Replication Protein A (RPA) is a single stranded DNA (ssDNA) binding protein that coordinates diverse DNA metabolic processes including DNA replication, repair, and recombination. RPA is a heterotrimeric protein with six functional oligosaccharide/oligonucleotide (OB) domains and flexible linkers. Flexibility enables RPA to adopt multiple configurations and is thought to modulate its function. Here, using single molecule confocal fluorescence microscopy combined with optical tweezers and coarse-grained molecular dynamics simulations, we investigated the diffusional migration of single RPA molecules on ssDNA under tension. The diffusion coefficient D is the highest (20,000 nucleotides2/s) at 3 pN tension and in 100 mM KCl and markedly decreases when tension or salt concentration increases. We attribute the tension effect to intersegmental transfer which is hindered by DNA stretching and the salt effect to an increase in binding site size and interaction energy of RPA-ssDNA. Our integrative study allowed us to estimate the size and frequency of intersegmental transfer events that occur through transient bridging of distant sites on DNA by multiple binding sites on RPA. Interestingly, deletion of RPA trimeric core still allowed significant ssDNA binding although the reduced contact area made RPA 15-fold more mobile. Finally, we characterized the effect of RPA crowding on RPA migration. These findings reveal how the high affinity RPA-ssDNA interactions are remodeled to yield access, a key step in several DNA metabolic processes. less

Control of the water freezing process is considerable in different fields of science and technology: from the artificial snow production to the cryopreservation of biological materials. To date, there is no conventional theory that predicts the influence of various biological and non-biological ice nucleators on the formation of ice and, accordingly, on the freezing point of supercooled water. In this work, we investigated the influence of bacterium Pseudomonas syringae, a biological ice nucleator, and heterodisperse insoluble powders of low molecular weight substances on the process of water freezing. AgCl, ZnO and SnO2 were found to be ice nucleators. This property has not been described previously in the literature. It has also been established that insoluble low molecular weight substances affect both the freezing point of water and the temperature of coexistence of water and ice. less

Constitutive heterochromatin, built on various types of repetitive DNA, is a fundamental feature of eukaryotic nucleus essential for transposon silencing and genome stability. However, the molecular programs driving its de novo establishment during early embryogenesis remain poorly understood. Here, we show that histone H3 lysine 14 acetylation (H3K14ac) is maternally inherited and partially colocalizes with hallmarks of constitutive heterochromatin, H3 lysine 9 trimethylation (H3K9me3) and its methyltransferase Eggless/SetDB1, around the mid-blastula transition in Drosophila early embryos. Concealing H3K14ac by either antibody injection or maternal knockdown of Gcn5 diminishes Eggless/SetDB1 nuclear foci and reduces the deposition of H3K9me3. Structural analysis reveals that Eggless/SetDB1 recognizes H3K14ac via its tandem Tudor domains, and disrupting the binding interface causes defects in Eggless/SetDB1 distribution and derepression of a subset of transposons. Therefore, H3K14ac, a histone modification associated with active transcription, is a crucial piece of the maternal programs that introduce constitutive heterochromatic features to the newly formed zygotic genome less

The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in freshwater and seawater, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131) and gut metagenomics (n=80). Bacterial genomes were taxonomically assigned into 14 different orders, including 28 distinctive genera and 31 potentially novel species. Benchmarking the SMGA, we functionally characterized key populations in the salmon gut that were detected in vivo. This included the ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects, which were validated by in vitro cultivation and untargeted metabolomics. Together, the SMGA enables high resolution functional insight into salmon gut microbiota with relevance for salmon nutrition and health. less

Background: The aminoglycoside apramycin has been proposed as a drug candidate for the treatment of critical Gram-negative systemic infections. However, its potential in the treatment of drug-resistant bloodstream infections (BSIs) has yet to be assessed. Methods: The resistance gene annotations of 26493 blood culture isolates were analyzed. In vitro profiling of apramycin comprised cell-free translation assays, broth microdilution, and frequency of resistance determination. The efficacy of apramycin was studied in a mouse peritonitis model for nine E. coli and K. pneumoniae isolates. Results: Genotypic aminoglycoside resistance was identified in 87.8% of all 6973 carbapenem-resistant Enterobacterales blood-culture isolates, in comparison to 46.4% of colistin and 2.1% of apramycin resistance. Apramycin activity against methylated ribosomes was > 100-fold higher than other aminoglycosides. Frequencies of resistance were < 109 at 8 x MIC. Tentative epidemiological cutoffs (ECOFFs) were determined as 8 g/mL for E. coli and 4 g/mL for K. pneumoniae. A single dose of 5 to 13 mg/kg resulted in a 1-log CFU reduction in the blood and peritoneum. Two doses of 80 mg/kg, resulting in an exposure that resembles the AUC observed for a single 30 mg/kg dose in humans, resulted in complete eradication of carbapenem- and aminoglycoside-resistant bacteremias. Conclusion: Encouraging coverage and potent in-vivo efficacy against a selection of highly drug-resistant Enterobacterales isolates in the mouse peritonitis model warrants further consideration of apramycin as a drug candidate for the treatment and prophylaxis of BSI. less

