The anti‐immunity system of phage‐plasmid N15: identification of the antirepressor gene and its control by a small processed RNA

Ravin, Nikolai V.; Svarchevsky, Alexander N.; Dehò, Gianni

doi:10.1046/j.1365-2958.1999.01658.x

Cited by 51 publications

(58 citation statements)

References 47 publications

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“…Their putative proteins are 74, 79, and 81% identical to the N15 antB-, antA-, and icd-encoded proteins, respectively; these N15 proteins have auxiliary antirepressor, antirepressor, and inhibition of cell division functions, respectively (81). The 5Ј portion of the N15 transcript is processed into a highly folded cA RNA that activates a terminator 5Ј to N15 genes 30, 31, and 32.…”

Section: Resultsmentioning

confidence: 99%

The pKO2 Linear Plasmid Prophage ofKlebsiella oxytoca

et al. 2004

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Temperate bacteriophages with plasmid prophages are uncommon in nature, and of these only phages N15 and PY54 are known to have a linear plasmid prophage with closed hairpin telomeres. We report here the complete nucleotide sequence of the 51,601-bp Klebsiella oxytoca linear plasmid pKO2, and we demonstrate experimentally that it is also a prophage. We call this bacteriophage KO2. An analysis of the 64 predicted KO2 genes indicate that it is a fairly close relative of phage N15; they share a mosaic relationship that is typical of different members of double-stranded DNA tailed-phage groups. Although the head, tail shaft, and lysis genes are not recognizably homologous between these phages, other genes such as the plasmid partitioning, replicase, prophage repressor, and protelomerase genes (and their putative targets) are so similar that we predict that they must have nearly identical DNA binding specificities. The KO2 virion is unusual in that its phage -like tails have an exceptionally long (3,433 amino acids) central tip tail fiber protein. The KO2 genome also carries putative homologues of bacterial dinI and umuD genes, both of which are involved in the host SOS response. We show that these divergently transcribed genes are regulated by LexA protein binding to a single target site that overlaps both promoters.Temperate bacteriophages usually physically integrate their prophage DNAs into the host bacterium's chromosome when they establish lysogeny. However, a few prophages, such as those of phages P1, N15, LE1, 20, and BB-1, are not integrated but replicate in the lysogen as low-copy-number plasmids (32,38,52,53,84). Of these, the Escherichia coli doublestranded DNA (dsDNA) tailed-phage N15 has an unusual linear prophage plasmid that has covalently closed hairpin telomeres (67, 68). Although N15 has been studied in some detail (83,85,87), few other phages with similar linear DNA prophages have been described. While this paper was being prepared, another linear plasmid prophage, PY54, was reported for Yersinia enterocolitica (48). Furthermore, the linear, hairpin-ended plasmids Lp28-2 and Lp54 in the spirochete Borrelia burgdorferi B31-MI carry sequence similarities to dsDNA phage virion assembly genes (19, 33); however, they have not yet been shown to be bone fide prophages. Linear plasmids are very rare in the ␥-Proteobacteria, but it has been reported that Klebsiella oxytoca strain CCUG 15788 (a nickelresistant bacterium isolated from the mineral oil-water coolant-lubricant emulsion of a metal working machine in Göte-borg, Sweden, in 1989 [69]) harbors a linear plasmid, pKO2, of about 50 kbp (95). Since this is close to the size of the N15 linear plasmid prophage, we were prompted to investigate the possibility that this plasmid could be a prophage. We report here the complete nucleotide sequence of pKO2, a linear plasmid prophage that encodes the synthesis of a tailed-phage particle, and the analysis of some of its properties. MATERIALS AND METHODSBacterial strains and plasmid construction. The bacterial st...

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Section: Resultsmentioning

confidence: 99%

The pKO2 Linear Plasmid Prophage ofKlebsiella oxytoca

et al. 2004

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“…The coupling of tandem promoters to the same operator is frequently observed in bacteria (examples are the rRNA operons [23,73], crp gene [22], and fis operon [53]) and offers a certain flexibility for differential gene regulation. In the autonomously replicating coliphage N15, for example, two adjacent promoters direct gene expression from the anti-immunity locus immA, and their differential control is important for the choice between lysis and lysogeny (56). Similarly arranged promoters regulate antiimmunity operons in distinct phages, such as P1, P4, and P7 (56), suggesting that this regulatory strategy is widespread among temperate phages.…”

