA substrates.

Overcoming the polycation dilemma - Explorative studies to characterise the efficiency and biocompatibility of newly designed lipofection reagents

In this explorative study of the novel cationic lipid OO4 in two different formulations the complex formation with DNA, the biopharmaceutical stability of the lipid/DNA complexes in physiological media, and the transfection efficiency were analysed. We investigated liposomes composed of two binary mixtures of OO4 with either DOPE or DPPE as co-lipids in the molar ratio of 1:3. These formulations were compared with regard to their ability to bind the DNA using gel retardation electrophoresis, ethidium bromide exclusion and zeta potential measurements. Colloidal stability of the lipoplexes in foetal bovine serum (FBS) and the protective effect against degradation by endonucleases were studied. Furthermore, the influence of different salt concentrations on the complex formation with DNA was examined. The DOPE mixture was markedly superior compared to the DPPE mixture. Finally, haemocompatibility studies and gene silencing experiments were performed on OO4:DOPE 1:3 (n:n). The experiments demonstrate that the lipoplex formulation OO4:DOPE 1:3 (n:n) at N/P 4 is a promising candidate for systemic application because of the high colloidal stability in serum without PEGylated lipids, high transfection efficiency, superior resistance against nucleases, reproducible complexation independent of ionic effects, and haemocompatibility.

The effects of DNA supercoiling on G-quadruplex formation

Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson–Crick duplex. Quadruplex formation must therefore first require local dissociation (melting) of the duplex strands. Since negative supercoiling is known to facilitate the formation of alternative DNA structures, we have investigated G-quadruplex formation within negatively supercoiled DNA plasmids. Plasmids containing multiple copies of (G₃T)_n and (G₃T₄)_n repeats, were probed with dimethylsulphate, potassium permanganate and S1 nuclease. While dimethylsulphate footprinting revealed some evidence for G-quadruplex formation in (G₃T)_n sequences, this was not affected by supercoiling, and permanganate failed to detect exposed thymines in the loop regions. (G₃T₄)_n sequences were not protected from DMS and showed no reaction with permanganate. Similarly, both S1 nuclease and 2D gel electrophoresis of DNA topoisomers did not detect any supercoil-dependent structural transitions. These results suggest that negative supercoiling alone is not sufficient to drive G-quadruplex formation.

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

Topological constraints, such as those associated with DNA supercoiling, play an integral role in genomic regulation and organization in living systems. However, physical understanding of the principles that underlie DNA organization at biologically relevant length scales remains a formidable challenge. We develop a coarse-grained simulation approach for predicting equilibrium conformations of supercoiled DNA. Our methodology enables the study of supercoiled DNA molecules at greater length scales and supercoiling densities than previously explored by simulation. With this approach, we study the conformational transitions that arise due to supercoiling across the full range of supercoiling densities that are commonly explored by living systems. Simulations of ring DNA molecules with lengths at the scale of topological domains in the Escherichia coli chromosome (∼10 kilobases) reveal large-scale conformational transitions elicited by supercoiling. The conformational transitions result in three supercoiling conformational regimes that are governed by a competition among chiral coils, extended plectonemes, and branched hyper-supercoils. These results capture the nonmonotonic relationship of size versus degree of supercoiling observed in experimental sedimentation studies of supercoiled DNA, and our results provide a physical explanation of the conformational transitions underlying this behavior. The length scales and supercoiling regimes investigated here coincide with those relevant to transcription-coupled remodeling of supercoiled topological domains, and we discuss possible implications of these findings in terms of the interplay between transcription and topology in bacterial chromosome organization.

The interplay between DNA topology and accessory factors in site-specific recombination in bacteria and their bacteriophages

Site-specific recombination is employed widely in bacteria and bacteriophage as a basis for genetic switching events that control phenotypic variation. It plays a vital role in the life cycles of phages and in the replication cycles of chromosomes and plasmids in bacteria. Site-specific recombinases drive these processes using very short segments of identical (or nearly identical) DNA sequences. In some cases, the efficiencies of the recombination reactions are modulated by the topological state of the participating DNA sequences and by the availability of accessory proteins that shape the DNA. These dependencies link the molecular machines that conduct the recombination reactions to the physiological state of the cell. This is because the topological state of bacterial DNA varies constantly during the growth cycle and so does the availability of the accessory factors. In addition, some accessory factors are under allosteric control by metabolic products or second messengers that report the physiological status of the cell. The interplay between DNA topology, accessory factors and site-specific recombination provides a powerful illustration of the connectedness and integration of molecular events in bacterial cells and in viruses that parasitise bacterial cells.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.

