Evolution for improved secretion and fitness may be the selective pressures leading to the emergence of two NDM alleles

• Published in: Biochemical and biophysical research communications Vol. 524; no. 3; pp. 555 - 560
• Main Authors: Zalucki, Yaramah M., Jen, Freda E.-C., Pegg, Cassandra L., Nouwens, Amanda S., Schulz, Benjamin L., Jennings, Michael P.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 09.04.2020
• Subjects: Antibiotic resistance; NDM-1; Protein export; Signal peptide; NDM-1; Signal peptide; Protein export; Antibiotic resistance
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2020.01.135

The New Delhi metallo-β-lactamase (NDM-1) mediates resistance to β-lactam antibiotics. NDM-1 was likely formed as the result of a gene fusion between sequences encoding the first six amino acids of cytoplasm-localised aminoglycosidase, AphA6, and a periplasmic metallo-β -lactamase. We show that NDM-1 has an atypical signal peptide and is inefficiently secreted. Two new blaNDM-1 alleles that have polymorphisms in the signal peptide; NDM-1(P9R), a proline to arginine substitution, and NDM-2, a proline to alanine substitution (P28A) were studied. Here, we show that both the P9R and P28A substitutions improve secretion compared to NDM-1 and display higher resistance to some β-lactam antibiotics. Mass spectrometry analysis of these purified NDM proteins showed that the P28A mutation in NDM-2 creates new signal peptide cleavage sites at positions 27 and 28. For NDM-1, we detected a signal peptide cleavage site between L21/M22 of the precursor protein. We find no evidence that NDM-1 is a lipoprotein, as has been reported elsewhere. In addition, expression of NDM-2 improves the fitness of E. coli, compared to NDM-1, in the absence of antibiotic selection. This study shows how optimization of the secretion efficiency of NDM-1 leads to increased resistance and increased fitness. •NDM-1 has an inefficient signal peptide for secretion to the periplasm.•NDM-1 is cleaved by signal peptidase I as verified by mass spectrometry.•Recently evolved signal peptide variants in NDM-1 have better secretion.•NDM-2 forms a new signal peptide I cleavage site.•NDM-2 has better secretion and fitness in E. coli compared to NDM-1.