ssDNA Viruses

Virus ssDNA synthesis is initiated by cleavage of the virion-sense strand by the virus-encoded replication-associated protein (Rep) immediately downstream of the 3′ thymidine residue in an absolutely conserved TAATATT/AC sequence located in the loop of a potential stem-loop structure within the intergenic region.

From: Virus Taxonomy , 2012

Molecular Cell Biology

I.P. O'Carroll , A. Rein , in Encyclopedia of Cell Biology, 2016

Group II: ssDNA Viruses

The ssDNA viruses include some of the smallest and simplest viruses, with genomes only approximately 2–6  kb in length. One of these viruses is the familiar dog pathogen, canine parvovirus. These small viruses rely on the host cell (and, for some ssDNA viruses, coinfecting larger viruses) for much of their replication machinery. These 'minimalist' viruses may encode only a single structural protein and a single protein involved in their DNA replication. It seems reasonable to speculate that the genome size of ssDNA viruses is limited because a single nick in viral DNA will be a fatal disruption of their genome, unlike in organisms whose information is carried in dsDNA. However, some ssDNA viruses are more complex: these include the Nanoviridae, in which the entire genome is composed of 6 to 8 ~1-kb ssDNA segments, each packaged in a separate particle; the Pleolipoviridae, which infect Archaea and contain a single circular ssDNA molecule ranging up to approximately 10   kb in size; and the Bidnaviridae, which infect silkworms and whose genomes consist of a 6   kb and a 6.5   kb DNA molecule, encapsidated separately.

The DNA in these viruses can be either circular or linear; in the latter case, 'hairpin' structures at the ends of the DNA participate in priming of DNA replication (Figure 2(c)). In some ssDNA viruses, either of the two complementary strands can be packaged, so that a virus preparation is a mixture of particles with either strand; in others, only one of the strands is packaged into virions. The DNAs of ssDNA viruses are replicated by a mechanism similar to 'rolling circle' replication, involving synthesis of dsDNA intermediates containing multiple tandem copies of the viral genome. It should be noted that the template for the mRNAs of ssDNA viruses is not the ssDNA that the infecting virion brings into the cell, but rather the dsDNA produced intracellularly in infected cells (Figure 1).

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Virus Assembly and Exit Pathways

Carlos P. Mata , ... José R. Castón , in Advances in Virus Research, 2020

Abstract

Mycoviruses are a diverse group that includes ssRNA, dsRNA, and ssDNA viruses, with or without a protein capsid, as well as with a complex envelope. Most mycoviruses are transmitted by cytoplasmic interchange and are thought to lack an extracellular phase in their infection cycle. Structural analysis has focused on dsRNA mycoviruses, which usually package their genome in a 120-subunit T  =   1 icosahedral capsid, with a capsid protein (CP) dimer as the asymmetric unit. The atomic structure is available for four dsRNA mycovirus from different families: Saccharomyces cerevisiae virus L-A (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). Their capsids show structural variations of the same framework, with asymmetric or symmetric CP dimers respectively for ScV-L-A and PsV-F, dimers of similar domains of a single CP for PcV, or of two different proteins for RnQV1. The CP dimer is the building block, and assembly proceeds through dimers of dimers or pentamers of dimers, in which the genome is packed as ssRNA by interaction with CP and/or viral polymerase. These capsids remain structurally undisturbed throughout the viral cycle. The T  =   1 capsid participates in RNA synthesis, organizing the viral polymerase (1–2 copies) and a single loosely packaged genome segment. It also acts as a molecular sieve, to allow the passage of viral transcripts and nucleotides, but to prevent triggering of host defense mechanisms. Due to the close mycovirus-host relationship, CP evolved to allocate peptide insertions with enzyme activity, as reflected in a rough outer capsid surface.

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Plant Viruses and Technology

Roger Hull , in Plant Virology (Fifth Edition), 2014

ii Geminivirus Rep Proteins

As described in Chapter 7, Section VIII, D , the genomes of plant ssDNA viruses do not encode polymerases, their replication requiring interaction between a viral replication-associated protein (Rep) and host polymerases.

