Complete Genome Sequence of Pectobacterium carotovorum subsp. carotovorum Bacteriophage My1

Lee, Dong Hwan; Lee, Ju-Hoon; Shin, Hakdong; Ji, Samnyu; Roh, Eunjung; Jung, Kyu-Suk; Ryu, Sangryeol; Choi, Jaehyuk; Heu, Sunggi

doi:10.1128/jvi.01987-12

Cited by 24 publications

(17 citation statements)

References 22 publications

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“…We report the first comprehensive description of T5 morphogenesis genes and the topology of their products in viral particles and assigned functions, and we highlight major new structural features of T5, which is the prototype of a large family of lytic siphophages infecting Gram-negative hosts (4)(5)(6)(7). New similarities between T5 and several families of Siphoviridae and Myoviridae are also identified, providing additional examples of the evolutionary connections between related viruses.…”

Section: Discussionmentioning

confidence: 99%

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

Zivanovic

Confalonieri

Ponchon

et al. 2014

J Virol

104

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Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T‫31؍‬ geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm. Bacteriophage T5 is a member of the Siphoviridae family infecting Escherichia coli. It consists of an icosahedral capsid containing a large molecule of double-stranded DNA (dsDNA) (121.75 kbp) attached to a long flexible noncontractile tail. The complete genomes of two wild-type T5 strains (GenBank accession numbers AY587007 [1] and AY543070) and of the heat-stable deletion mutant T5st0 (GenBank accession number AY692264 [this study]) have been sequenced. Moreover, the genomes of T5-related phages H8 (2), EPS7 (3), SPC35 (4), AKVF3 (5), pVp-1 (6), and My1 (7) exhibit high sequence similarity to T5. Of the 159 to 174 genes predicted in each genome, about 70 were assigned functions on the basis of similarity searches and/or previous genetic studies. Most of the identified genes are related to nucleotide metabolism, DNA replication, recombination, and various enzymatic functions. Despite the fact that the major structural proteins of T5 have been identified (8), the functions of 13 of the 23 late genes encoding the structural and morphogenesis proteins remain to be ascertained.The overall structure of T5 was solved by cryo-electron microscopy (cryo-EM) and image reconstruction (9). The large icosahedral capsid consists of the coat protein pb8, arranged as 11 pentamers at the vertices and 120 hexamers on the faces. The 12th vertex is occupied by a dodecamer of the portal protein pb7. The early events of T5 capsid assembly have been partly deciphered (10). The initial shell (prohead I) is assemb...

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Section: Discussionmentioning

confidence: 99%

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

Zivanovic

Confalonieri

Ponchon

et al. 2014

J Virol

104

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“…Recently, T5-related viruses were identified also in non- Enterobacteriaceae hosts. At the moment, T5-like phages are considered a genus in the Siphoviridae family with at least 11 representatives with fully sequenced genomes annotated in GenBank as “T5likeviruses”: coliphages T5, BF23, CEV2, H8, and bv_EcoS_AKF33; Salmonella phages SPC35, EPS7, and Stitch; Yersinia phage phiR201; Pectobacterium phage My1, and Vibrio phage pVp1 [ 2 , 3 , 4 , 5 , 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis

Golomidova

Kulikov

Prokhorov

et al. 2016

Viruses

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The T5-like siphoviruses DT57C and DT571/2, isolated from horse feces, are very closely related to each other, and most of their structural proteins are also nearly identical to T5 phage. Their LTFs (L-shaped tail fibers), however, are composed of two proteins, LtfA and LtfB, instead of the single Ltf of bacteriophage T5. In silico and mutant analysis suggests a possible branched structure of DT57C and DT571/2 LTFs, where the LtfB protein is connected to the phage tail via the LtfA protein and with both proteins carrying receptor recognition domains. Such adhesin arrangement has not been previously recognized in siphoviruses. The LtfA proteins of our phages are found to recognize different host O-antigen types: E. coli O22-like for DT57C phage and E. coli O87 for DT571/2. LtfB proteins are identical in both phages and recognize another host receptor, most probably lipopolysaccharide (LPS) of E. coli O81 type. In these two bacteriophages, LTF function is essential to penetrate the shield of the host’s O-antigens. We also demonstrate that LTF-mediated adsorption becomes superfluous when the non-specific cell protection by O-antigen is missing, allowing the phages to bind directly to their common secondary receptor, the outer membrane protein BtuB. The LTF independent adsorption was also demonstrated on an O22-like host mutant missing O-antigen O-acetylation, thus showing the biological value of this O-antigen modification for cell protection against phages.

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“…A Siphidoviridae lytic phage targeting the plant pathogenic bacterium Pectobacterium carotovorum subsp. carotovorum , My1, was recently sequenced (Lee et al, 2012). Although no stx genes were found in the genome of this phage, it illustrates the possibility that lytic phages released from plant-pathogenic bacteria can infect plant-invasive Escherichia coli strains.…”

Section: Horizontal Gene Transfer Between Human Pathogens and Their (mentioning

confidence: 99%

The arable ecosystem as battleground for emergence of new human pathogens

et al. 2014

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Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the “classical” routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.

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Complete Genome Sequence of Pectobacterium carotovorum subsp. carotovorum Bacteriophage My1

Cited by 24 publications

References 22 publications

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis

The arable ecosystem as battleground for emergence of new human pathogens

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