Species-specific supercoil dynamics of the bacterial nucleoid

Bacteria organize DNA into self-adherent conglomerates called nucleoids that are replicated, transcribed, and partitioned within the cytoplasm during growth and cell division. Three classes of proteins help condense nucleoids: (1) DNA gyrase generates diffusible negative supercoils that help compact DNA into a dynamic interwound and multiply branched structure; (2) RNA polymerase and abundant small basic nucleoid-associated proteins (NAPs) create constrained supercoils by binding, bending, and forming cooperative protein-DNA complexes; (3) a multi-protein DNA condensin organizes chromosome structure to assist sister chromosome segregation after replication. Most bacteria have four topoisomerases that participate in DNA dynamics during replication and transcription. Gyrase and topoisomerase I (Topo I) are intimately involved in transcription; Topo III and Topo IV play critical roles in decatenating and unknotting DNA during and immediately after replication. RNA polymerase generates positive (+) supercoils downstream and negative (-) supercoils upstream of highly transcribed operons. Supercoil levels vary under fast versus slow growth conditions, but what surprises many investigators is that it also varies significantly between different bacterial species. The MukFEB condensin is dispensable in the high supercoil density (σ) organism Escherichia coli but is essential in Salmonella spp. which has 15 % fewer supercoils. These observations raise two questions: (1) How do different species regulate supercoil density? (2) Why do closely related species evolve different optimal supercoil levels? Control of supercoil density in E. coli and Salmonella is largely determined by differences encoded within the gyrase subunits. Supercoil differences may arise to minimalize toxicity of mobile DNA elements in the genome.

Supercoiling Effects on Short-Range DNA Looping in E. coli

DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades. Here we adapt this model to test the hypothesis that negative superhelical strain facilitates the formation of short-range (6-8 DNA turns) repression loops in E. coli. The natural negative superhelicity of E. coli DNA is regulated by the interplay of gyrase and topoisomerase enzymes, adding or removing negative supercoils, respectively. Here, we measured quantitatively DNA looping in three different E. coli strains characterized by different levels of global supercoiling: wild type, gyrase mutant (gyrB226), and topoisomerase mutant (ΔtopA10). DNA looping in each strain was measured by assaying repression of the endogenous lac operon, and repression of ten reporter constructs with DNA loop sizes between 70-85 base pairs. Our data are most simply interpreted as supporting the hypothesis that negative supercoiling facilitates gene repression by small DNA-protein loops in living bacteria.

Ni exposure impacts the pool of free Fe and modifies DNA supercoiling via metal-induced oxidative stress in Escherichia coli K-12

The biology of nickel has been widely studied in mammals because of its carcinogenic properties, whereas few studies have been performed in microorganisms. In the present work, changes accompanying stress caused by nickel were evaluated at the cellular level using RNA-Seq in Escherichia coli K-12. Interestingly, a very large number of genes were found to be deregulated by Ni stress. Iron and oxidative stress homeostasis maintenance were among the most highly enriched functional categories, and genes involved in periplasmic copper efflux were among the most highly upregulated. These results suggest that the deregulation of Fe and Cu homeostatic genes is caused by a release of free Cu and Fe ions in the cell which in turn activate the Cu and Fe homeostatic systems. The content of Cu was not significantly affected upon the addition of Ni to the growth medium, nor were the Cus and CopA Cu-efflux systems important for the survival of bacteria under Ni stress In contrast the addition of Ni slightly decreased the amount of cellular Fe and activated the transcription of Fur regulated genes in a Fur-dependent manner. Cu or Fe imbalance together with oxidative stress might affect the structure of DNA. Further experiments revealed that Ni alters the state of DNA folding by causing a relaxed conformation, a phenomenon that is reversible by addition of the antioxidant Tiron or the Fe chelator Dip. The Tiron-reversible DNA relaxation was also observed for Fe and to a lesser extent with Cu but not with Co. DNA supercoiling is well recognized as an integral aspect of gene regulation. Moreover our results show that Ni modifies the expression of several nucleoid-associated proteins (NAPs), important agents of DNA topology and global gene regulation. This is the first report describing the impact of metal-induced oxidative on global regulatory networks.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.