Bacteriophage replication modules

Weigel, Christoph; Seitz, Harald

doi:10.1111/j.1574-6976.2006.00015.x

Cited by 155 publications

(133 citation statements)

References 288 publications

(328 reference statements)

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“…Genomes of most simple viruses are composed of two functional modules, one for the virion structure and the other one for genome replication (142). While the genome replication modules in viruses are prone to horizontal transfer between distinct types of MGEs as well as their host cells (140,150,286), the virion structure module is unique to viruses, thereby defining their identity and distinguishing viruses from other types of MGEs (10, 145). …”

Section: Genomic Relationship To 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

218

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: Genomic Relationship To 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

218

176

View full text Add to dashboard Cite

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“…Only five archaeal ssDNA viruses, i.e., Aeropyrum coil-shaped virus (ACV), Halorubrum pleomorphic virus (HRPV1/2/6), and Haloarcula hispanica pleomorphic virus 2 (HHPV2), have been isolated so far. All known ssDNA viruses replicate, or are believed to replicate, their genome in an RCR (for a circular genome) or RHR (for a linear genome) mode (297). In bacterial circular ssDNA viruses (e.g., X174, M13, and fd), the single-stranded genome is first converted into a double-stranded replicative form (RF).…”

Section: Genome Replicationmentioning

confidence: 99%

Archaeal Extrachromosomal Genetic Elements

Wang

Peng

Shah

et al. 2015

Microbiol Mol Biol Rev

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SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.

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“…2 Interestingly, the resemblance to T4 extends beyond the mere morphological level: like T4, bacteriophage T5 encodes an ensemble of replication and recombination factors within a dedicated section of its genome, the so-called replication module. 5 Even though only a subset of these factors show obvious homology to T4 counterparts, the co-localization of the two types of genes in the replication module strongly suggests that T5 uses a recombination-dependent replication (RDR) mechanism similar to that of T4. 5 In apparent agreement with this idea, T5 contains large terminal redundancies in the form of direct repeats, while replication intermediates detected by electron microscopy show the highly complex, branched concatenates that are the hallmark of RDR.…”

Section: Introductionmentioning

confidence: 99%

“…5 Even though only a subset of these factors show obvious homology to T4 counterparts, the co-localization of the two types of genes in the replication module strongly suggests that T5 uses a recombination-dependent replication (RDR) mechanism similar to that of T4. 5 In apparent agreement with this idea, T5 contains large terminal redundancies in the form of direct repeats, while replication intermediates detected by electron microscopy show the highly complex, branched concatenates that are the hallmark of RDR. 6 In contrast to T5, the DNA replication mechanism of T4 has been studied intensively, resulting in successful reconstitution of RDR reactions in vitro and detailed knowledge of the roles of the factors involved.…”

Section: Introductionmentioning

confidence: 99%

“…6 In contrast to T5, the DNA replication mechanism of T4 has been studied intensively, resulting in successful reconstitution of RDR reactions in vitro and detailed knowledge of the roles of the factors involved. 5,7,8 In short, early rounds of T4 replication are initiated at several specific origins via transcription priming by the host RNA polymerase, followed by leading strand synthesis by the phage replisome. Concomitant lagging strand synthesis is primed by the viral primase, gp61, assisted by the helicase p41 and the helicase loader p59.…”

Section: Introductionmentioning

confidence: 99%

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