Reconfiguring the quorum-sensing regulator sdiA of escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones

SdiA is a homolog of quorum-sensing regulators that detects N-acylhomoserine lactone (AHL) signals from other bacteria. Escherichia coli uses SdiA to reduce its biofilm formation in the presence of both AHLs and its own signal indole. Here we reconfigured SdiA (240 amino acids) to control biofllm formation using protein engineering. Four SdiA variants were obtained with altered biofllm formation, including truncation variants SdiAlEll (F7L, F59L, Y70C, M94K, and K153X) and SdiA14C3 (W9R, P49T, N87T, frameshift at N96, and L123X), which reduced biofllm formation by 5- to 20-fold compared to wild-type SdiA in the presence of endogenous indole. Whole-transcriptome profiling revealed that wild-type SdiA reduced biofllm formation by repressing genes related to indole synthesis and curli synthesis compared to when no SdiA was expressed, while variant SdiAlEll induced genes related to indole synthesis in comparison to wild-type SdiA. These results suggested altered indole metabolism, and corroborating the DNA microarray results in regard to indole synthesis, variant SdiAlEll produced ninefold more indole, which led to reduced swimming motility and cell density. Also, wild-type SdiA decreased curli production and tnaA transcription, while SdiAlEll increased tnaA transcription (tnaA encodes tryptophanase, which forms indole) compared to wild-type SdiA. Hence, wild-type SdiA decreased biofllm formation by reducing curli production and motility, and SdiAlEll reduced biofllm formation via indole. Furthermore, an AHL-sensitive variant (SdiA2D10, having four mutations at E31G, Y42F, R116H, and L165Q) increased biofllm formation sevenfold in the presence of N-octanoyl-DL-homoserine lactone and N-(3-oxododecatanoyl)-L-homoserine lactone. Therefore, SdiA can be evolved to increase or decrease biofllm formation, and biofllm formation may be controlled by altering sensors rather than signals.