Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility

Abstract

YdiV is a negative regulator of cell motility. It interacts with FlhD4C2 complex, a product of flagellar master operon, which works as the transcription activator of all other flagellar operons. Here, we report the crystal structures of YdiV and YdiV2–FlhD2 complex at 1.9 Å and 2.9 Å resolutions, respectively. Interestingly, YdiV formed multiple types of complexes with FlhD4C2. YdiV1–FlhD4C2 and YdiV2–FlhD4C2 still bound to DNA, while YdiV3–FlhD4C2 and YdiV4–FlhD4C2 did not. DNA bound FlhD4C2 through wrapping around the FlhC subunit rather than the FlhD subunit. Structural analysis showed that only two peripheral FlhD subunits were accessible for YdiV binding, forming the YdiV2–FlhD4C2 complex without affecting the integrity of ring-like structure. YdiV2–FlhD2 structure and the negative staining electron microscopy reconstruction of YdiV4–FlhD4C2 suggested that the third and fourth YdiV molecule bound to the FlhD4C2 complex through squeezing into the ring-like structure of FlhD4C2 between the two internal D subunits. Consequently, the ring-like structure opened up, and the complex lost DNA-binding ability. Thus, YdiV inhibits FlhD4C2 only at relatively high concentrations.

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

“…Some proteins with highly diverged GGDEF, EAL, or PilZ domains participate in regulatory interactions despite a total loss of enzymatic activity or the ability to bind c-di-GMP. Examples include the GGDEF domain protein GdpS (SA0701) from Staphylococcus aureus, the E. coli EAL domain proteins BluF (YcgF) and CdgR (YdiV), and the E. coli carbon storage regulator CsrD (YhdA), which contains both GGDEF and EAL domains (64)(65)(66)(67). A potentially even more striking example is the interaction between the X. campestris response regulator RpfG, which combines a two-component receiver (REC) domain with the c-di-GMP-degrading HD-GYP domain, and various GGDEF domain-containing proteins, which then recruits a PilZ domain protein to form a tripartite HD-GYP-GGDEF-PilZ complex that effectively controls pilus motility (68,69).…”

Progress in Understanding the Molecular Basis Underlying Functional Diversification of Cyclic Dinucleotide Turnover Proteins

“…Several well-investigated class IIIb proteins of Escherichia coli and Salmonella enterica serovar Typhimurium, YdiV and Salmonella-specific STM1697, bind to the major flagellin regulator FlhDC with apparently similar but highly distinct interfaces (51)(52)(53). Furthermore, the class IIIb protein YdiV interacts in complex with FlhDC with the ClpXP protease, guiding FlhDC for degradation (54), and it regulates other physiological traits besides motility (55).…”

Involvement of Two-Component Signaling on Bacterial Motility and Biofilm Development

“…Likewise, the negative effect of the phosphodiesterase YdiV on FlhD/FlhC is indicated by the red dashed line with a blunt end. This effect is one of posttranslation, where YdiV binds to the FlhD/FlhC complex at high concentrations to inhibit its transcriptional activity (67).…”