Accessory Genes in thedarAOperon of Bacteriophage P1 Affect Antirestriction Function, Generalized Transduction, Head Morphogenesis, and Host Cell Lysis

Iida, Shigeru; Hiestand-Nauer, Rosemarie; Sandmeier, H.; Lehnherr, Hansjörg; Arber, Werner

doi:10.1006/viro.1998.9405

“…Analysis of the complete sequence of P1 has revealed 112 protein-coding genes and five genes encoding untranslated RNA (Tables 2 and 3 see also Table S1 in the supplemental material). Of these, complete sequences of 42 protein-coding genes and two RNA genes had been determined previously (149,187,190,346). The remaining 73 genes were identified as described in Materials and Methods.…”

Section: Methodsmentioning

confidence: 99%

Genome of Bacteriophage P1

Łobocka

¹

,

Rose

²

,

Plunkett

³

et al. 2004

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P1 is a bacteriophage of Escherichia coli and other enteric bacteria. It lysogenizes its hosts as a circular, low-copy-number plasmid. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. Protein-coding genes occupy 92% of the genome and are organized in 45 operons, of which four are decisive for the choice between lysis and lysogeny. Four others ensure plasmid maintenance. The majority of the remaining 37 operons are involved in lytic development. Seventeen operons are transcribed from 70 promoters directly controlled by the master phage repressor C1. Late operons are transcribed from promoters recognized by the E. coli RNA polymerase holoenzyme in the presence of the Lpa protein, the product of a C1-controlled P1 gene. Three species of P1-encoded tRNAs provide differential controls of translation, and a P1-encoded DNA methyltransferase with putative bifunctionality influences transcription, replication, and DNA packaging. The genome is particularly rich in Chi recombinogenic sites. The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication.

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“…/supD thi ⌬(lac-proAB) (13), wild-type strains WA3110 (16) and MC4100 (43), the rpoS strain RH90 (23), and strain RDP268/pRPZ146 (35). The last strain is a derivative of AB1157 (F Ϫ thr-1 leuB6 proA2 his-4 arg E3thi-1 ara-14 lacY1 galK2 xyl-5 mtl-1 tsx-33 supE44 Ϫ ) carrying a kanamycin cassette (aphA) inserted in the chromosomal ssb gene.…”

Section: Methodsmentioning

confidence: 99%

“…Large bacteriophages like T4 (20) or P1 (47) contain a plethora of genes which are not absolutely required for normal phage development under standard laboratory conditions. Though the function(s) of most of these genes is unknown, many are proposed to ensure the survival of the phage in different habitats or under various growth conditions (16).…”

mentioning

confidence: 99%

Phylogenetic and Functional Analysis of the Bacteriophage P1 Single-Stranded DNA-Binding Protein

Bendtsen

¹

,

Nilsson

²

,

Lehnherr

³

2002

J Virol

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Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit and does not represent a recent acquirement of the phage. The P1 and E. coli SSB proteins are fully functionally interchangeable. SSB-P1 is nonessential for phage growth in an exponentially growing E. coli host, and it is sufficient to promote bacterial growth in the absence of the E. coli SSB protein. Expression studies showed that the P1 ssb gene is transcribed only, in an rpoS-independent fashion, during stationary-phase growth in E. coli. Mixed infection experiments demonstrated that a wild-type phage has a selective advantage over an ssb-null mutant when exposed to a bacterial host in the stationary phase. These results reconciled the observed evolutionary conservation with the seemingly redundant presence of ssb genes in many bacteriophages and conjugative plasmids.Single-stranded DNA-binding proteins (SSBs) have been found in all investigated organisms from bacteria to humans (7,36). These proteins have no enzymatic activity, but as their name indicates, they bind nonspecifically and stoichiometrically to single-stranded DNA, hold the single strands in an open conformation, and protect them from degradation by nucleases. In Escherichia coli, the assembly and propagation of the DNA replication fork, RecA-mediated homologous recombination, and the DNA base excision repair mechanism depend on the presence of SSB (see Chase [6], Meyer and Laine [29], and Lohmann and Ferrari [26] for reviews on E. coli SSB). SSB is an essential protein, and a functional copy of an ssb gene is present in every viable bacterial cell. Despite this fact, many E. coli bacteriophages and conjugative plasmids encode their own SSBs (9). Most of these episomal SSBs show strong conservation of key residues important for SSB function (24), and among them, several were shown to be able to reverse the temperature-sensitive growth defect of an ssb-1 mutant E. coli strain (9,10,12,24,29,34). The exact function of the episomal SSBs, however, was unclear, and the fact that most of them appeared to be dispensable remained puzzling (7,10,12).Under harsh natural conditions, bacteria more often than not encounter limited resources allowing only minimal or no growth (33). E. coli drastically adapts the expression of its genetic information in order to endure and survive such periods of stationary-phase growth (17, 48). The response of bacteriophages to such growth conditions varies (1). Some phages are unable to grow or acquire a stationary-phase dormant state, called pseudolysogeny (37), and resume growth once the host cells obtain fresh nutrients (21, 37). Others seem to be able to grow, albeit with reduced efficiency compared to exponential growth conditions (19,42). Large bacteriophages like T4 (20) or P1 (47) contain a plethora of genes which are not absol...