Section: Discussionmentioning

confidence: 99%

Phage-Borne Factors and Host LexA Regulate the Lytic Switch in Phage GIL01

2011

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The Bacillus thuringiensis temperate phage GIL01 does not integrate into the host chromosome but exists stably as an independent linear replicon within the cell. Similar to that of the lambdoid prophages, the lytic cycle of GIL01 is induced as part of the cellular SOS response to DNA damage. However, no CI-like maintenance repressor has been detected in the phage genome, suggesting that GIL01 uses a novel mechanism to maintain lysogeny. To gain insights into the GIL01 regulatory circuit, we isolated and characterized a set of 17 clear plaque (cp) mutants that are unable to lysogenize. Two phage-encoded proteins, gp1 and gp7, are required for stable lysogen formation. Analysis of cp mutants also identified a 14-bp palindromic dinBox1 sequence within the P1-P2 promoter region that resembles the known LexA-binding site of Gram-positive bacteria. Mutations at conserved positions in dinBox1 result in a cp phenotype. Genomic analysis identified a total of three dinBox sites within GIL01 promoter regions. To investigate the possibility that the host LexA regulates GIL01, phage induction was measured in a host carrying a noncleavable lexA (Ind ؊ ) mutation. GIL01 formed stable lysogens in this host, but lytic growth could not be induced by treatment with mitomycin C. Also, mitomycin C induced ␤-galactosidase expression from GIL01-lacZ promoter fusions, and induction was similarly blocked in the lexA (Ind ؊ ) mutant host. These data support a model in which host LexA binds to dinBox sequences in GIL01, repressing phage gene expression during lysogeny and providing the switch necessary to enter lytic development.

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“…3), is located between the protelomerase gene and replication operon (31). Three genes at the immA form an operon and encode an inhibitor of cell division (Icd), an antirepressor protein, (AntA) and a protein that may play an ancillary role in antirepression (AntB).…”

Section: Control Of Lysogeny and Plasmid Replicationmentioning

confidence: 99%

Replication and Maintenance of Linear Phage-Plasmid N15

Ravin

2015

Microbiol Spectr

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The lambdoid phage N15 of Escherichia coli is very unusual among temperate phages in that its prophage is not integrated into the chromosome but is a linear plasmid molecule with covalently closed ends (telomeres). Upon infection, the phage DNA circularizes via cohesive ends, and then a special phage enzyme of the tyrosine recombinase family, protelomerase, cuts at another site and joins the ends, forming hairpin telomeres of the linear plasmid prophage. Replication of the N15 prophage is initiated at an internally located ori site and proceeds bidirectionally, resulting in the formation of duplicated telomeres. The N15 protelomerase cuts them, generating two linear plasmid molecules with hairpin telomeres. Stable inheritance of the plasmid prophage is ensured by a partitioning operon similar to the F factor sop operon. Unlike the F centromere, the N15 centromere consists of four inverted repeats dispersed in the genome. The multiplicity and dispersion of centromeres are required for efficient partitioning of a linear plasmid. The centromeres are located in the N15 genome regions involved in phage replication and control of lytic development, and binding of partition proteins at these sites regulates these processes. The family of N15-like linear phage-plasmids includes lambdoid phages ϕKO2 and pY54, as well as Myoviridae phages ΦHAP-1, VHML, VP882, Vp58.5, and vB_VpaM_MAR of marine gamma-proteobacteria. The genomes of these phages contain similar protelomerase genes, lysogeny control modules, and replication genes, suggesting that these phages may belong to a group diverged from a common ancestor. THE FAMILY OF LINEAR N15-LIKE PHAGE-PLASMIDSAll cells with linear chromosomes must employ special mechanisms to replicate the extreme termini of their chromosomes, since DNA polymerases alone are unable to perform this function (1).Most eukaryotes have openended DNA and employ special "telomerase" enzymes for this purpose, but there are other solutions that ensure complete replication of linear DNA: protein priming, recombination, and covalently closed terminal hairpins (reviewed in reference 2). Prokaryotes usually posses circular plasmids and chromosomes, but examples of linear replicons are known. Bacteriophage N15 belongs to the small group of organisms known to replicate as linear DNA with covalently closed telomeres. Besides N15 and related phage-plasmids, only a few examples of such replicons from bacteria are known, including the linear plasmids and chromosomes common in the spirochete genus Borrelia (3-5) and one of the two chromosomes of Agrobacterium tumefaciens (6, 7). In this review I will summarize the most relevant work on N15 and related phages, with a special emphasis on the mechanism of replication, generation of hairpin telomeres, control of lysogeny, and plasmid prophage maintenance.Phage N15 was isolated by Victor Ravin in 1964 (8). N15 belongs to the lambdoid phage family on the basis of cross-hybridization of their DNA (9) and is similar to phage λ with respect to the morphology of phag...

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The anti‐immunity system of phage‐plasmid N15: identification of the antirepressor gene and its control by a small processed RNA

Cited by 51 publications

References 47 publications

The pKO2 Linear Plasmid Prophage ofKlebsiella oxytoca

The pKO2 Linear Plasmid Prophage ofKlebsiella oxytoca

Phage-Borne Factors and Host LexA Regulate the Lytic Switch in Phage GIL01

Replication and Maintenance of Linear Phage-Plasmid N15

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