A Single Residue within the MCR-1 Protein Confers Anticipatory Resilience

• Published in: Microbiology spectrum 2023-06, Vol.11 (3), p.e0359222-e0359222
• Main Authors: Frantz, Renate, Gwozdzinski, Konrad, Gisch, Nicolas, Doijad, Swapnil Prakash, Hudel, Martina, Wille, Maria, Abu Mraheil, Mobarak, Schwudke, Dominik, Imirzalioglu, Can, Falgenhauer, Linda, Ehrmann, Michael, Chakraborty, Trinad
• Format: Article
• Language: English
• Subjects: Bacteriology; E. coli; envelope stress response (ESR); lipid A; MCR-1; pH-enhanced resistance; plasmid elimination; Research Article
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.03592-22

The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role toward antimicrobials, but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here, we report interactions between a central regulator of ESR , the two-component signal transduction system CpxRA ( onjugative ilus e pression), and the recently described mobile colistin resistance protein (MCR-1). Purified MCR-1 is specifically cleaved within its highly conserved periplasmic bridge element, which links its N-terminal transmembrane domain with the C-terminal active-site periplasmic domain, by the CpxRA-regulated serine endoprotease DegP. Recombinant strains harboring cleavage site mutations in MCR-1 are either protease resistant or degradation susceptible, with widely differing consequences for colistin resistance. Transfer of the gene encoding a degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying plasmids. As CpxRA directly senses acidification, growth of strains at moderately low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A and colistin resistance levels. Strains expressing MCR-1 are also more resistant to antimicrobial peptides and bile acids. Thus, a single residue external to its active site induces ESR activity to confer resilience in MCR-1-expressing strains to commonly encountered environmental stimuli, such as changes in acidity and antimicrobial peptides. Targeted activation of the nonessential protease DegP can lead to the elimination of transferable colistin resistance in Gram-negative bacteria. The global presence of transferable genes in a wide range of Gram-negative bacteria from clinical, veterinary, food, and aquaculture environments is disconcerting. Its success as a transmissible resistance factor remains enigmatic, because its expression imposes fitness costs and imparts only moderate levels of colistin resistance. Here, we show that MCR-1 triggers regulatory components of the envelope stress res