(Re)Defining the Proline-Rich Antimicrobial Peptide Family and the Identification of Putative New Members

Abstract

As we rapidly approach a post-antibiotic era in which multi-drug resistant bacteria are ever-pervasive, antimicrobial peptides (AMPs) represent a promising class of compounds to help address this global issue. AMPs are best-known for their membrane-disruptive mode of action leading to bacteria cell lysis and death. However, many AMPs are also known to be non-lytic and have intracellular modes of action. Proline-rich AMPs (PrAMPs) are one such class, that are generally membrane permeable and inhibit protein synthesis leading to a bactericidal outcome. PrAMPs are highly effective against Gram-negative bacteria and yet show very low toxicity against eukaryotic cells. Here, we review both the PrAMP family and the past and current definitions for this class of peptides. Computational analysis of known AMPs within the DRAMP database (http://dramp.cpu-bioinfor.org/) and assessment of their PrAMP-like properties have led us to develop a revised definition of the PrAMP class. As a result, we subsequently identified a number of unknown and unclassified peptides containing motifs of striking similarity to known PrAMP-based DnaK inhibitors and propose a series of new sequences for experimental evaluation and subsequent addition to the PrAMP family.

Keywords: 70S ribosome; AMPs; DnaK; PrAMP; antimicrobial peptides; host defense peptides; proline-rich antimicrobial peptide.

Figure 1

Left: DnaK forward binding mode shown by superposition of A3-APO (1–20) (cyan), Onc72 (orange), PR-39 (1–15) (purple), and pyrrhocoricin (1–20) (salmon). Right: DnaK reverse peptide binding mode shown by superposition of pyrrhocoricin (12–20) (green) and drosocin (12–19) (purple). Reproduced from Zahn et al. (2013) with permission.

Figure 2

PrAMP binding at the 70S ribosome. (A) Api137 locates within the ribosomal large subunit polypeptide exit tunnel (NPET) in the presence of peptidyl-transfer RNA (P-tRNA) and release factor 1 (RF1). (B) Api137 binds in an inverted orientation relative to pyrrhocoricin (Pyr) and Tur1A with the N-termini and C-termini marked by N and C, respectively. Reproduced from Graf and Wilson (2019) with permission.

Figure 3

Phylogenetic tree of naturally occurring PrAMPs identified from the literature.

Figure 4

Analysis of the DRAMP database. PrAMP-like peptides that are putative new members of the PrAMP family are shown in green and currently reported PrAMP members are shown in blue. All other AMPs from the DRAMP database are shown in gray.