Intramolecular signal transduction of the sensor histidine kinase DcuS and the aerobic and anaerobic fumarate proteome in the regulation of the Escherichia coli C4-dicarboxylate metabolism

Abstract

The aerobic and anaerobic utilization of C4-dicarboxylates in Escherichia coli is regulated by the DcuSR two-component system. Depending on oxygen availability, the transcription of the genes of fumarate respiration or the aerobic transporter DctA are induced. The C4-dicarboxylate transporters DctA and DcuB act as co-regulators of DcuS and convert DcuS to its responsive state in the DcuS-transporter sensor complex. C4-dicarboxylates bound at the periplasmic domain of DcuS and trigger a signal cascade across the membrane, emanating from the sensory PASP domain through TM2, a short Linker and the cytoplasmic PASC domain that results in cytoplasmic autophosphorylation at the C-terminal kinase domain of DcuS. TM2 was already shown to transduce the signal across the membrane via a piston type shift, but the entire mechanism in DcuS transmembrane signaling is unknown. The structure and dynamics of the domains in DcuS intramolecular signal transduction were investigated by oxidative cysteine cross-linking. This revealed a membrane spanning dimeric continuous helix that is mostly stable in both DcuS signaling states. The continuous helix comprises the C-terminal α6 helix of PASP, TM2, the linker, and the N-terminal α1 helix of PASC and thus connects periplasmic signal input with the cytoplasmic signal output domains. The structural dynamics of selected DcuS residues in the DcuS signal transfer were tested by time-resolved cysteine cross-linking. TM2 was shown to be a rigid homo-dimer confirming the piston-type shift as major transmembrane signaling mechanism by TM2. In contrast, the linker represents a dynamic region in signal transduction. PASC also seems to undergo a restructuring in α1 and β1 upon DcuS activation. Furthermore, time-resolved cysteine crosslinking in the absence of the co-regulator DctA showed that DcuS adopts cross-linking reactivity resembling the fumarate activated state. It seems likely that DctA stabilizes homo-dimerization of the linker and α1 of PASC by direct interaction via the DctA helix 8b and thus converts DcuS in its responsive state in the DcuS-DctA sensor complex. In addition, the aerobic and anaerobic E. coli fumarate proteome was investigated in a ‘shotgun proteomics’ approach. The transcriptional regulation by DcuSR was displayed in the proteomic results. Upregulation of almost all TCA cycle enzymes, anaplerotic reactions, and gluconeogenesis under aerobic conditions was observed. This regulatory effect can be related to an EIIA-P/EIIA ratio-dependent indirect regulation by cAMP/CRP, but a previously unknown regulation by DcuSR is also possible in some cases. The most abundant category of proteins, which was upregulated by fumarate under anaerobic conditions, can be assigned to chemotaxis and motility.