Transformation of N. benthamiana and tomato with a truncated TYLCV-Sar Rep protein gene strongly inhibits virus replication in protoplasts and induces protection when expressed at high levels (Noris et al., 1996; Brunetti et al., 1997). This dominant negative mutant, lacking a conserved NTP-binding domain, confers protection through two distinct molecular mechanisms depending on the challenging virus. In protecting against the homologous virus the transgenic protein inhibits the expression of the viral Rep protein; when transgenic plants are challenged with the heterologous TYLCV the transgenic protein forms dysfunctional complexes with the viral Rep protein (Lucioli et al., 2003). However, the resistance is in some cases unstable due to transgene silencing. In contrast, tomato plants transgenic with a similar construct from a mild strain of TYLCV are protected against the homologous virus but are susceptible to a severe strain of the virus (Antignus et al., 2004).

Similar strategies with Rep proteins mutated in the ori- or NTP-binding sites gave plants protected against other geminiviruses, such as BGMV (Hanson and Maxwell, 1999) or ACMV (Sangaré et al., 1997).

Silencing the Rep gene of a nanovirus has also proved to give resistance against the cognate virus. Transgenic expression of an introns-hairpin-RNA construct the babuvirus BBTV Rep gene in banana plants confers a high level of resistance to virus infection (Shenhawat et al., 2012).

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Anellovirus

P. Biagini , P. de Micco , in Encyclopedia of Virology (Third Edition), 2008

Phylogenetic and Taxonomic Aspects

The genetic diversity among anelloviruses is far larger than within any other defined group of ssDNA viruses. The considerable genetic heterogeneity is exemplified by the large number of highly divergent full-length sequences progressively identified as TTV, TTMV, and 'small anellovirus' genomes.

Historically, primer extension of the initial sequence (∼500   nt, N22 clone) to about 3700   nt (TA278 clone) primarily suggested a distant resemblance of TTV to parvoviruses, based on the apparent linear nature of the characterized genome. The circular nature of the genome was subsequently elucidated (TTV-1a clone), leading to the possible assignment of TTV members to the families of viruses possessing a circular single-stranded DNA genome. This initiated studies on circular single-stranded DNA viruses infecting humans.

Concomitant comparisons of short nucleotide sequences obtained by PCR in the N22 region allowed to identify three distinct genotypes (differing by 27–30% nucleotide divergence) describing TTV genetic diversity in early 1999. The progressive characterization of partial and complete nucleotide sequences had not only demonstrated the existence of a large number of genotypes but has also allowed to classify these genotypes into five distinct clusters (∼50% nucleotide divergence) representing the TTV major phylogenetic groups, as defined in 2002 ( Figure 2 ). The creation of the genus Anellovirus by ICTV in 2004   has officially presented such classification, but it is possible that the next ICTV report will bring significant changes to the taxonomic status of anelloviruses, such as the creation of a specific family hosting several genera accommodating many species, and modify phylogenetic clusters due to the description of new genomic sequences.

Figure 2. Phylogenetic relations among members of species Torque teno virus (neighbor-joining tree built with full-length nucleotide sequences).

Despite the fact that genomic sequences from TTMV and 'small anellovirus' are not as well described as those of TTV, they revealed a high genetic heterogeneity, at least of the same magnitude of that identified for TTV or greater. In 2005, the available full-length TTMV sequences clustered in four major phylogenetic groups (∼40% nucleotide divergence), whereas the only two 'small anellovirus' complete sequences described exhibited a nucleotide divergence reaching 46%. Extremely divergent isolates (as compared to human TTV, TTMV, and 'small anellovirus') have been also identified in nonhuman primates and low-order mammals.

A low degree of sequence homology exists between TTV, TTMV, the 'small anellovirus', and animal isolates. However, there is a ∼130 nt long sequence that is relatively well conserved between the viral groups, which is located within the UTR downstream of the GC-rich region ( Figure 3 ). Moreover, the genome organization of anelloviruses globally appears similar. It includes a coding region containing at least two main ORFs, and a UTR generally having a GC-rich stretch. The respective sizes of each of these components is however variable between isolates.