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“…The E. coli K-12 strains used were UT580 (FЈ Tet r tra⌬36 lacI q ⌬(lacZ)M15 proA ϩ B ϩ /supD thi ⌬(lac-proAB) (13), wild-type strains WA3110 (16) and MC4100 (43), the rpoS strain RH90 (23), and strain RDP268/pRPZ146 (35). The last strain is a derivative of AB1157 (F Ϫ thr-1 leuB6 proA2 his-4 arg E3thi-1 ara-14 lacY1 galK2 xyl-5 mtl-1 tsx-33 supE44 Ϫ ) carrying a kanamycin cassette (aphA) inserted in the chromosomal ssb gene.…”

Section: Methodsmentioning

confidence: 99%

Single-Stranded DNA Binding Protein

2006

Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine

0

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Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit and does not represent a recent acquirement of the phage. The P1 and E. coli SSB proteins are fully functionally interchangeable. SSB-P1 is nonessential for phage growth in an exponentially growing E. coli host, and it is sufficient to promote bacterial growth in the absence of the E. coli SSB protein. Expression studies showed that the P1 ssb gene is transcribed only, in an rpoS-independent fashion, during stationary-phase growth in E. coli. Mixed infection experiments demonstrated that a wild-type phage has a selective advantage over an ssb-null mutant when exposed to a bacterial host in the stationary phase. These results reconciled the observed evolutionary conservation with the seemingly redundant presence of ssb genes in many bacteriophages and conjugative plasmids.Single-stranded DNA-binding proteins (SSBs) have been found in all investigated organisms from bacteria to humans (7,36). These proteins have no enzymatic activity, but as their name indicates, they bind nonspecifically and stoichiometrically to single-stranded DNA, hold the single strands in an open conformation, and protect them from degradation by nucleases. In Escherichia coli, the assembly and propagation of the DNA replication fork, RecA-mediated homologous recombination, and the DNA base excision repair mechanism depend on the presence of SSB (see Chase [6], Meyer and Laine [29], and Lohmann and Ferrari [26] for reviews on E. coli SSB). SSB is an essential protein, and a functional copy of an ssb gene is present in every viable bacterial cell. Despite this fact, many E. coli bacteriophages and conjugative plasmids encode their own SSBs (9). Most of these episomal SSBs show strong conservation of key residues important for SSB function (24), and among them, several were shown to be able to reverse the temperature-sensitive growth defect of an ssb-1 mutant E. coli strain (9,10,12,24,29,34). The exact function of the episomal SSBs, however, was unclear, and the fact that most of them appeared to be dispensable remained puzzling (7,10,12).Under harsh natural conditions, bacteria more often than not encounter limited resources allowing only minimal or no growth (33). E. coli drastically adapts the expression of its genetic information in order to endure and survive such periods of stationary-phase growth (17, 48). The response of bacteriophages to such growth conditions varies (1). Some phages are unable to grow or acquire a stationary-phase dormant state, called pseudolysogeny (37), and resume growth once the host cells obtain fresh nutrients (21, 37). Others seem to be able to grow, albeit with reduced efficiency compared to exponential growth conditions (19,42). Large bacteriophages like T4 (20) or P1 (47) contain a plethora of genes which are not absol...

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Accessory Genes in thedarAOperon of Bacteriophage P1 Affect Antirestriction Function, Generalized Transduction, Head Morphogenesis, and Host Cell Lysis

Cited by 29 publications

References 46 publications

Genome of Bacteriophage P1

Genome of Bacteriophage P1

Phylogenetic and Functional Analysis of the Bacteriophage P1 Single-Stranded DNA-Binding Protein

Single-Stranded DNA Binding Protein

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