Characterization of the role of YidC in Escherichia coli membrane protein biogenesis

YidC, an essential protein in E. coli with homologs in other bacteria, mitochondria, chloroplasts and some Archaea, functions by incompletely understood mechanisms in the insertion and folding of certain cytoplasmic membrane proteins. Using a genome-scale approach, we identified 50 E. coli membrane proteins that, in the absence of YidC, exhibited aberrant localization by microscopy as well as biochemical defects in membrane insertion, indicating their dependence on YidC for proper membrane insertion or folding. Membrane proteins that possessed a characteristic unfavorable distribution of positively charged residues uniformly depended on YidC for membrane insertion. Correcting the charge distribution of a charge-unbalanced YidC-dependent membrane protein abrogated its requirement for YidC, while perturbing that of a charge-balanced YidC-independent membrane protein rendered it YidC-dependent, demonstrating that charge distribution can be a necessary and sufficient determinant of YidC dependence. These findings provide insights into the mechanism by which YidC promotes proper membrane protein biogenesis. Localization of proteins to specific sites within bacterial cells is often critical to their function. In rod-shaped bacteria, proteins involved in diverse and important cell processes localize to the cell poles. The molecular mechanisms by which these proteins are targeted to the pole, however, are poorly understood. The Shigella autotransporter protein IcsA, which is localized to the pole on the surface of the bacterium, is targeted to the pole in the cytoplasm by a mechanism that is conversed across multiple Gram-negative bacterial species, and has thus served as an important and informative model for studying polar localization. Here, I present evidence that the establishment of polar positional information recognized by IcsA requires the activity of YidC. This requirement is most likely mediated by one or a small number of substrate membrane proteins that are required for IcsA polarity and themselves require YidC for proper membrane insertion. A likely candidate is the cell division protein FtsQ, a YidC substrate that has recently been shown to be required for polar localization of IcsA.