Figure 3. Alignment of the nucleotide sequence of TTV, TTMV, and 'small anellovirus' representative isolates identified in humans (conserved zone, UTR region).

Accurate phylogenetic analyses inside each viral group are feasible by comparing full-length ORF1, and to a lesser extent ORF2 nucleotide sequences. By contrast, phylogenetic analysis of short nucleotide sequences located in the N22 region or on the UTR proved to be unreliable. The latter approach is also biased by the occurrence of recombination events which are statistically more frequent in this location than in the rest of the genome.

The amino acid sequence comparisons of translated ORF1 or ORF2 proved to be reliable for phylogenetic analyses, and is the only approach for taxonomic studies combining all Anellovirus members which markedly differ in sequence and size. Such comparisons at the amino acids level have also highlighted that most, if not all, of the anelloviruses possess an ORF1 with an arginine-rich N-terminal part and motifs related to the Rep protein, while the ORF2 exhibits the well-conserved motif WX7HX3CX1CX5H. Interestingly, the same features are found in the chicken anemia virus (CAV), the type species of the genus Gyrovirus of the family Circoviridae. CAV possesses a negative-sense genome, a similar genome organization to anelloviruses, with overlapping ORFs, and several viral proteins with functions supposedly similar to their counterparts in members of the genus Anellovirus.

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Nanoviridae

In Virus Taxonomy, 2012

Similarity with other taxa

All Rep proteins of the assigned species have most of the aa domains characteristic of Rep proteins of geminiviruses and other ssDNA viruses. The nanovirus Rep proteins differ from those of members of the family Geminiviridae in being smaller (about 33   kDa), having a slightly different dNTP-binding motif (GPQ/NGGEGKT), lacking the retinoblastoma-like protein (Rb)-binding motif (LxCxE) and sharing aa sequence identities of only 17 to 22% with them. Moreover, the assigned species are clearly distinct from geminiviruses in particle morphology, genome size, number and size of DNA components, mode of transcription, and in vector species. Although circo- and nanovirids possess closely related Rep proteins and morphologically similar virions, circovirids infect vertebrates and have a much smaller genome (1.8–2.3   kb) that is not only monopartite but also bidirectionally transcribed. All these ssDNA viruses have a conserved nonanucleotide motif at the apex of the stem-loop sequence which is consistent with the operation of a rolling circle model for DNA replication.

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Genome Composition, Organization, and Expression

Roger Hull , in Plant Virology (Fifth Edition), 2014

8 mRNAs

Viral genomes are expressed from mRNAs that are either the nucleic acid of (+)-sense ssRNA viruses or transcripts from (−)-sense or dsRNA or from ds or ssDNA viruses. Baltimore (1971) pointed out that the expression of all viral genomes, be they RNA or DNA, ss or ds, (+)- or (−)-sense, converge on the mRNA stage (Figure 6.2).

Figure 6.2. Routing of viral genome expression through mRNA. Route I is transcription of dsDNA usually by the host DNA-dependent RNA polymerase; route II is transcription of ssDNA to give a dsDNA template for I (e.g., geminiviruses); route III is transcription of dsRNA, usually by virus-coded RdRp (e.g., reoviruses); route IV is replication of (+)-strand RNA via a (−)-strand template by virus-coded RdRp—the viral (+)-strand is often the template for early translation (the (+)-strand RNA viruses); route V is transcription of (−)-strand RNA viral genome by virus-coded RdRp (e.g., tospoviruses); route VI is reverse transcription of the RNA stage of retro- and pararetroviruses leading to a dsDNA template for mRNA transcription (for pararetroviruses the input viral dsDNA can be the template.

 From Baltimore (1971) with permission of the publishers.

Figure 6.3. Diagrammatic representation of a protease and its substrate showing the nomenclature of Schechter and Berger (1967). The substrate residues are labeled progressively from P1 N-terminal of the cleavage site and P1′, etc., C-terminal of the cleavage site. The corresponding binding pockets of the protease are labeled S1 and S1′.

