The Analysis of OmpA and Rz/Rz1 of Lytic Bacteriophage from Surabaya, Indonesia

Abstract

A good strategy to conquer the Escherichia coli-cause food-borne disease could be bacteriophages. Porins are a type of β-barrel proteins with diffuse channels and OmpA, which has a role in hydrophilic transport, is the most frequent porin in E. coli; it was also chosen as the potential receptor of the phage. And the Rz/Rz1 was engaged in the breakup of the host bacterial external membrane. This study aimed to analyze the amino acid of OmpA and Rz/Rz1 of lytic bacteriophage from Surabaya, Indonesia. This study employed a sample of 8 bacteriophages from the previous study. The OmpA analysis method was mass spectrometry. Rz/Rz1 was analyzed using PCR, DNA sequencing, Expasy Translation, and Expasy ProtParam. The result obtained 10% to 29% sequence coverage of OmpA, carrying the ligand-binding site. The Rz/Rz1 gene shares a high percentage of 97.04% to 98.89% identities with the Siphoviridae isolate ctTwQ4, partial genome, and Myoviridae isolate cthRA4, partial genome. The Mann–Whitney statistical tests indicate the significant differences between Alanine, Aspartate, Glycine, Proline, Serine ( p = 0.011 ), Asparagine, Cysteine ( p = 0.009 ), Isoleucine ( p = 0.043 ), Lysine ( p = 0.034 ), Methionine ( p = 0.001 ), Threonine ( p = 0.018 ), and Tryptophan ( p = 0.007 ) of OmpA and Rz/Rz1. The conclusion obtained from this study is the fact that OmpA acts as Phage 1, Phage 2, Phage 3, Phage 5, and Phage 6 receptors for its peptide composition comprising the ligand binding site, and Rz/Rz1 participates in host bacteria lysis.

Genetic development of Stx phage

“…A 4 μL sample of each PCR product was electrophoresed on a 2% agarose gel at 100 volts for 30 min. The developing bands were visualized using a UV transilluminator (Sjahriani et al 2021b).…”

“…Purification and sequencing of DNA were conducted according to previous report (Thung et al 2017;Sjahriani et al 2021b). They were demonstrated using Thermo Fisher Scientific, California, USA.…”

“…Previous study has showed the findings of molecular identification using the PCR technique (Sjahriani et al 2021b).…”

Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics

“…Phage infection poses a selective pressure for the bacteria to lose the AMR transporters and become sensitive to antibiotics. Surface modifications can also indirectly impact bacterial fitness and antibiotic tolerance [ 157 , 158 ]. Westra et al demonstrated that Pseudomonas aeruginosa PA14 evolves immunity to phage DMS3vir under high-phage conditions through loss of the pilus [ 159 ], which can impair biofilm formation and, therefore, may reduce antibiotic tolerance [ 142 , 160 , 161 , 162 ] ( Figure 3 B).…”