Endonuclease VII is a key component of the mismatch repair mechanism in bacteriophage T4

Shcherbakov, Victor P.; Plugina, Lidiya; Shcherbakova, Tamara

doi:10.1016/j.dnarep.2010.12.006

Cited by 8 publications

(5 citation statements)

References 44 publications

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“…The six genomes had in common enzymes involved in DNA metabolism, such as thymidylate synthase, dihydrofolate reductase, exodeoxyribonuclease, deoxyribonuclease monophosphate kinase, and proteins associated with replication such as DNA polymerase, DNA ligase, and DNA primase/helicase. Phage FSL-SP107 had a putative integration and excision endonuclease VII (ACLAME 151), which has been described in the phage T4 as a key component of the mismatch repair mechanism [52]. .…”

Section: Similar Genomic Backbone In Felixounaviruses That Infect Salmonellamentioning

confidence: 99%

Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis

et al. 2021

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Salmonella spp. is one of the most common foodborne pathogens worldwide; therefore, its control is highly relevant for the food industry. Phages of the Felixounavirus genus have the characteristic that one phage can infect a large number of different Salmonella serovars and, thus, are proposed as an alternative to antimicrobials in food production. Here, we describe two new members of the Felixounavirus genus named vB_Si_35FD and vB_Si_DR94, which can infect Salmonella Infantis. These new members were isolated and sequenced, and a subsequent comparative genomic analysis was conducted including 23 publicly available genomes of Felixounaviruses that infect Salmonella. The genomes of vB_Si_35FD and vB_Si_DR94 are 85,818 and 85,730 bp large and contain 129 and 125 coding sequences, respectively. The genomes did not show genes associated with virulence or antimicrobial resistance, which could be useful for candidates to use as biocontrol agents. Comparative genomics revealed that closely related Felixounavirus are found in distinct geographical locations and that this genus has a conserved genomic structure despite its worldwide distribution. Our study revealed a highly conserved structure of the phage genomes, and the two newly described phages could represent promising biocontrol candidates against Salmonella spp. from a genomic viewpoint.

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Section: Similar Genomic Backbone In Felixounaviruses That Infect Salmonellamentioning

confidence: 99%

Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis

et al. 2021

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“…There is also a homologue of recombination endonuclease VII of Escherichia phage T4 (CB7_214). In phage T4, this protein is involved in DNA mismatch repair and assists in DNA packaging by removing branched replicative DNA [27].…”

Section: Dna Replication Methylation and Nucleotide Metabolismmentioning

confidence: 99%

“…Functional inferences for predicted ORF gene products were obtained by searches conducted using BLASTp (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins; [62]), Pfam (http://pfam.xfam.org/search#tabview=tab1; [63]), InterProScan (https://www.ncbi.nlm.nih.gov/ pmc/articles/PMC3998142/; [64]) and HHpred (https://toolkit.tuebingen.mpg.de/#/tools/hhpred; [65]). Transmembrane domains and lipoprotein cleavage signal were identified using TMHMM v.2 (http://www.cbs.dtu.dk/services/TMHMM/; [27]) and LipoP v.1 (http://www.cbs.dtu.dk/services/ LipoP/; [66]), respectively. Translated ORFs from phage ϕM1 were searched against hidden Markov model profiles downloaded from the pVOGs database (ref) using hmmscan (version), with an E-value cut off of 10 −5 .…”

Section: Bioinformatic Analysismentioning

confidence: 99%

Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus

et al. 2020

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To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins—20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.

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“…ORF5 is predicted to be the endonuclease VII. It is a component of the mismatch repair mechanism in the genome (Shcherbakov et al, 2011 ). ORF7 and ORF10 are predicted to be the 5'-3' exonuclease.…”

Section: Resultsmentioning

confidence: 99%

Isolation, characterization and therapeutic evaluation of a new Acinetobacter virus Abgy202141 lysing Acinetobacter baumannii

Tian,

Liu,

Zhou

et al. 2024

Front. Microbiol.

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Acinetobacter baumannii is an opportunistic pathogen that easily resists currently available antibiotics. Phages are considered alternative therapeutic agents to conventional antibiotics for the treatment of multidrug-resistant bacteria. We isolated an Acinetobacter virus Abgy202141 from underground sewage in a residential area of Guiyang City in China. Transmission electron microscopy (TEM) analysis showed that Acinetobacter virus Abgy202141 has an icosahedral head attached to a tail. This phage infects A. baumannii strain GY-4, and was found to have a short latent period of 5 min and with a burst size of 189 particles per infected host cell. Additionally, Acinetobacter virus Abgy202141 remained stable at different concentrations of chloroform and varying pH levels and temperatures. Based on SDS-PAGE analysis, it contained 14 proteins with molecular weights ranging from 12 to 125 kDa. The double-strand (ds) DNA genome of Acinetobacter virus Abgy202141 consisted of 41,242 bp with a GC content of 39.4%. It contained 50 open reading frames (ORFs), of which 29 ORFs had identified functions, but no virulence-related genes, antibiotic-resistance genes, or tRNAs were found. Phylogenetic analysis indicated that Acinetobacter virus Abgy202141 was a new phage in the Friunavirus genus. Acinetobacter virus Abgy202141 also showed the ability to prevent A. baumannii infections in the Galleria mellonella in vivo model.

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Endonuclease VII is a key component of the mismatch repair mechanism in bacteriophage T4

Cited by 8 publications

References 44 publications

Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis

Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis

Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus

Isolation, characterization and therapeutic evaluation of a new Acinetobacter virus Abgy202141 lysing Acinetobacter baumannii

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