 From Adams et al. (2005) with permission of the publishers.

Figure 6.4. Structure and function of a VPg. Panel (A) Primary structure and properties of CPMV VPg. VPg is released from longer precursors by the 24-kDa protease at Glu/Ser and Glu/Met cleavage sites, respectively. Basic and acidic amino acids are indicated by+and−signs, respectively. Panel (B) Diagram of a VPg phosphodiester-linked to the 5′ nucleotide residue of a TRSV genomic RNA and of the expected VPg-derived product of a base-catalyzed β-elimination reaction in the presence of ethanediol. The VPg amino terminal sequence was determined by Edman degradation. An S-ethylcysteine residue was detected at cycle 5 for the VPg derivative obtained after treatment of VPg-5′-oligo with ethanediol. From this result, position 5 is deduced to be a serine linked by a phosphodiester to the 5′-uridylate residue of each genomic RNA of TRSV. Panel (C) Schematic ribbon drawing illustrating interactions of PVY VPg with RNA fragment. The RNA backbone and Tyr-64 of the VPg are shown in space-filling representation. The side-chain residues that are in close contact with RNA are shown in blue.

 Panel (A) from Jaegle et al. (1987); panel (B) from Zalloua et al. (1996); and panel (C) from Plochocka et al. (1996) with permission of the publishers.

Figure 6.5. Interactive map of the potyvirus VPg. Small circles depicted in orange are viral proteins and in green are plant proteins. Interactions connecting the protein nodes are represented by color-coded lines: in blue are interactions uncovered by one assay (e.g., yeast two hybrid); in red are interactions supported by two or more assays; in black are interactions reported in the Predicted Arabidopsis Interactome Resource (PAIR) database; in magenta are protein–RNA interactions. Interactions taking place within viral replication factories are shown within the larger green circle while interactions taking place in the nucleus are shown within the black circle. As the cellular localization for the interaction between VPg and PVIP and between eIF4E and DBP1 are unknown, the host proteins have been positioned arbitrarily in the cytosol.

 From Jiang and Laliberté (2011) with permission of the publishers.

The mRNAs from genomes of DNA viruses must be identified in nucleic acids isolated from infected tissue and matched for sequence with the genomic DNA. Many plant viruses with ss (+)-sense RNA genomes have some ORFs that are translated only from a subgenomic mRNA (sg mRNA) (discussed in Section IV, C, 2, b). These too must be identified to establish the strategy of the genome.

It may be a difficult task to establish whether a viral RNA of subgenomic size is a functional mRNA or merely a partly degraded or partly synthesized piece of genomic RNA. Sequence data on an RNA isolated from an infected plant, especially if it is isolated from a polysome fraction, can give a strong indication of whether it is an sg mRNA. A sequence determination that reveals a single termination nucleotide rather than several is a good indication that the sg mRNA under study is a single distinct species and not a set of heterogeneous molecules (Sulzinski et al., 1985). This should be followed by in vitro translation to confirm that it can express the viral gene product.

Not infrequently, genuine viral sg mRNAs are encapsidated along with the genomic RNAs. These can then be isolated from purified virus preparations and characterized. When the sequence of the genomic nucleic acid is known there are two techniques available to locate precisely the 5′ terminus of a presumed sg mRNA. In the S1 nuclease protection procedure, the mRNA is hybridized with a complementary DNA sequence that covers the 5′ region of the sg mRNA. The ss regions of the hybridized molecule are removed with S1 nuclease. The DNA that has been protected by the mRNA is then sequenced. In the second method, primer extension, a suitable ss primer molecule is annealed to the mRNA. Reverse transcriptase is then used to extend the primer as far as the 5′ terminus of the mRNA and the DNA produced sequence. Carrington and Morris (1986) used both these procedures to locate the 5′ termini of the two sgRNAs of CarMV.

