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Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction

Youngju Kim1,2, Sang-Mok Lee3, Linh Khanh Nong3

  • 1Optipharm Inc., Cheongju-si, Chungcheongbuk-do, Republic of Korea.

Frontiers in Microbiology
|February 10, 2023
PubMed

Insights

Novel bacteriophages KP1 and KP12 targeting Klebsiella pneumoniae were characterized. Their genomic context and lytic proteins were analyzed, offering new tools for phage therapy development against antibiotic-resistant bacteria.

Area of Science:

  • Microbiology and Virology
  • Biotechnology and Bioinformatics

Background:

  • Rising antibiotic resistance in Klebsiella pneumoniae necessitates alternative treatments.
  • Bacteriophage therapy is a promising alternative, requiring detailed phage genomic understanding.

Purpose of the Study:

  • To sequence, annotate, characterize, and compare two Klebsiella phages, KP1 and KP12.
  • To analyze the genomic context and lytic proteins of these novel phages for therapeutic applications.

Main Methods:

  • Genomic sequencing and annotation of KP1 and KP12.
  • Physiological stability and host specificity assays.
  • Bioinformatic analysis of lytic proteins, including 3D structure prediction using AlphaFold.

Main Results:

  • KP1 and KP12 are Myoviridae family members, stable across a wide pH/temperature range.
  • Both phages exhibit K. pneumoniae specificity with broad intraspecies host range.
  • Phylogenetic analysis shows distant relation; AlphaFold models confirm T4-like and P1/P2-like lysis proteins.

Conclusions:

  • KP1 and KP12 represent novel bacteriophages with potential for phage therapy development.
  • This study provides essential genomic data for K. pneumoniae phage therapy research and development.
Keywords:
3D structure predictionAlphaFoldKlebsiella pneumoniaebacteriophagecomparative genomic analysislysis-associated proteinprotein structure alignment

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