Steric clashes with bound OMP peptides activate the DegS stress-response protease

• Published in: Proceedings of the National Academy of Sciences - PNAS 2015-03, Vol.112 (11), p.3326-3331
• Main Authors: de Regt, Anna K., Baker, Tania A., Sauer, Robert T.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino Acid Substitution; Bacterial Outer Membrane Proteins - chemistry; Bacterial Outer Membrane Proteins - metabolism; beta-Galactosidase - metabolism; Binding sites; Biological Sciences; E coli; Enzyme Activation; Enzymes; Escherichia coli; Escherichia coli - enzymology; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Genes; Gram-negative bacteria; Models, Biological; Molecular Sequence Data; Mutant Proteins - metabolism; Mutation - genetics; Peptides; Peptides - chemistry; Peptides - metabolism; Protein Binding; Protein Multimerization; Protein Structure, Secondary; Protein Structure, Tertiary; proteinases; proteins; proteolysis; signal transduction; Stress response
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1502372112

Significance Gram-negative bacteria sense and respond to compromised outer-membrane assembly to maintain cell integrity. In Escherichia coli , outer-membrane stress is sensed via regulated intramembrane proteolysis, a universal signal-transduction system. The C-terminal peptides of unassembled outer-membrane proteins (OMPs) bind and activate DegS, a periplasmic protease that cleaves a transmembrane anti-sigma factor, increasing transcription of stress-response genes. The molecular mechanism by which OMPs allosterically activate DegS has been unclear. We show that OMP-peptide binding to DegS initiates a steric clash that breaks autoinhibitory interactions, resulting in proteolytic activation. This mechanism does not require strong sequence conservation. As proteases related to DegS play important roles in protein-quality control and regulation in most organisms, these studies provide an important step forward in understanding these enzymes. Escherichia coli senses envelope stress using a signaling cascade initiated when DegS cleaves a transmembrane inhibitor of a transcriptional activator for response genes. Each subunit of the DegS trimer contains a protease domain and a PDZ domain. During stress, unassembled outer-membrane proteins (OMPs) accumulate in the periplasm and their C-terminal peptides activate DegS by binding to its PDZ domains. In the absence of stress, autoinhibitory interactions, mediated by the L3 loop, stabilize inactive DegS, but it is not known how this autoinhibition is reversed during activation. Here, we show that OMP peptides initiate a steric clash between the PDZ domain and the L3 loop that results in a structural rearrangement of the loop and breaking of autoinhibitory interactions. Many different L3-loop sequences are compatible with activation but those that relieve the steric clash reduce OMP activation dramatically. Our results provide a compelling molecular mechanism for allosteric activation of DegS by OMP-peptide binding.