New Site-Specific Endonucleases F-TflI, F-TflII, and F-TflIV Encoded by Bacteriophage T5

Nv, Akulenko; Ивашина, Т. В.; La, Shaloĭko; Mg, Shliapnikov; Vn, Ksenzenko

doi:10.1023/b:mbil.0000037005.52556.0f

Cited by 6 publications

(4 citation statements)

References 32 publications

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“…Proteins from this group are similar to the F-TflII endodeoxyribonuclease of E . coli T5 phage, described to act on asymmetric DNA substrates (coding or template) to introduce single-strand breaks 33 . HHPRED analysis allowed the determination of structural homology of the identified HNHEs to the catalytic motif of Bacillus phage SPO1 HNH, I-HmuI (E-values: 1.6e-30 for GP23 5g1 and 4.8e-27 for the remaining products).…”

Section: Resultsmentioning

confidence: 99%

Molecular, physiological and phylogenetic traits of Lactococcus 936-type phages from distinct dairy environments

Chmielewska-Jeznach

Bardowski

Szczepankowska

2018

Sci Rep

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Bacteriophage infection of Lactococcus species can cause serious disruption of dairy fermentation processes. The most common isolates from the dairy environment are Siphoviridae lytic 936-type phages. To gain specific knowledge about this group of phages in Polish dairies, we examined 90 isolates from 8 different locations. Based on restriction fragment length polymorphism analysis, coupled with physiological and molecular studies, the isolated phages were divided into 8 distinct groups. Whole-genome sequencing of single representatives from each phage group provided data about their biology and genetic composition. The phages present an overall conserved genome organization. High sequence homology to another Polish isolate, Lactococcus phage bIBB29, indicates their close phylogenetic relatedness to this strain. Such similarity may be suggestive of a general genome conservation among phages persisting in Polish dairies. Comparative genome analyses with other 936-type phages revealed several discriminative traits, including the presence and position of HNH endonuclease genes, varying number of orfs in the early gene region, and a putative TpeX gene. Interestingly, host range of the sequenced phages was restricted to L. lactis subsp. lactis biovar. diacetylactis strains. The results provide new data regarding phages present in the Polish dairy environment and permit analysis of their biology, genome composition and relatedness to other Lactococcus 936-type phages.

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Section: Resultsmentioning

confidence: 99%

Molecular, physiological and phylogenetic traits of Lactococcus 936-type phages from distinct dairy environments

Chmielewska-Jeznach

Bardowski

Szczepankowska

2018

Sci Rep

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“…Similarly, a T5-like phage, SPC35 with activity against Salmonella and E. coli exhibited the highest nucleotide similarity (86%) to AKFV33 and was found to possess genes encoding for two HEs [26] , while another T5-like phage EPS7, only possessed a single HE [27] . To date, only three HEs belonging to H-N-H subfamily have been revealed to be located in the tRNA gene region of T5 phage (ATCC11303-B5) [28] . All three of these were not identified in the genome of AKFV33.…”

Section: Discussionmentioning

confidence: 99%

Genomic, Proteomic and Physiological Characterization of a T5-like Bacteriophage for Control of Shiga Toxin-Producing Escherichia coli O157:H7

et al. 2012

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Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33), a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli . Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31×10 −9 ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C), containing 160 open reading frames (ORFs), 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (<60%) to proteins in the National Centre for Biotechnology Information database. AKVF33 also lacked the L-shaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37–41%) to tail fibers of E. coli phage phiEco32 of Podoviridae , a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein ( pb5 ) shared an overall identify of 29–72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip ( pb2 ). The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre- and post-harvest biocontrol agent.

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“…In contrast to bacteria, where tRNA genes are favorite sites for insertion of mobile group I introns (6), the presence of homing endonuclease genes in a tRNA gene cluster of phages is rarely observed (17,18). In this work we show that the segB gene codes for a site-specific endonuclease.…”

Section: Introductionmentioning

confidence: 99%

“…The segB gene is located between tRNA Ile and tRNA Arg genes of T4 in the tRNA gene region ( 13 , 17 ) and encodes a protein of unknown function. In contrast to bacteria, where tRNA genes are favorite sites for insertion of mobile group I introns ( 6 ), the presence of homing endonuclease genes in a tRNA gene cluster of phages is rarely observed ( 17 , 18 ). In this work we show that the segB gene codes for a site-specific endonuclease.…”

Section: Introductionmentioning

confidence: 99%

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage

Brok-Volchanskaya

Kadyrov

Sivogrivov

et al. 2008

Nucleic Acids Research

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Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3′ 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA TψC stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages.

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New Site-Specific Endonucleases F-TflI, F-TflII, and F-TflIV Encoded by Bacteriophage T5

Cited by 6 publications

References 32 publications

Molecular, physiological and phylogenetic traits of Lactococcus 936-type phages from distinct dairy environments

Molecular, physiological and phylogenetic traits of Lactococcus 936-type phages from distinct dairy environments

Genomic, Proteomic and Physiological Characterization of a T5-like Bacteriophage for Control of Shiga Toxin-Producing Escherichia coli O157:H7

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage

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