The microviridae: Diversity, assembly, and experimental evolution

Doore, Sarah M.; Fane, Bentley A.

doi:10.1016/j.virol.2016.01.020

Cited by 52 publications

(45 citation statements)

References 101 publications

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“…The sequencing of the microviruses is peculiar, as library preparation with the Nextera ® XT DNA kit applies transposons targeting dsDNA. However, during microvirus infection the host polymerase converts the viral ssDNA into an intermediate state of covalently closed dsDNA, which is then replicated in rolling circle by viral replication proteins transcribed by the host RNA polymerase [65]. This intermediate state may have enabled the library preparation.…”

Section: Resultsmentioning

confidence: 99%

Exploring the remarkable diversity ofEscherichia coliPhages in the Danish Wastewater Environment, Including 91 Novel Phage Species

Olsen

Kot

Junco

et al. 2020

Preprint

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Phages drive bacterial diversity -profoundly influencing diverse microbial communities, from 14 microbiomes to the drivers of global biogeochemical cycling. The vast genomic diversity of phages is 15 gradually being uncovered as >8000 phage genomes have now been sequenced. Aiming to broaden our 16 understanding of Escherichia coli (MG1655, K-12) phages, we screened 188 Danish wastewater samples (0.5 17 ml) and identified 136 phages of which 104 are unique phage species and 91 represent novel species, 18 including several novel lineages. These phages are estimated to represent roughly a third of the true diversity 19 of Escherichia phages in Danish wastewater. The novel phages are remarkably diverse and represent four 20 different families Myoviridae, Siphoviridae, Podoviridae and Microviridae. They group into 14 distinct clusters 21 and nine singletons without any substantial similarity to other phages in the dataset. Their genomes vary 22 drastically in length from merely 5 342 bp to 170 817 kb, with an impressive span of GC contents ranging 23 from 35.3% to 60.0%. Hence, even for a model host bacterium, in the go-to source for phages, substantial 24 diversity remains to be uncovered. These results expand and underlines the range of Escherichia phage 25 diversity and demonstrate how far we are from fully disclosing phage diversity and ecology. 26 27 28 108 6 R studio version 1.1.456 [48] was used for rarefaction, species diversity (q = 0, datatype: incidence_raw), 109 extrapolation hereof (estimadeD) and estimation of sample coverage. The visualisation of genome sizes and 110 GC contents was prepared in Excel version 16.31.111 3. Results and Discussion 112 3.2. Phylogenetics, taxonomy and species richness 113 The sequenced phages were analysed strictly in silico, focusing on their relatedness to known phages, 114 their taxonomy and any distinctive characteristics. Based on the confirmed morphology of closely related 115 phages, at least four different families are represented, Myoviridae (58%), Siphoviridae (25%), Podoviridae (7.4%) 116 and even the single stranded DNA (ssDNA) Microviridae (5.9%) (Table 1). Five (3.7%) of the phages are so 117 distinct that they could not with certainty be assigned to any family. A similar distribution was found by Korf 118 et al., (2019), i.e. 70% Myoviridae, 22% Siphoviridae and 8% Podoviridae, just as an analysis of the genomes of 119 Caudovirales infecting Enterobacteriaceae, by Grose & Casjens (2014), also identified more clusters belonging to 120 the Myoviridae, than the Siphoviridae and fewest of the Podoviridae [8,22]. Jurczak-Kurek et al., (2016) found more 121 siphoviruses than myovirus, but also found the Podoviridae to be the least abundant [23]. Nonetheless, these 122 distributions are just as likely to be caused by culture or isolation methods, as they are to reflect true 123 abundances. Based on DNA homology and phylogenetic analysis, the 104 unique phages identified in this 124 study group into 14 distinct clusters and nine singletons, having a <1% Gegenees score...

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Section: Resultsmentioning

confidence: 99%

Exploring the remarkable diversity ofEscherichia coliPhages in the Danish Wastewater Environment, Including 91 Novel Phage Species

Olsen

Kot

Junco

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…Experiments used to study phage evolution have typically included a variety of model systems. Examples include phages φ6 ( Burch and Chao 2000 ), φX174 and its relatives ( Doore and Fane 2016 ), T7 ( Bull and Molineux 2008 ), and λ ( Meyer et al 2012 ). Experimental evolution studies using these systems have uncovered important trends in phage evolution.…”

Section: Introductionmentioning

confidence: 99%

Evolved Populations ofShigella flexneriPhage Sf6 Acquire Large Deletions, Altered Genomic Architecture, and Faster Life Cycles

et al. 2016

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Genomic architecture is the framework within which genes and regulatory elements evolve and where specific constructs may constrain or potentiate particular adaptations. One such construct is evident in phages that use a headful packaging strategy that results in progeny phage heads packaged with DNA until full rather than encapsidating a simple unit-length genome. Here, we investigate the evolution of the headful packaging phage Sf6 in response to barriers that impede efficient phage adsorption to the host cell. Ten replicate populations evolved faster Sf6 life cycles by parallel mutations found in a phage lysis gene and/or by large, 1.2- to 4.0-kb deletions that remove a mobile genetic IS911 element present in the ancestral phage genome. The fastest life cycles were found in phages that acquired both mutations. No mutations were found in genes encoding phage structural proteins, which were a priori expected from the experimental design that imposed a challenge for phage adsorption by using a Shigella flexneri host lacking receptors preferred by Sf6. We used DNA sequencing, molecular approaches, and physiological experiments on 82 clonal isolates taken from all 10 populations to reveal the genetic basis of the faster Sf6 life cycle. The majority of our isolates acquired deletions in the phage genome. Our results suggest that deletions are adaptive and can influence the duration of the phage life cycle while acting in conjunction with other lysis time-determining point mutations.

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“…The bacteriophage ϕX174 belonging to Microviridae family was chosen as an example of icosahedral viruses with ssDNA genome packaging (for a review see, e.g., Doore & Fane, 2016).…”

Section: Large-scale Periodic Patterns In ϕX174 Genomementioning

confidence: 99%

Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

Chechetkin

Lobzin

2018

Journal of Biomolecular Structure and Dynamics

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The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studied the quasi-regular large-scale segmentation in genomic sequences of different ssRNA, ssDNA, and dsDNA viruses. The particular representatives included satellite tobacco mosaic virus (STMV) and the strains of satellite tobacco necrosis virus (STNV), STNV-C, STNV-1, STNV-2, Escherichia phages MS2, ϕX174, α3, and HK97, and Simian virus 40. In all their genomes, we found the significant quasi-regular segmentation of genomic sequences related to the virion assembly and the genome packaging within icosahedral capsid. We also found good correspondence between our results and available cryo-electron microscopy data on capsid structures and genome packaging in these viruses. Fourier analysis of genomic sequences provides the additional insight into mechanisms of hierarchical genome packaging and may be used for verification of the concepts of 3-fold or 5-fold intermediates in virion assembly. The results of sequence analysis should be taken into account at the choice of models and data interpretation. They also may be helpful for the development of antiviral drugs. Communicated by Ramaswamy H. Sarma.

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The microviridae: Diversity, assembly, and experimental evolution

Cited by 52 publications

References 101 publications

Exploring the remarkable diversity ofEscherichia coliPhages in the Danish Wastewater Environment, Including 91 Novel Phage Species

Exploring the remarkable diversity ofEscherichia coliPhages in the Danish Wastewater Environment, Including 91 Novel Phage Species

Evolved Populations ofShigella flexneriPhage Sf6 Acquire Large Deletions, Altered Genomic Architecture, and Faster Life Cycles

Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

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