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Unclassified and Unassigned Aquatic Animal Viruses

F.S.B. Kibenge , in Aquaculture Virology, 2016

3.3.1.2 Virus Characteristics

ShrimpCDV is a novel virus with similarities to members of the family Circoviridae (genera Circovirus and Cyclovirus) that possess circular ssDNA (Ng et al., 2013). The ShrimpCDV genome is 1956 nucleotides long (GenBank accession no. KC441518), of ambisense organization, and it encodes two genes, putative Rep and Cap proteins. A putative DNA hairpin structure containing a sequence (AAG TAT TAC) similar to the conserved nonanucleotide motif of Circoviridae (TAG TAT TAC) exists in the short intergenic region (Ng et al., 2013 ). The canonical nonanucleotide motif (NAN TAT TAC) is at the apex of the potential stem-loop structure of Rep protein–encoding ssDNA viruses ( Rosario et al., 2012). However, the ShrimpCDV Rep protein was only 21–34% identical to the cognate protein of Circoviridae and other unclassified ssDNA viruses, and in phylogenetic analysis, it was clustered separately from the genera Circovirus and Cyclovirus (Ng et al., 2013). Thus, the Rep protein, a conserved feature of many ssDNA viruses, does not provide adequate taxonomic resolution for classification (Rosario et al., 2012). Moreover, according to the classification scheme for ssDNA viruses based on genomic features that have been detected through metagenomic studies (Rosario et al., 2012), ShrimpCDV is a Type IV genome (Ng et al., 2013) in contrast to Circoviridae members of genera Circovirus and Cyclovirus, which are Type I and Type II genomes, respectively (Rosario et al., 2012). The Type IV genome is one of five novel genome architectures not previously classified by the International Committee for Taxonomy of Viruses (ICTV) (King et al., 2012). The Type IV genome displays ambisense organization, but the intergenic region containing a potential stem-loop structure is found at the 3′ end of the major ORFs. Type I and Type II genomes also have ambisense organization, but the intergenic region containing the potential stem-loop structure is found at the 5′ end of the major ORFs. In Type II genome, the conserved nonanucleotide sequence is not found on the Rep-encoding strand (Rosario et al., 2012).

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Satellite RNAs

Chikara Masuta , Hanako Shimura , in Viroids and Satellites, 2017

Introduction

"Satellites" comprise satellite viruses and satellite nucleic acids, and the satellite nucleic acids are further divided into satellite DNAs and satellite RNAs (satRNAs) (Briddon et al., 2012 ). In plants, circular single-stranded (ss) DNA satellites (satDNA) are often associated with ssDNA viruses, geminiviruses ( Nawaz-ul-Rehman and Fauquet, 2009). Plant satRNAs are apparently molecular parasites depending for their replication and encapsidation on their helper viruses (Hu et al., 2009; Roossinck et al., 1992; Simon et al., 2004). SatRNAs often attenuate the viral symptoms but some cause more severe symptoms. Here we overview the molecular mechanisms for the symptom attenuation/exacerbation induced by several satellite nucleic acids, paying special attention to the role played by the host RNA silencing.

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Environmental Virology and Virus Ecology

