Copper (Cu) is involved in key biological processes, but it is also toxic to cells. The antimicrobial effect of Cu is used by the immune system and also for human activities in agriculture, hospitals, etc. The accumulation of Cu in the environment is a threat to health and ecosystems and leads to the emergence of resistant organisms. Bacteria have different Cu detoxification systems. The photosynthetic bacterium Rubrivivax gelatinosus present an original system of Cu resistance1, the mechanism of which has yet to be elucidated, and which is also found in other bacteria, some of which are pathogenic to humans (e.g. Vibrio cholerae or Pseudomonas aeruginosa). This system involves an operon encoding for three proteins, CopI, CopJ and CopH. CopI is a monodomain cupredoxin able to bind up to 3 Cu ions1,2. CopJ has a conserved CxCC motif whose sulphur ligands can coordinate a copper ion. It is homologous to CopG from V. cholerae and P. aeruginosa. CopH is predicted as an intrinsically disordered protein and has not been studied experimentally yet.

The internship project aims at first retrieve sequences in data bases by using an HMM profiles-based search and secondly reconstructing a phylogenetic tree (concatenated or not) using these three proteins. An interesting feature is that the homologues are not always found together or encoded in the same operon in the different bacteria which possess the CopI protein. In addition, the Master student will build structural models with Alphafold and perform molecular dynamics studies of the different proteins either isolated or in interaction, in order to study in silico not only the Cu binding modules in the different bacteria which possesses such a system but also the possible protein-protein complex formation and the structural rearrangement of the proteins it implies.

References on the CopI protein studied experimentally in the laboratory

[1] Durand, A.;  Fouesnard, M.;  Bourbon, M. L.;  Steunou, A. S.;  Lojou, E.;  Dorlet, P.; Ouchane, S., A periplasmic cupredoxin with a green CuT1.5 center is involved in bacterial copper tolerance. Metallomics 2021, 13, mfab067

[2] Rossotti, M.; Arceri, D.; Mansuelle, P; Bornet, O.; Durand, A.; Ouchane, S.; Launay, H.; Dorlet, P., The green cupredoxin CopI is a multicopper protein able to oxidize Cu(I). J. Inorg. Biochem. 2024, 254, 112503