Figure 2. Lambda-encoded sRNAs are predominantly expressed during the lytic cycle.

(A) Genome browser view of the preS region from RIL-seq of lambda-infected E. coli (30 min). Hfq IP (green) and total RNA (gray) tracks are shown with normalized ranges. Two biological repeats are overlaid. PreS chimeras are displayed below; blue indicates PreS as RNA2.

(B) Predicted PreS secondary structure (drawn using Forna¹⁰²). Numbering reflects positions from the 5′ end. Shaded bases represent the predicted seed sequence.

(C) E. coli MG1655 (ML001) (OD₆₀₀ = 0.4) was infected with lambda (MOI = 0.0015). Samples collected every 30 min were probed for PreS, LPR2, and lambda 6S RNA, which appear at 30-60 min post-infection. 5S RNA served as loading control. A longer PreS exposure is shown in Fig. S2A; the same 5S panel is reused.

(D) Lysogenic E. coli carrying lambda cI857 (ML007) was grown to OD₆₀₀ = 0.6 at 30 °C and split to 30 °C (lysogenic) or 42 °C (lytic). PreS, LPR2, and lambda 6S RNA are detected throughout the lytic cycle, while lambda 6S also appears in the lysogenic state. RNAs were sequentially probed on the same membrane with 5S RNA as loading control.

(E) PreS engages lambda- and E. coli-encoded RNAs. Circos plot of PreS chimeras at 30 min represents the E. coli genome (right) and lambda genome (left). Blue edges denote E. coli-lambda chimeras; red denotes lambda-lambda chimeras. Scale bars represent 100 kb (E. coli) and 1 kb (lambda).