Fig. 4: Phage transcription and DNA replication are collectively organized within nucleoid-free regions.
From: Emerging heterogeneous compartments by viruses in single bacterial cells
a, b DNA FISH labels phage and bacterial DNA. Representative images of DNA FISH experiments targeting phage DNA and attB at 10 min (a) and 50 min (b) post-infection with cells stained with DAPI. Representative cells chosen from six independent infection experiments. All scale bars in this figure are 2 μm. c, d Violin plots of whole-cell phage DNA signal (c) and sizes of phage DNA clusters (d). In the violin plots, the solid line represents the median, and the dashed lines mark the bounds of the interquartile range of the data. e, f RNA FISH labels phage pR transcript at 6 min (e) and 40 min (f) post-infection. Cells stained with DAPI. Representative cells chosen from six independent infection experiments. g–i Phage DNA (g), DAPI (h), and E. coli attB (i) heat maps arranged by the location of peak brightness of phage DNA at 10 min post-infection. Cell below (g) shows how locations are represented for g–n. Fluorescence of each cell is normalized to its own peak brightness for g–i and l, m. n = 907 cells for g–i. j, k Phage DNA prefers nucleoid-free locations and avoids attB. j Difference maps (see Supplementary Discussion), calculated as g, h, show contrast in locations of phage DNA and DAPI. Negative values are set to 0. k Difference maps as in j, except showing differences between phage DNA and attB. n for j and k = n of c for each time point. l–n Phage mRNA prefers nucleoid-free locations. pR RNA FISH (l) and DAPI (m) heat maps arranged by the location of peak brightness of pR at 15 min post-infection. n Difference map of l, m, similar to j–k. n = 2035 for l–n. o–q Phage DNA and mRNA colocalize away from E. coli DNA. o Histograms of peak location of pR and DAPI from RNA FISH in l, m. p Histograms of peak location of phage DNA and DAPI from DNA FISH (g, h). q Histogram of peak location of SeqA signal from experiments in Fig. 1 (lytic cells, combined first three time points). Cell below (q) shows how locations are represented for o–q. Source data are provided as a Source Data file.
