This study focuses on CI repressor of bacteriophage 901-1 (TP901-1) that infects the Lactococcus lactis host cells. As the authors emphasize in the Introduction, the classic lambda lysis/lysogeny switch is - although studied extensively - merely one of many phage switches. Comparative studies, such as the one presented in this manuscript, allow us to compare and contrast the different mechanisms available.
Previous studies of the repressor have demonstrated that length of the linker plays a critical role in the ability of the protein to interact with both promoters by binding to adjacent major grooves of the DNA from opposing sides. Wild-type and linker-region variants were therefore investigated using a combination of biochemical, biophysical and computational techniques.

In general terms, the paper is very well written, and the experimental work appears to have been conducted carefully. The figures document the results comprehensively and are visually effective. The wide range of experimental and theoretical methods is highly commendable.
The background and experimental rationale are clearly explained in the Introduction. The CD, thermal unfolding and SAXS experiments are well described, appropriately interpreted and provide consistent insights.
The last sentence of the “Concluding Remarks” sums up the main message of the manuscript very well by stating that flexible linkers are bona fide functional regions of transcription factors and important for their biological function. This is an important message of more general interest that probably applies to many other similar systems.

Suggestions for improvements:

page 4: it may be a good idea to show a schematic diagram of the lysogenic PR and the lytic PL promoters and the different transcription programs directed by them to supplement the information presented in the text visually.

page 6, line 26: I do not like it if investigators say that they use SEC to “estimate the apparent molecular mass of each variant."
SEC only provides information about the dimension of a macromolecule (and even that may be influenced by hydrophobic and/or electrostatic interaction with the matrix) - I suggest that this phrase is altered

page 9: For the molecular dynamics experiments, it would be useful to the reader to be given some (brief) information about the force field and water model/solvation methods used here in the main text, not just in the Materials and Methods.