Two Families of Rep-Like Genes That Probably Originated by Interspecies Recombination Are Represented in Viral, Plasmid, Bacterial, and Parasitic Protozoan Genomes

Gibbs, Mark J.; Smeianov, Vladimir V.; Steele, J. L.; Upcroft, Peter; Ефимов, Б. А.

doi:10.1093/molbev/msj122

Cited by 51 publications

(55 citation statements)

References 14 publications

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“…Genomes within CDS group 6 share a rolling-circle replication protein commonly found in circoviruses and nanoviruses. A similar replication protein is also found in geminiviruses (Gronenborn, 2004) and some plasmids (Gibbs et al, 2006). The translated proteins contained all five conserved replicase motifs involved in rolling-circle replication (Supplementary Figure 3), including the motif involved in the initiation and termination of rollingcircle DNA replication (motif 2), a DNA-linking tyrosine (motif 3) and the Walker A motif, which is a Figure 2 FFP analyses of ssDNA virus isolates from the NCBI database and genomes from this study.…”

Section: Resultsmentioning

confidence: 66%

Previously unknown and highly divergent ssDNA viruses populate the oceans

2013

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Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.

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Section: Resultsmentioning

confidence: 66%

Previously unknown and highly divergent ssDNA viruses populate the oceans

2013

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“…Comparative analysis of the Rep protein sequences of circoviruses and nanoviruses reveals a complex network of relationships between viruses, plasmids, and transposons (30,135,139). A plausible hypothesis has been proposed that recombination events between ssDNA genetic elements and RNA viruses are pervasive in the evolution of ssDNA replicons and underlie the evolutionary success of this class of selfish elements (140).…”

Section: Rolling Circle Replicons: Multiple Transitions From Viruses mentioning

confidence: 99%

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Koonin

Dolja

2014

Microbiol Mol Biol Rev

219

211

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SUMMARY Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus “self” that defines the identity of deep, ancient viral lineages. However, several other widespread viral “hallmark genes” encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.

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“…Plasmids are not commonly detected in bifidobacteria, with approximately 20% of isolated bifidobacteria containing detectable plasmids (281 (97). Some plasmids have been sequenced completely, revealing primarily rolling circular plasmids varying in size from 1.8 to 10.2 kb (Table 5).…”

Section: Plasmid Analysismentioning

confidence: 99%

Genomic Insights into Bifidobacteria

Lee

O’Sullivan

2010

Microbiol Mol Biol Rev

249

197

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SUMMARY Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.

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Two Families of Rep-Like Genes That Probably Originated by Interspecies Recombination Are Represented in Viral, Plasmid, Bacterial, and Parasitic Protozoan Genomes

Cited by 51 publications

References 14 publications

Previously unknown and highly divergent ssDNA viruses populate the oceans

Previously unknown and highly divergent ssDNA viruses populate the oceans

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Genomic Insights into Bifidobacteria

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