Genomic sequence and analysis of the atypical temperate bacteriophage N15 1 1Edited by M. Gottesman

Равин, В. К.; Ravin, Nikolai V.; Casjens, Sherwood; Ford, Michael E.; Hatfull, Graham F.; Hendrix, Roger W.

doi:10.1006/jmbi.2000.3731

Cited by 121 publications

(121 citation statements)

References 77 publications

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“…It therefore seems that His2 or HHPV-1 donated a block of structural protein-coding genes to a linear plasmid and a circular plasmid, respectively, thereby transforming a plasmid into a virus. A similar evolutionary scenario was also proposed to be accountable for the origin of plant geminiviruses (151) as well as bacterial siphovirus N15 (228,229). The circular ssDNA genome of another haloarchaeal pleomorphic virus, Halorubrum pleomorphic virus 1 (HRPV-1), presented an even greater amazement.…”

Section: Euryarchaeal Virusesmentioning

confidence: 80%

“…The two types of elements not only share a gene pool (143,229,253) but also depend on each other (8,60,119,283) or, on the contrary, compete (14) inside the host cell. A single cell thus represents a unique ecosystem where viruses, plasmids, integrons, and transposable elements all come together and where each one of these genetic elements tries to survive and stay fit.…”

Section: Interplay Between Viruses and Other Mobile Genetic Elementsmentioning

confidence: 99%

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Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Krupovìč

Prangishvili

Hendrix

et al. 2011

Microbiol Mol Biol Rev

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216

176

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SUMMARY Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

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Section: Euryarchaeal Virusesmentioning

confidence: 80%

Section: Interplay Between Viruses and Other Mobile Genetic Elementsmentioning

confidence: 99%

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Krupovìč

Prangishvili

Hendrix

et al. 2011

Microbiol Mol Biol Rev

Self Cite

216

176

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“…An alternative strategy, also proposed in Bacteriophage N15 (Ravin et al, 2000), may exist: as new virions are assembled during the lytic phase, the replicated DNA is methylated before packaging. Host lysis.…”

Section: Genome Features and Annotationsmentioning

confidence: 99%

Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

et al. 2010

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Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed 'ecogenomic' patterns of Pseudoalteromonas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intragenomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most 'host'-adapted proteins also have the strongest bacterial tetra signature, whereas the least 'host'-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules. Finally, analysis of the structural proteome identified seven proteins that make up the mature virion, four of which were previously unknown. This integrated approach combines both novel and classical strategies and serves as a model to elucidate ecological inferences and evolutionary relationships from phage genomes that typically abound with unknown gene content.

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“…The complete nucleotide sequence of the 46-kb genome is known (2). Upon infection of E. coli, the DNA circularizes via the cos ends.…”

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confidence: 99%

Phage N15 Telomere Resolution

Deneke

Ziegelin

Lurz

et al. 2002

Journal of Biological Chemistry

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The Escherichia coli prophage N15 exists as a linear DNA molecule with covalently closed ends. Purified N15 protelomerase TelN is the only protein required to convert circular DNA substrates to the linear form with hairpin termini. Within the center of the telomerase occupancy site tos, the target for TelN is the 56-bp telRL consisting of the central 22-bp palindrome telO and two 14-bp flanking inverted sequence repetitions. DNase I footprinting of TelN-telRL complexes shows a segment of ϳ50 bp protected by TelN. Surface plasmon resonance studies demonstrate that this extended footprint is caused by two TelN molecules bound to telRL. Stable TelN-target DNA complexes are achieved with telRL; however, the additional sequences of tos stabilize the TelN-target complexes. TelO alone is not sufficient for specific stable complex formation. However, processing can occur, i.e. generation of the linear covalently closed DNA. Within the context of telRL, sequences of telO are involved in specific TelN-telRL complex formation, in processing itself, and/or in recognition of the processing site. The sequence of the central (CG) 3 within telO that is part of a 14-bp stretch proposed to have Z-DNA conformation is essential for processing but not for formation of specific TelN-telRL complexes. The concerted action of both TelN molecules at the target site is the basis for telomere resolution. Capturing of reaction intermediates demonstrates that TelN binds covalently to the 3-phosphoryl of the cleaved strands.N15 is a lambdoid, temperate Escherichia coli phage that has double-stranded DNA with cohesive ends packaged in the virion (1). The complete nucleotide sequence of the 46-kb genome is known (2). Upon infection of E. coli, the DNA circularizes via the cos ends. In contrast to other temperate phages, N15 does not integrate into the host genome. Lysogeny is established by processing the telomere resolution site telRL to form a linear genome with covalently closed, hairpin-like ends telL and telR (see "Discussion"). The proposed telomerase occupancy site tos (1) contains a series of inverted repeats centered on the 56-bp palindromic telRL. This palindrome or part of it could form a potential cruciform structure that may function as the real substrate of the telomerase TelN. In vivo replication of linear N15 plasmids requires three N15-derived components as follows: the origin of replication ori, the replication initiation protein RepA, and TelN protein for resolution of the replicated telomeres (3). Ori probably is located immediately upstream of repA. repA is essential in N15 lytic replication and for maintenance of the linear prophage. Both lytic and lysogenic replication is independent of at least dnaA, dnaJ, dnaK, grpE, and recA (1, 4, 5). For telomere resolution, in vitro purified TelN and a telRL substrate are sufficient (6). In contrast to eukaryotic telomerases, TelN seems to be purely proteinaceous, lacking DNA synthesizing activity. The cleavingjoining activity of TelN resembles a specialized type of integrase that u...

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Genomic sequence and analysis of the atypical temperate bacteriophage N15 1 1Edited by M. Gottesman

Cited by 121 publications

References 77 publications

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

Phage N15 Telomere Resolution

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