Complement proteins eliminate Gram-negative bacteria in serum via the formation of membrane attack complex (MAC) pores in the outer membrane. However, it remains unclear how outer membrane poration leads to inner membrane permeation and cell lysis. Using atomic force microscopy (AFM) on living Escherichia coli (E. coli), we probed MAC-induced changes in the cell envelope and correlated these with subsequent cell death. Initially, bacteria survived despite the formation of hundreds of MACs randomly distributed over the cell surface. This was followed by larger-scale disruption of the outer membrane, including propagating defects and fractures, and by an overall swelling and stiffening of the bacterial surface, which precede inner membrane permeation. We conclude that bacterial cell lysis is only an indirect effect of MAC formation; outer membrane poration leads to mechanical destabilization of the cell envelope, reducing its ability to contain the turgor pressure, causing inner membrane permeation and cell death. This represents a previously unknown route to bacterial cell death that could be exploited by novel antibiotic treatments. less

Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase towards the end of pregnancy and comprise reduced -diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1{triangleup}IEC mice carrying an intestinal epithelial deletion of the Crohn\'s disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1{triangleup}IEC pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. In addition, functional inference of metagenomic data suggest a reduced potential to biosynthesize mucosal protective polyamines and reduced capacity to metabolize acidic polysaccharides (ketogluconate metabolism). On the host side, we found that the immunological response of Atg16l1{triangleup}IEC mice is characterized by higher colonic mRNA levels of TNFA, and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improving precision care for managing pregnancies in IBD patients. less

Nucleolar ribosomal DNA (rDNA) repeats control ribosome manufacturing. rDNA harbors a ribosomal RNA (rRNA) gene and an intergenic spacer (IGS). RNA polymerase (Pol) I transcribes rRNA genes yielding the rRNA components of ribosomes. Pol II at the IGS induces rRNA production by preventing Pol I from excessively synthesizing IGS non-coding RNAs (ncRNAs) that can disrupt nucleoli. At the IGS, Pol II regulatory processes and whether Pol I function can be beneficial remain unknown. Here, we identify IGS Pol II regulators, uncovering nucleolar optimization via IGS Pol I. Compartment-enriched proximity-dependent biotin identification (compBioID) showed enrichment of the TATA-less promoter-binding TBPL1 and transcription regulator PAF1 with IGS Pol II. TBPL1 localizes to TCT motifs, driving Pol II and Pol I and maintaining its baseline ncRNA levels. PAF1 promotes Pol II elongation, preventing unscheduled R-loops that hyper-restrain IGS Pol I and its ncRNAs. PAF1 or TBPL1 deficiency disrupts nucleolar organization and rRNA biogenesis. In PAF1-deficient cells, repressing unscheduled IGS R-loops rescues nucleolar organization and rRNA production. Depleting IGS Pol I-dependent ncRNAs is sufficient to compromise nucleoli. We present the interactome of nucleolar Pol II and show its control by TBPL1 and PAF1 ensures IGS Pol I ncRNAs maintaining nucleolar structure and operation. less

Planktonic (free-floating) cells are typically assumed to be oblivious to any flow that carries them. Here we discover that planktonic bacteria can sense flow to induce gene expression changes that are beneficial in flow. Specifically, planktonic P. aeruginosa induce shear-rate-dependent genes that promote growth in low oxygen environments. Untangling this mechanism revealed that in flow, motile P. aeruginosa spatially redistribute, leading to cell density changes that activate quorum sensing, which in turn enhances oxygen uptake rate. In diffusion-limited environments, including those commonly encountered by bacteria, flow-induced cell density gradients also independently generate oxygen gradients that alter gene expression. Mutants deficient in this newly-discovered flow sensing mechanism exhibit decreased fitness in flow, suggesting that this dynamic coupling of biological and mechanical processes can be physiologically significant. less

Bacterial persisters are a multidrug-tolerant subpopulation capable of surviving and resuscitating after lethal antibiotic treatment, leading to relapsing infections and the emergence of antibiotic resistance. We hypothesize that multiple persister subpopulations are within an isogenic Escherichia coli population, allowing them to survive lethal antibiotic stress. We conducted transcriptomic analyses at multiple time points with lethal ampicillin (Amp) antibiotic, and as expected, several genes were differentially expressed over time. We identified a subset of genes consistently upregulated by comparing transcription levels at different time points of Amp-treated to untreated. Some genes had previously been associated with persisters, while others were new. Subsequently, network analysis showed the gene response between networks, but could not map hypothetical genes. So, we overexpressed seven hypothetical genes, which resulted in slow growth or no growth, indicating that high production harmed the cell. We then made single gene knockouts, which dramatically reduced persister level by ~4-6 fold at 3 h and ~10-15 fold at 6 h of Amp treatment. However, no significant difference in survival rates was observed at 24 h, indicating the presence of multiple persister subpopulations. Our mathematical model demonstrated a 20-fold decrease in the slow-decaying fraction in the mutant, suggesting the importance of decay kinetics in bacterial survival. These results support the existence of multiple subpopulations of persisters, each characterized by distinct decay rates. These results challenge the idea of complete dormancy, suggest the presence of intricate, multifaceted survival mechanisms, and indicate that the persister population itself is heterogeneous. Keywords Antibiotic tolerance, antibiotic persistence, antibiotic resistance, phenotypic heterogeneity, cell-state transitions, phenotypic switching less