Origin, Evolution and Diversity of φ29-like Phages—Review and Bioinformatic Analysis

Origin, Evolution and Diversity of φ29-like Phages—Review and Bioinformatic Analysis Review

Journal

International Journal of Molecular Sciences
ISSN: 1661-6596 , E-ISSN: 1422-0067

Output data

Year: 2024, Volume: 25, Number: 19, Article number : 10838, Pages count : DOI: 10.3390/ijms251910838

Authors

Evseev Peter ^1,2 , Gutnik Daria ³ , Evpak Alena ² , Kasimova Anastasia ⁴ , Miroshnikov Konstantin ²

Affiliations

1	Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117997 Moscow, Russia
2	Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, 117997 Moscow, Russia
3	Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorsakaya Street, 3, 664033 Irkutsk, Russia
4	Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, 119991 Moscow, Russia

Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.

Evseev P. , Gutnik D. , Evpak A. , Kasimova A. , Miroshnikov K.
Origin, Evolution and Diversity of φ29-like Phages—Review and Bioinformatic Analysis
International Journal of Molecular Sciences. 2024. V.25. N19. 10838 . DOI: 10.3390/ijms251910838 Scopus OpenAlex

Scopus:	2-s2.0-85206435613
OpenAlex:	W4403252995

Пока нет цитирований