DOI: 10.5061/dryad.zgmsbcck8
title: Data from: Stability and gene strand bias of lambda prophages and chromosome organization in Escherichia coli

description: Temperate phage-mediated horizontal gene transfer is a potent driver of
 genetic diversity in the evolution of bacteria. Most lambdoid prophages in
 E. coli are integrated into the chromosome with the same orientation with
 respect to the direction of chromosomal replication, and their location on
 the chromosome is far from homogeneous. To understand better these
 features, we studied the interplay between lysogenic and lytic states of
 phage lambda in both native and inverted integration orientations, at the
 wild-type integration site, as well as at other sites on the bacterial
 chromosome. Measurements of free phage released by spontaneous induction
 showed that the stability of lysogenic states is affected by location and
 orientation along the chromosome, with stronger effects near the origin of
 replication. Competition experiments and range expansions between
 lysogenic strains with opposite orientations and insertion loci indicated
 that there are no major differences in growth. Using single-molecule
 fluorescence in situ hybridization we quantified the level of
 transcriptional bursts of the cI gene coding for the lambda phage
 repressor. These measurements indicate that the stability of the lysogenic
 states at native and inverted orientations are different. We postulate
 that the preference for a given orientation and location is a result of a
 balance between the maintenance of lysogeny and the ability to lyse.
 Together, our findings shed light on key mechanisms that determine the
 genomic architecture in the bacterial chromosome.
description: # Stability and gene strand bias of lambda prophages and chromosome
 organization in Escherichia coli \[Dataset]
 [https://doi.org/10.5061/dryad.zgmsbcck8](https://doi.org/10.5061/dryad.zgmsbcck8) Deposited data includes the following data files used to generate different figures in the main text, with their respective description. Files of .opju type can be opened with OriginPro software (OriginLab Corporation). **Distributions of cI and gal transcripts in Figs. 2 and S1** **measured in different genetic backgrounds.** Origin file containing the smFISH data used to generate the histograms in Figs. 2 and S1 for the indicated experiments. The name of the workbooks denotes the figure of the respective normalized histograms. For each strain, the calculated mean and standard error (SE) per bin are given. **Flow cytometry of labelled lysogenic *E. coli* strains with lambda prophage integrated at the wild‐type *attB* site (17.4’) in Fig. 3**. The data used to plot Fig. 3, in the workbook Flowcytometry, gives bar heights (columns B and D, sheet Figure3) and standard deviation (sd) (columns C and E). The calculation of means and SD for YFP and CFP labeled strains are given in the indicated sheets in the same workbook. **Range expansions data and analysis in Fig. 4.** Origin file containing the ratios of areas of  CFP- and YFP-labelled sectors in the range expansion assays shown in Fig. 4, corresponding to bacterial lysogenic strains bearing prophages integrated at the wild-type site.  The raw data and its analysis are given in workbook Baredata. The data of weighted mean and standard errors from four independent experiments in workbook Statistics are given (columns I and J respectively). **Sequencing of the lambda phage in different strains and backgrounds.** Text files (.txt) of nanopore sequencing of the indicated strains: XTL856 (MG1655), XTL855 (MG1655), XTL894 (MG1655), XTL893 (MG1655), and the recA-deleted strains: XTL862 and XTL863.