DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch

Feiss, Michael; Min, Jea Young; Sultana, Sawsan; Patel, Priyal; Sippy, Jean

doi:10.1371/journal.pone.0141934

Cited by 3 publications

(9 citation statements)

References 68 publications

(98 reference statements)

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“…The order of subsites is R3-I1-R2-R1, where R2 is oriented opposite to R3 and R1. An exception is phage N15, the cosB of which consists of a single R sequence, R3-N15, analogous in location to R3-λ [19,20] (Figures 1C and 2).…”

Section: Terminase:cos-λ Interactionsmentioning

confidence: 99%

“…The Rpps in the Rpp-TerS complexes are proposed to bind specifically to R3-PICI sites. Given the absence of I1, R2, and R1 sequences, PICIs cosBs architecture resembles cosB-N15, which contains only an R3 equivalent [19,20]. Interestingly, the putative R3 sequences of cos-PICI-A and cos-PICI-C differ in just a few positions.…”

Section: The Pici Cosmentioning

confidence: 99%

“…Therefore, in both cases, the ΔG ladder would be composed of only two steps: binding to cosN and R3. TerS-N15 DBD is dimeric [19]. Presumably, one of the TerS molecules binds to R3 specifically, but in the absence of I1 and R2, the other subunit of the TerS dimer may not bind DNA or could bind non-specifically perhaps to DNA in a region corresponding to R2 in phage λ DNA.…”

Section: Architecture Of the Cosn-pici Nicking Complexmentioning

confidence: 99%

“…It remains puzzling the necessity (or advantage) for the TerS-N15 dimer to bind, in addition to R3, to a non-specific DNA site. The ability of phage N15 to package λ DNA shows that N15 TerS recognizes λ R3 [19,20]. If dimeric TerS-N15 indeed binds non-specifically to a second site, then the presence of R2 in λ DNA would be irrelevant.…”

Section: Architecture Of the Cosn-pici Nicking Complexmentioning

confidence: 99%

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Enteric Chromosomal Islands: DNA Packaging Specificity and Role of λ-like Helper Phage Terminase

Murialdo

Feiss

2022

Viruses

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The phage-inducible chromosomal islands (PICIs) of Gram-negative bacteria are analogous to defective prophages that have lost the ability to propagate without the aid of a helper phage. PICIs have acquired genes that alter the genetic repertoire of the bacterial host, including supplying virulence factors. Recent work by the Penadés laboratory elucidates how a helper phage infection or prophage induction induces the island to excise from the bacterial chromosome, replicate, and become packaged into functional virions. PICIs lack a complete set of morphogenetic genes needed to construct mature virus particles. Rather, PICIs hijack virion assembly functions from an induced prophage acting as a helper phage. The hijacking strategy includes preventing the helper phage from packaging its own DNA while enabling PICI DNA packaging. In the case of recently described Gram-negative PICIs, the PICI changes the specificity of DNA packaging. This is achieved by an island-encoded protein (Rpp) that binds to the phage protein (TerS), which normally selects phage DNA for packaging from a DNA pool that includes the helper phage and host DNAs. The Rpp–TerS interaction prevents phage DNA packaging while sponsoring PICI DNA packaging. Our communication reviews published data about the hijacking mechanism and its implications for phage DNA packaging. We propose that the Rpp–TerS complex binds to a site in the island DNA that is positioned analogous to that of the phage DNA but has a completely different sequence. The critical role of TerS in the Rpp–TerS complex is to escort TerL to the PICI cosN, ensuring appropriate DNA cutting and packaging.

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Section: Terminase:cos-λ Interactionsmentioning

confidence: 99%

Section: The Pici Cosmentioning

confidence: 99%

Section: Architecture Of the Cosn-pici Nicking Complexmentioning

confidence: 99%

Section: Architecture Of the Cosn-pici Nicking Complexmentioning

confidence: 99%

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Enteric Chromosomal Islands: DNA Packaging Specificity and Role of λ-like Helper Phage Terminase

Murialdo

Feiss

2022

Viruses

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“…Their structural and packing proteins are also highly analogous, making it likely that N15 DNA packing follows a pathway similar to that of lambda [1]. It has even been demonstrated that the N15 specific terminase can package lambda DNA with reasonable efficiency [41].…”

Section: Lytic Replicationmentioning

confidence: 99%

The Unusual Linear Plasmid Generating Systems of Prokaryotes

Knott¹,

Rothwell²

2020

Bacteriophages - Perspectives and Future

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Linear DNA is vulnerable to exonuclease degradation and suffers from genetic loss due to the end replication problem. Eukaryotes overcome these problems by locating repetitive telomere sequences at the end of each chromosome. In humans and other vertebrates this noncoding terminal sequence is repeated between hundreds and thousands of times, ensuring important genetic information is protected. In most prokaryotes, the end-replication problem is solved by utilizing circular DNA molecules as chromosomes. However, some phage and bacteria do store genetic information in linear constructs, and the ends of these structures form either invertrons or hairpin telomeres. Hairpin telomere formation is catalyzed by a protelomerase, a unique protein that modifies DNA by a two-step transesterification reaction, proceeding via a covalent protein bound intermediate. The specifics of this mechanism are largely unknown and conflicting data suggests variations occur between different systems. These proteins, and the DNA constructs they produce, have valuable applications in the biotechnology industry. They are also an essential component of some human pathogens, an increased understanding of how they operate is therefore of fundamental importance. Although this review will focus on phage encoded protelomerase, protelomerases found from Agrobacterium and Borellia will be discussed in terms of mechanism of action.

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DNA Packaging Specificity in the λ-like Phages: Gifsy-1

Feiss,

Sippy

2024

Preprint

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DNA viruses recognize viral DNA and package it into virions. Specific recognition is needed to distinguish viral DNA from host cell DNA. The λ-like phages are interesting and good models to examine viral DNA packaging, and the Escherichia coli phage λ has been extensively studied. Gifsy-1 is a Salmonella phage largely genetically isolated from coliphage λ due to their different host ranges. In this present work, Gifsy-1’s DNA packaging specificity was studied using a Gifsy-1-λ hybrid phage with the Gifsy-1 recognition elements – the TerS protein’s winged helix-turn-helix DNA binding motif and cosB, the TerS binding site. In vivo packaging studies showed Gifsy-1 packages λ DNA at ⁓50% and λ packages Gifsy-1 DNA at ⁓ 30% efficiency, and thus share the same DNA packaging specificity. N15 is a third phage that shares phage λ’s packaging specificity. Here N15 is shown to package Gifsy-1 DNA. Phage 21 fails to package λ and Gifsy-1 DNAs; the efficiencies are 0.01% and 1%, resp. A known incompatibility between the 21 helix-turn-helix motif and cosB is also proposed to account for the inability of 21 to package Gifsy-1 DNA.

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DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch

Cited by 3 publications

References 68 publications

Enteric Chromosomal Islands: DNA Packaging Specificity and Role of λ-like Helper Phage Terminase

Enteric Chromosomal Islands: DNA Packaging Specificity and Role of λ-like Helper Phage Terminase

The Unusual Linear Plasmid Generating Systems of Prokaryotes

DNA Packaging Specificity in the λ-like Phages: Gifsy-1

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