Two endolysins with high anti-pneumococcal activity have been structurally and functionally characterized by scientists from the IQFR, CIB and Salamanca University.

Endolysins, encoded by bacteriophages to allow the phage progeny exit the host bacterial cell, constitute a novel class of anti-infective and one of the main alternatives to classical antibiotics in the fight against antibiotic multi-resistant bacteria. We have structurally and functionally characterized the Skl and Pal endolysins, shown to be goodantibacterial agents that efficiently and selectively kill Streptococcus pneumoniae, a world’s leading cause of deathly diseases. They comprise a homologous choline-binding domain (CBDs) and a catalytic domain of CHAP or Amidase_5 type, respectively. We have shown, for the first time, that Amidase_5 domains are cysteine-peptidases, as are the CHAP domains. Indeed, Skl and Pal catalytic domains share a similar fold with a papain-like topology, and residues relevant for substrate binding and intermediate stabilization have been inferred from in silico models, including a calcium-binding site accounting for Skl dependence on this cation for activity. Also, the dimerization mode promoted by choline binding has been characterized and six conserved choline-binding loci identified. Interestingly, Pal and Skl dimers display a common overall architecture, preserved as well in choline-bound dimers of pneumococcal lysins with other catalytic domains and bond specificities, evidencing their adaptation to the pneumococcal cell wall. Finally, our biochemical studies helped to understand how Pal and Skl may accede to the target bonds in the lysis from without of S. pneumoniae, and revealed that activation of both cysteine-peptidases by DTT does not take place, solely, through reversal of catalytic-cysteine oxidation. Understanding these processes at the molecular level is key in our comprehension of how endolysin efficiency as antibacterials is finely tuned or even nullified by the overall cell-wall structure of a given pathogen, of relevance in the clinical or technological settings.

Reference: C. Gallego-Páramo, N. Hernández-Ortiz, R. M. Buey, P. Rico-Lastres, G. García, J. F. Díaz, P. García, M. Menéndez. (2021) Structural and functional insights into Skl and Pal endolysins, two cysteine-amidases with anti-pneumococcal activity. Dithiothreitol (DTT) effect on lytic activity. Front. Microbiol. 12:740914. doi: 10.3389/fmicb.2021.740914.