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Varming et al. Microbiome Res Rep 2024;3:15 https://dx.doi.org/10.20517/mrr.2023.50 Page 3 of 16

Figure 1. Overview of different genetic switches. (A) Simplified view of the λ phage lysogeny switch showing the interplay between CI,
its antirepressor Cro, and the bacterial RecA. CI consists of two domains, the DNA-binding NTD and a protease domain at its CTD,
which is activated and results in autocleavage on interaction with RecA. Here and in the diagrams below, longer bars on specific
operator sites indicate higher affinity. Only CI dimers are shown, but higher oligomerization states exist and have functional roles; (B)
simplified view of TP901-1 lysogeny switch. Here, Mor rather than Cro acts as a counterpart to CI. However, Mor does not seem to
interact directly with DNA, but rather with the CI-NTD, blocking its binding to O and functioning as a corepressor at a composite site
L
around O . It is furthermore known that induction by the SOS response is RecA mediated, but it is not understood how, since TP901-1 CI
R
does not undergo autocleavage, not having a protease domain or autocleavage site in its CTD. As above, higher oligomerization states
of CI are not shown for simplicity; (C) overview of lysogeny switch region of φ13. The switch has a similar operator site and gene
organization as TP901-1 with Mor instead of Cro; however, the C-terminal region of the CI resembles much more closely the one of λ
(see color coding of domains). The φ13 switch is much less characterized at the molecular level, but it has been recently established
that CI can bind to the putative operator sites with high affinity in vitro [28] ; (D) overview of interaction between TP901-1 CI-NTD (in light
green) and Mor (dark green) in the crystal structure (PDB 6TRI). The interface regions identified in [24] are highlighted in yellow (CI) and
magenta (Mor). CI: Phage repressor; NTD: N-terminal domain; CTD: C-terminal domain.