Molecular insights into quorum sensing in Acidithiobacillus ferrooxidans bacteria via molecular modelling of the transcriptional regulator AfeR and of the binding mode of long-chain acyl homoserine lactones Laurent Soulère & Nicolas Guiliani & Yves Queneau & Carlos A. Jerez & Alain Doutheau Abstract Amino acid sequence alignments of the tran- scriptional regulator AfeR, which is involved in type 1 quorum sensing (QS) in Acidithiobacillus ferrooxidans bacteria, with other acyl homoserine lactone (AHL)- dependent QS regulators, revealed the presence of strictly or highly conserved residues located in the active site of these proteins. As a consequence, a model of AfeR was constructed to study the binding mode of long-chain AHLs using molecular dynamics and subsequent rigid ligand docking. This study, performed on the tetradecanoyl homoserine lactone C14-AHL, showed that the binding mode involved a curved conformation. Based on these results, the binding mode of tetradec-7-Z enoyl homoserine lactone, an AHL that is conformationally constrained due to the presence of the cis double bond, was investigated. This mono-unsaturated AHL with its preferential curved shape conformation was found to be particularly well adapted to the active site of AfeR. These results should be helpful in the rational design of QS modulators with potential biotechnological applications and especially in the im- provement of industrial bioleaching from ores. Keywords Quorum sensing . Long-chain acyl homoserine lactones . AfeR . Modulators . Conformational analysis . Docking Introduction Quorum sensing (QS) is a communication system that allows bacteria to adapt their behaviour to their cell density [1–5]. This system regulates the expression of genes encoding important phenotypes such as biofilm formation, virulence and bioluminescence. QS is based on signalling molecules called auto-inducers, including cyclic peptides in Gram-positive bacteria [ 6], acyl homoserine lactone (AHLs) in Gram-negative bacteria, and 4,5-dihydroxy-2,3- pentanedione (DPD)-derived compounds in both Gram- positive and -negative bacteria [7]. QS has recently aroused great interest as a novel target for interference with biological functions of bacteria, with potential medical or biotechnological applications [8–12]. The design and L. Soulère : Y. Queneau : A. Doutheau Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Laboratoire de Chimie Organique, INSA Lyon, Bât J. Verne, 20 av A. Einstein, 69621 Villeurbanne Cedex, France L. Soulère : Y. Queneau : A. Doutheau CNRS, UMR 5246 ICBMS, INSA Lyon, CPE Lyon, Université Lyon 1, Bât CPE, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France N. Guiliani : C. A. Jerez Unidad de Comunicación Bacteriana, Laboratorio de Microbiología Molecular y Biotecnología, Departamento de Biología, Instituto de Dinámica Celular y Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras, Ñuñoa, 3425 Santiago, Chile L. Soulère (*) Laboratoire de Chimie Organique, INSA Lyon, 20 av A. Einstein, 69621 Villeurbanne Cedex, France e-mail: laurent.soulere@insa-lyon.fr