Phage Endolysins as Promising and Effective Candidates for Use Against Uropathogenic Escherichia coli

Abstract

The presented in silico and phylogenetic analysis of putative endolysins potentially produced by phages infecting uropathogenic Escherichia coli (UPEC) demonstrates their remarkable diversity. These proteins exhibit significant variations in sequence length, molecular weight, isoelectric point, and stability, as well as diverse functional domains determining their enzymatic activity, including lysin, lysozyme, hydrolase, amidase, and peptidase functions. Due to their predicted lytic properties, endolysins hold great promise in combating UPEC bacteria, including those within biofilms, which are often highly resistant to conventional treatments. Despite their potential, several challenges hinder the full utilization of endolysins. These include the relatively small number of identified proteins, challenges in the annotation process, and the scarcity of studies evaluating their efficacy in vitro and in vivo against Gram-negative bacteria. In this work, we emphasize these challenges while also underlining the potential of endolysins as an effective tool against UPEC infections. Their effectiveness could be significantly enhanced when combined with agents that disrupt the outer membrane of these bacteria, making them a promising alternative or complement to existing antimicrobial strategies. Further research is necessary to fully explore their therapeutic potential.

Keywords: bacteriophages; phage endolysins; phage therapy; urinary tract infections (UTIs); uropathogenic Escherichia coli (UPEC).

Figure 1

The phylogenetic tree is generated based on the first orthologous group determined by OMA and contains endolysins (YP_009620148.1, YP_010749568.1, QVR48622.1, WWY66481.1, YP_010749155.1, QYU43915.1, and WVW77834.1), with autolysin domains derived from phages Golestan, phiEc3, 590B, UTEC10, NTEC3, phiEc4, and SHAK7858, respectively. The tree was made as described in the text, using the maximum likelihood method with 1000 bootstrap replications. Panel (A) presents a tree with all grouped proteins. Panel (B) shows a modified tree, where proteins derived from phages CH5UKE2, 101114BS4, 22664B1, 101114B2, and CHD2B1 were removed to highlight the particular distances on the tree. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.

Figure 2

The phylogenetic tree is generated based on the second orthologous group estimated by OMA and contains a selected endolysin (WEU67899.1) of the Killian anti-UPEC phage. The tree was made using the maximum likelihood method with 1000 bootstrap replications. Panel (A) presents a tree with all grouped proteins. Panel (B) shows a modified tree, where proteins derived from phages KMB37, LNA2, 172859UKE1, KMB38, CHD94UKE2, and ZCEC14 were removed to highlight the particular distances on the tree. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.

Figure 3

The phylogenetic tree is generated based on the third orthologous group determined by OMA and contains endolysin (YP_006987885.1) derived from phage ACG-M12. The tree was made using the maximum likelihood method. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.

Figure 4

The phylogenetic tree is generated based on the fourth orthologous group estimated by OMA and contains endolysins with an amidase domain (QZI79721.1, QZI79903.1, QZI79784.1, QZI79844.1, QZI78465.1, and QZI78611.1). The tree was made using the maximum likelihood method with 1000 bootstrap replications. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number. The ‘self’-labeled proteins were annotated by us using Pharokka version 1.6.1 [42].

Figure 5

The phylogenetic tree is generated based on the fifth orthologous group determined by OMA and contains endolysins with peptidase domain (WPK27911.1, WVW77668.1, self_RMKP5, and YP006987811.1) derived from phages KMB14, SHAK7163, SHAK7704, and ACG-C91, respectively. The tree was made using the maximum likelihood method with 1000 bootstrap replications. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number. The ‘self’-labeled endolysin was annotated by us using Pharokka version 1.6.1 [42].

Figure 6

The phylogenetic tree is generated based on the sixth orthologous group determined by OMA and contains internal virion proteins with endolysin domain, such as EG-derived protein YP_009795842.1, and four other annotated and assigned by us: self_TCEH45, self_ZENB53, self_GXIJ6, and self_DNYN53. The tree was constructed using the maximum likelihood method with 1000 bootstrap replications. Panel (A) presents a tree with all grouped proteins. Panel (B) shows a modified tree, where proteins derived from phages EG1 and LNA3 were removed to highlight the particular distances on the tree. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.

Figure 7

The phylogenetic tree is generated based on the seventh orthologous group established by OMA and contains internal virion proteins with a coiled-coil domain (WVW77660.1 and, annotated by us, self_RMKP62). It was made using the maximum likelihood method with 1000 bootstrap replications. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.

Figure 8

The phylogenetic tree is generated based on the eighth orthologous group established by OMA and contains putative endolysin of Killian phage (WEU67851.1). The tree was made using the maximum likelihood method with 1000 bootstrap replications. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.

Figure 9

The phylogenetic tree is generated based on the ninth orthologous group determined by OMA and contains Killian’s putative endolysin no. WEU68017.1 and ZCEC14 putative endolysin no. UVD33329.1. It was constructed using the maximum likelihood method with 1000 bootstrap replications. Panel (A) presents a tree with all grouped proteins. Panel (B) shows a modified tree, in which proteins of phages KMB43, LNA2, KMB38, and 172859UKE1 were removed to highlight the particular distances on the tree. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.

Figure 10

The phylogenetic tree is based on the tenth orthologous group identified by OMA and includes the ZCEC14-derived putative endolysin (UVD33388.1). It was constructed using the maximum likelihood method with 1000 bootstrap replications. Panel (A) displays the tree with all grouped proteins, while panel (B) presents a modified version in which the phage KMB43 protein was removed to emphasize specific distances within the tree. The names on the tree consist of the protein name and its accession number, followed by the phage name and its accession number.

Figure 11

The phylogenetic tree is generated based on the eleventh orthologous group determined by OMA and contains two putative endolysins of Killian and ZCEC14 phages (WEU67833.1 and UVD33512.1). It was made using the maximum likelihood method with 1000 bootstrap replications. Panel (A) presents a tree with all grouped proteins. Panel (B) shows a modified tree, in which the proteins of phages LNA2, 172859UKE1, and KMB38 were removed to highlight the particular distances on the tree. The names indicated on the tree include the protein name and its accession number, followed by the phage name and its accession number.