TY - JOUR

T1 - CI:Mor interactions in the lysogeny switches of Lactococcus lactis TP901-1 and Staphylococcus aureus φ13 bacteriophages

AU - Varming, Anders K.

AU - Huang, Zhiyu

AU - Hamad, Ghofran M.

AU - Rasmussen, Kim K.

AU - Ingmer, Hanne

AU - Kilstrup, Mogens

AU - Lo Leggio, Leila

N1 - Funding Information: This work was supported by a Lundbeck Foundation PhD scholarship to AKV (R249-2017-977) and an Independent Research Fund Denmark project grant “Molecular mechanisms and structural dynamics in the TP901-1 genetic switch and related pathogen systems” (DFF - 4002-00107). The structure of CI-NTD was elucidated during the development of a course on Integrative Structural Biology at University of Copenhagen, funded by an educational initiative of the Novo Nordisk Foundation (grant NNF22SA0076513 to Kresten Lindorff-Larsen). We thank the Danish Agency for Science, Technology, and Innovation for funding the instrument center DanScatt. Publisher Copyright: © The Author(s) 2024.

PY - 2024

Y1 - 2024

N2 - Aim: To structurally characterize in detail the interactions between the phage repressor (CI) and the antirepressor (Mor) in the lysis-lysogeny switches of two Gram-positive bacteriophages, the lactococcal TP901-1 and staphylococcal φ13. Methods: We use crystallographic structure determination, computational structural modeling, and analysis, as well as biochemical methods, to elucidate similarities and differences in the CI:Mor interactions for the two genetic switches. Results: By comparing a newly determined and other available crystal structures for the N-terminal domain of CI (CI-NTD), we show that the CI interface involved in Mor binding undergoes structural changes upon binding in TP901-1. Most importantly, we show experimentally for the first time the direct interaction between CI and Mor for φ13, and model computationally the interaction interface. The computational modeling supports similar side chain rearrangements in TP901-1 and φ13. Conclusion: This study ascertains experimentally that, like in the TP901-1 lysogeny switch, staphylococcal φ13 CI and Mor interact with each other. The structural basis of the interaction of φ13 CI and Mor was computationally modeled and is similar to the interaction demonstrated experimentally between TP901-1 CI-NTD and Mor, likely involving similar rearrangement of residue side chains during the formation of the complex. The study identifies one CI residue, Glu69, which unusually interacts primarily through its aliphatic chain with an aromatic residue on Mor after changing its conformation compared to the un-complexed structure. This and other residues at the interface are suggested for investigation in future studies.

AB - Aim: To structurally characterize in detail the interactions between the phage repressor (CI) and the antirepressor (Mor) in the lysis-lysogeny switches of two Gram-positive bacteriophages, the lactococcal TP901-1 and staphylococcal φ13. Methods: We use crystallographic structure determination, computational structural modeling, and analysis, as well as biochemical methods, to elucidate similarities and differences in the CI:Mor interactions for the two genetic switches. Results: By comparing a newly determined and other available crystal structures for the N-terminal domain of CI (CI-NTD), we show that the CI interface involved in Mor binding undergoes structural changes upon binding in TP901-1. Most importantly, we show experimentally for the first time the direct interaction between CI and Mor for φ13, and model computationally the interaction interface. The computational modeling supports similar side chain rearrangements in TP901-1 and φ13. Conclusion: This study ascertains experimentally that, like in the TP901-1 lysogeny switch, staphylococcal φ13 CI and Mor interact with each other. The structural basis of the interaction of φ13 CI and Mor was computationally modeled and is similar to the interaction demonstrated experimentally between TP901-1 CI-NTD and Mor, likely involving similar rearrangement of residue side chains during the formation of the complex. The study identifies one CI residue, Glu69, which unusually interacts primarily through its aliphatic chain with an aromatic residue on Mor after changing its conformation compared to the un-complexed structure. This and other residues at the interface are suggested for investigation in future studies.

KW - antirepressor

KW - corepressor

KW - human adaptation

KW - Lysogeny switch

KW - pathogen

KW - repressor

KW - temperate phage

U2 - 10.20517/mrr.2023.50

DO - 10.20517/mrr.2023.50

M3 - Journal article

AN - SCOPUS:85183350808

VL - 3

JO - Microbiome Research Reports

JF - Microbiome Research Reports

SN - 2771-5965

IS - 2

M1 - 15

ER -