Journal: bioRxiv

Article Title: Nanopore direct RNA sequencing (DRS) of MS2 bacteriophages in E.coli throughout its life cycle reveals a complex transcriptional activity to control and maintain its growth

doi: 10.1101/2025.03.30.646209

Figure Lengend Snippet: A. MS2 replication pattern. The MS2 replicase complex contains host factors EF-Tu, EF-Ts and S1 ribosomal protein. B. Schematic presentation of the MS2 full-length genomic RNA coding regions organisation and composition. NTD, N-terminal domain, CTD, C-terminal domain. The 5′ UTR of MS2 contains ∼130 nt, and the 3′ UTR of MS2 contains 171 nt. C. Growth curves of bacterial cells (DSM5695 E. coli ) infected with MS2 RNA phage at MOI = 200 (red line) and bacteria cells without infection (blue). Phages were added at t = 0. Cells were harvested at 0h, 3h, and 6h post-infection (p.i.), and RNAs were extracted. Each growth curve represents the mean values and standard deviations obtained from biological triplicates. D. MS2 plaques on the host E. coli DSM5695 at 0h, 3h, 6h, 10h p.i. Plaques were pointed with white arrows. E. Plaque PFU and size change at 0h, 3h, 6h, 10h p.i. All pair-wise comparisons (3h vs. 6h vs. 10h at each diameter) were done after observing a significant Analysis of Variance (ANOVA) test result and showed statistically significant results ( P value <0.05 after accounting for multiple comparisons), except the 3h vs. 6h (1 mm diameter) and the 3h vs. 6h (2 mm diameter) one. Data are presented as means ± standard deviation (n = 3).

Article Snippet: The bacteria host E. coli DSM 5695 (also called E. coli W1485) (F + ) and MS2 bacteriophages DSM 13767 were obtained from the DSMZ-German Collection of Microorganisms and Cell Culture.

Techniques: Infection, Bacteria, Standard Deviation

Journal: bioRxiv

Article Title: Nanopore direct RNA sequencing (DRS) of MS2 bacteriophages in E.coli throughout its life cycle reveals a complex transcriptional activity to control and maintain its growth

doi: 10.1101/2025.03.30.646209

Figure Lengend Snippet: A. Read counts from nanopore direct RNA sequencing of total RNA from DSM5695 E. coli cells infected with MS2 phage at different time points (0h, 3h, 6h p.i.). B. Principal component analysis (PCA) plot of MS2 samples at 0h, 3h, 6h p.i., each with three biological replicates to visualise the batch effects. C. Differential expression patterns for four MS2 genes at different time points (0h, 3h and 6h p.i.), analysed by DESeq2 with ‘median of ratios’ to normalise the read count. Adjusted P -value (after accounting for multiple hypothesis testing using the Benjamini-Hochberg method) <0.05, *; <0.01, **. D. Coverage map for MS2 total reads at 0h, 3h, 6h p.i. E-G. MS2 raw read length distribution at 0h, 3h and 6h p.i.

Article Snippet: The bacteria host E. coli DSM 5695 (also called E. coli W1485) (F + ) and MS2 bacteriophages DSM 13767 were obtained from the DSMZ-German Collection of Microorganisms and Cell Culture.

Techniques: RNA Sequencing, Infection, Expressing

Journal: bioRxiv

Article Title: Persistence of large conjugative plasmids relies on the combination of active partitioning and addiction mechanisms

doi: 10.1101/2025.02.11.637630

Figure Lengend Snippet: (A) Presence of partition (Par) and TA systems in KES plasmid taxonomic units. PTUs of small plasmids (<19Kb) are written in gray; PTUs of large plasmids (≥19Kb) are written in black. Horizontal stacked bar graphs show the fraction of plasmid mobility in the PTU and the systems presence in plasmids and the distribution of system instances per plasmid. (B) Structure of a conserved syntenic block including dinQ -like gene in X3 plasmids. The chromosomal dinQ in E. coli is presented together with the agrB - dqlB locus in plasmid pOXA-484 in E. coli strain EC-JS316. (C) Toxicity assay of the agrB-dqlB locus from pOXA-484. Growth of E. coli DH5α cells carrying either no plasmid, the empty vector control plasmid (pBAD30), the argB - dqlB locus from plasmid pOXA-484 in E. coli EC-JS316 (pBAD30- agrB - dqlB ), or the dqlB carrying plasmid (pBAD30- dqlB ). The samples were plated on medium selective for ampicillin resistance (LB+Amp 100 ) and selective plates supplemented with Arabinose (LB+Amp 100 +Ara 0,2% ). The expression of dqlB locus is induced in the presence of Arabinose via P BAD . The presented results are representative of three independent replicates. (D) Stability of plasmid pCONn-TD comprising the agrB - dqlB locus from plasmid pOXA-484 as evaluated in a serial transfer experiment under non-selective conditions (n=6).

Article Snippet: The E. coli strain MG1655 recA :: tetA derived from the E. coli strain MG1655 (DSM No. 18039, German Collection of Microorganisms and Cell Cultures, DSMZ) was used as plasmid host in all competition experiments.

Techniques: Plasmid Preparation, Blocking Assay, Control, Expressing