The Structure and Function of Biomaterial Endolysin EFm1 from E. faecalis Phage

Abstract

The endolysin EFm1 from the E. faecalis 002 (002) phage IME-EF1 efficiently lyses E. faecalis, a gram-positive bacterium that severely threatens human health. Here, the structure and lytic activity of EFm1 toward E. faecalis were further investigated. Lytic activity shows that EFm1 specifically lyses 002 and 22 other clinically isolated E. faecalis, but not E. faecalis 945. Therefore, EFm1 may be an alternative biomaterial to prevent and treat diseases caused by E. faecalis. A structural analysis showed that EFm1D166Q is a tetramer consisting of one full-length unit with additional C-terminal domains (CTDs), while EFm1166–237 aa is an octamer in an asymmetric unit. Several crucial domains and novel residues affecting the lytic activity of EFm1 were identified, including calcium-binding sites (D20, D22 and D31), a putative classic amidohydrolase catalytic triad (C29, H90 and D108), a tetramerization site (M168 and M227), putative ion channel sites (IGGK, 186–198 aa), and other residues (R208 and Y209). Furthermore, EFm1 exhibited no significant activity when expressed alone in vivo, and IME-EF1 lytic activity decreased when efm1 was knocked down. These findings provide valuable insights into the molecule mechanism of a potential functional biomaterial for the treatment of the disease caused by the opportunistic pathogen E. faecalis.

Bioinformatics analysis of the potential receptor and therapeutic drugs for Alzheimer’s disease with comorbid Parkinson’s disease

“…Semagacestat was found to be embedded in the cavity formed by the EGFR NTD domain I, II, and III regions, which agreed with a previous study ( Sabbah et al, 2020 ). Seven hydrogen bonds and one hydrophobic bond formed between semagacestat and EGFR NTD , and these bonds are key for the effect of semagacestat on the activity of EGFR NTD ( Zhou et al, 2022 ; Zheng et al, 2023 ). Although semamacestat can inhibit the activity of gamma-secretase and potentially improve the pathology of AD combined with PD through EGFR, it can also exacerbate side effects by inhibiting the cleavage of Notch.…”

SARS‐CoV‐2 NSP12 utilizes various host splicing factors for replication and splicing regulation

“…The structures of SLU7, PPIL3, and AKAP8 predicted by AlphaFold2 and the structure of NSP12 (PDB: 6XQB) were used for molecule docking (https://gramm.compbio.ku.edu/gramm). The interacting residues were indicated by PyMOL 26 …”

“…The protein expression and purification were performed as previously described with minor modifications. 26,28 The plasmid pET21b-NSP12 or pET32a-NSP8, was separately transformed into Escherichia coli BL21 (DE3). The plasmid pET21b-NSP7 was transformed into E. coli Rosetta-gami2 (DE3).…”

“…The interacting residues were indicated by PyMOL. 26 2.6 | Fluorescence microscopy A549, A549-SLU7 KO , A549-PPIL3 KO , or A549-AKAP8 KO cells seeded on the surface of coverslips placed in six-well plates were alone transfected with one plasmid, such as pEGFP-NSP12 or cotransfected with two plasmids, such as pEGFP-NSP12+ pDsRed2-SLU7. At 24 hpt, cells were fixed with 4% paraformaldehyde, permeabilized with 0.2% Triton X-100, stained by Hoechst 33342 and observed under a Leica DMi8 fluorescence microscope (objective ×64) or a Leica Stellaris laser confocal microscope (objective ×100), as described previously.…”

“…The protein expression and puri cation were performed as previously described with minor modi cations [28,29]. The plasmid pET21b-NSP12 or pET32a-NSP8, was separately transformed into E. coli BL21 (DE3).…”