Distinctive features of large complex virus genomes and proteomes

Mrázek, Jan; Karlin, Samuel

doi:10.1073/pnas.0700429104

Cited by 30 publications

(27 citation statements)

References 29 publications

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“…The lack of long contigs and discontinuous coverage at the nucleotide level suggests that the SM1 nucleotide sequence was highly variable between individuals, within individuals, or both. Temperate phage adopt the oligonucleotide usage patterns of their hosts, which can lead to sequence divergence at the nucleotide level if multiple different hosts are present (28,29). Because the oropharyngeal metagenomes were constructed from pooled samples from 19 individuals, it is likely that phage with varied hosts and host ranges were sampled.…”

Section: Resultsmentioning

confidence: 99%

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

Willner¹,

Furlan²,

Schmieder³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

129

118

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The human oropharynx is a reservoir for many potential pathogens, including streptococcal species that cause endocarditis. Although oropharyngeal microbes have been well described, viral communities are essentially uncharacterized. We conducted a metagenomic study to determine the composition of oropharyngeal DNA viral communities (both phage and eukaryotic viruses) in healthy individuals and to evaluate oropharyngeal swabs as a rapid method for viral detection. Viral DNA was extracted from 19 pooled oropharyngeal swabs and sequenced. Viral communities consisted almost exclusively of phage, and complete genomes of several phage were recovered, including Escherichia coli phage T3, Propionibacterium acnes phage PA6, and Streptococcus mitis phage SM1. Phage relative abundances changed dramatically depending on whether samples were chloroform treated or filtered to remove microbial contamination. pblA and pblB genes of phage SM1 were detected in the metagenomes. pblA and pblB mediate the attachment of S. mitis to platelets and play a significant role in S. mitis virulence in the endocardium, but have never previously been detected in the oral cavity. These genes were also identified in salivary metagenomes from three individuals at three time points and in individual saliva samples by PCR. Additionally, we demonstrate that phage SM1 can be induced by commonly ingested substances. Our results indicate that the oral cavity is a reservoir for pblA and pblB genes and for phage SM1 itself. Further studies will determine the association between pblA and pblB genes in the oral cavity and the risk of endocarditis.endocarditis | metagenomics | oropharyngeal viruses | phage-encoded virulence | streptococcal phage

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Section: Resultsmentioning

confidence: 99%

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

Willner¹,

Furlan²,

Schmieder³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

129

118

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“…V-psbA sequences could also be separated from the bacterial psbA genes based on nucleotide linguistics (Mrazek and Karlin, 2007; Figures 3a and b); we searched for the distribution of the predicted v-D1 triplet signatures (EQE, ENE, EEV, EEE, EDV, EVE, EQV and EDE) in the different groups separated by the principal components analysis (see Methods). These v-D1 motifs could also be confirmed based on the principal components analysis separation, as they were preferentially found on viral-assigned psbAs (Figures 3c and d).…”

Section: Resultsmentioning

confidence: 99%

Viral photosynthetic reaction center genes and transcripts in the marine environment

et al. 2007

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Cyanobacteria of the genera Synechococcus and Prochlorococcus are important contributors to photosynthetic productivity in the open ocean. The discovery of genes (psbA, psbD) that encode key photosystem II proteins (D1, D2) in the genomes of phages that infect these cyanobacteria suggests new paradigms for the regulation, function and evolution of photosynthesis in the vast pelagic ecosystem. Reports on the prevalence and expression of phage photosynthesis genes, and evolutionary data showing a potential recombination of phage and host genes, suggest a model in which phage photosynthesis genes help support photosynthetic activity in their hosts during the infection process. Here, using metagenomic data in natural ocean samples, we show that about 60% of the psbA genes in surface water along the global ocean sampling transect are of phage origin, and that the phage genes are undergoing an independent selection for distinct D1 proteins. Furthermore, we show that different viral psbA genes are expressed in the environment.

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“…The diversities include genome size, number of genes, mode of replication, level of virulence, and host range. Furthermore, the number of proteins encoded by a single viral genome range from two to about a thousand (3,4). Though there have been multiple theories about the origin of viruses yet the debate over this subject is far from settled.…”

Section: Introductionmentioning

confidence: 99%

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

Alam

Iqbal²,

Tripathi

et al. 2017

Gene Cell Tissue

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The present study focused on Staphylococcus phage genomes, which have been classified to 3 categories on the basis of their size. Overall, 18 classes of II Staphylococcus phage genomes with genome size around 40 kbp were investigated to elucidate the presence, distribution, and complexity of SSRs therein. The full length genome sequences from NCBI were analyzed using the IMEx software. A total of 3656 simple sequence repeats (SSRs) and 213 compound SSRs (cSSR) were present in the studied genomes. The incident frequency of SSR and cSSR per genome ranged from 183 to 308 and 8 to 19, respectively. The SSRs distribution across genomes was non-linear and so was its conversion to cSSR (the range of cSSR percentage was from 4.15 to 9.13) implicating a non-uniform incidence and clustering in genomes. The AT rich content of genomes was reflected in the prevalence of repeats with A, AT/TA, and AAG/GAA being the highest represented mono-, di-, and tri-nucleotide repeat motifs, respectively. An increase in dMAX was accompanied by greater cSSRs in the genomes yet the increase was neither uniform across genomes nor linear. The SSRs and cSSRs are predominantly localized on the coding region. The non-coding region accounts for~19% in SSR and~30% in cSSR while a hypothetical protein accounted for~30% in SSRs as well as cSSR. The relative frequencies and distribution of different classes of simple and compound microsatellites within and across genomes are suggestive of these sequences being involved in genome evolution and adaptation.

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Distinctive features of large complex virus genomes and proteomes

Cited by 30 publications

References 29 publications

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

Viral photosynthetic reaction center genes and transcripts in the marine environment

Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

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