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TitleIdentifying the core genome of the nucleus-forming bacteriophage family and characterization of phage RAY.
Journal, issue, pagesbioRxiv, Year 2023
Publish dateFeb 25, 2023
PubMed AbstractWe recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic ...We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn't degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
External linksbioRxiv / PubMed:36865095 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution8.9 - 38.0 Å
Structure data

EMDB-27973: Erwinia amylovora 70S Ribosome
Method: EM (subtomogram averaging) / Resolution: 8.9 Å

EMDB-27993: Erwinia amlyavora 50S ribosome
Method: EM (subtomogram averaging) / Resolution: 13.1 Å

EMDB-28003: Erwinia phage vB_EamM_RAY (RAY) Capsid Vertex
Method: EM (subtomogram averaging) / Resolution: 19.0 Å

EMDB-28004: Erwinia phage vB_EamM_RAY (RAY) Capsid Collar
Method: EM (subtomogram averaging) / Resolution: 38.0 Å

EMDB-28005: Erwinia phage vB_EamM_RAY (RAY) Tail Sheath
Method: EM (subtomogram averaging) / Resolution: 10.0 Å

EMDB-28006: Erwinia phage vB_EamM_RAY (RAY) Baseplate
Method: EM (subtomogram averaging) / Resolution: 36.0 Å

EMDB-28007: Erwinia phage vB_EamM_RAY (RAY) Chimallin
Method: EM (subtomogram averaging) / Resolution: 20.0 Å

EMDB-28008: Erwinia phage vB_EamM_RAY (RAY) Putative PhuZ Filament
Method: EM (subtomogram averaging) / Resolution: 25.0 Å

EMDB-28009: Pseudomonas chlororaphis phage 201phi2-1 PhuZ Filament
Method: EM (subtomogram averaging) / Resolution: 26.0 Å

EMDB-28010: Pseudomonas phage phiKZ PhuZ Filament
Method: EM (subtomogram averaging) / Resolution: 22.0 Å

Source
  • Erwinia amylovora (bacteria)
  • Erwinia phage vB_EamM_RAY (virus)
  • Pseudomonas phage 201phi2-1 (virus)
  • Pseudomonas phage phiKZ (virus)

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