Alberto Rastrojo , Antonio Alcamí , in Advances in Virus Research, 2018

3.1 DNA Viruses in Antarctic Lakes

The first metagenomics study of DNA viruses in Antarctica was carried out in Limnopolar Lake (Byers Peninsula, Livingston Island) (Fig. 1E). Byers Peninsula is an Antarctic Specially Protected Area of scientific interest because it is the largest ice-free area in the South Shetland Islands. The Peninsula expanded for approximately 8000   years BP as the Rotch Dome glacier retreated, leaving a unique area with numerous freshwater lakes that display some of the greatest microbial biodiversity in Antarctica (Oliva et al., 2016; Toro et al., 2007). Initial analysis by electron microscopy showed a large diversity of viral capsids in Limnopolar Lake (Lopez-Bueno et al., 2009) (Fig. 2). DNA sequencing of viral genomes with 454-Roche technology revealed a large percentage (81%–94%) of new viruses unrelated to viruses previously described in other aquatic environments (Lopez-Bueno et al., 2009 ). Phages infecting bacteria were identified, but small viruses with circular ssDNA viruses, related to circoviruses, geminiviruses, or satellites, were abundant in the samples. The abundance of circular ssDNA viruses may be overrepresented due to the preferential amplification of circular genomes when using multiple displacement amplification. However, circular ssDNA viruses are evidently abundant in these ecosystems even if a 100-fold overamplification is considered to have been introduced by this methodology and after the data were corrected for genome length. These viruses have unique genomic organizations compared to other ssDNA viruses previously described, with open reading frames transcribed unidirectionally, and are separated phylogenetically, suggesting that they may represent new viruses adapted to extreme polar environments ( Lopez-Bueno et al., 2009).

Fig. 2

Fig. 2. Electron microscopy of viruses present in Limnopolar Lake (Byers Peninsula, Livingston Island, Antarctica). Upper panel: bacteriophages such as siphoviruses (s), podoviruses (p), and myoviruses (m). Lower panels: virus particles with spikes, and lemon shape and small size virions.

 Reproduced with permission from Lopez-Bueno, A., Tamames, J., Velazquez, D., Moya, A., Quesada, A., Alcami, A., 2009. High diversity of the viral community from an Antarctic lake. Science 326, 858–861.

Extreme ecosystems were expected to harbor low biodiversity and they could facilitate the study of the role of viruses in simple ecosystems with reduced number of species (Convey and Stevens, 2007; Convey et al., 2008). By contrast, the first viral metagenomics study in Antarctica uncovered a viral community with unexpectedly high diversity (Lopez-Bueno et al., 2009). Computer analysis estimated the presence of nearly 10,000 viral species as compared to less than 800 viral species estimated in North American lakes. This study also showed a change in the composition of the viral community between the spring, when the lake is covered with a thick ice layer, and the summer, when algae-infecting phycodnaviruses increase as a result of ice melt. An increase in light provides the necessary energy for primary production and generates organic matter that promotes algal survival during the winter (Cavicchioli, 2015; Wilkins et al., 2013). Seasonal environmental changes select for microbial populations that use different survival strategies (i.e., autotrophs vs heterotrophs). Thus, over the annual cycle, the growth of different hosts determines seasonal changes in the viral community present in the lake. Mathematical models of the influence of light cycles in polar regions on virus–host interactions have identified potential devastating effects of viruses on bacterial populations (Lauro et al., 2011). On the other hand, mathematical models predict that the interaction of virophages—viruses that parasitize other viruses—and phycodnaviruses may benefit ecosystems. A virophage that preys on phycodnaviruses that infect prasinophytes (flagellated algae) may reduce the virulence of phycodnaviruses and the overall mortality of algal hosts. This will increase the frequency of algal blooms during polar summer light periods and stimulate secondary production (Yau et al., 2011).

The initial viral metagenomics studies in Limnopolar Lake were expanded with a comparative study of the viral community in eight lakes along the Antarctic Peninsula (Fig. 1E) (Aguirre de Carcer et al., 2016). This study confirmed the presence of a high diversity of viruses in Antarctic aquatic ecosystems unrelated to known viruses, and an abundance of circular ssDNA viruses. Viral diversity did not correlate with the geographical location of the lakes, indicating that the latitudinal gradient of biodiversity described for macroorganisms and in viral metagenomics studies in oceans is not observed in these Antarctic viral communities (Angly et al., 2006).

Small circular ssDNA viruses have also been identified in a freshwater pond on the McMurdo Ice Shelf (Fig. 1E), and their low sequence similarity to ssDNA viruses sequenced in Limnopolar Lake suggests high diversity of these viruses in Antarctica (Zawar-Reza et al., 2014). Other studies on Antarctic viruses have been carried out in a pristine, meromictic (permanently stratified) lake, Ace Lake, located in the Vestfold Hills of East Antarctica (Fig. 1E) (Lauro et al., 2011; Wilkins et al., 2013). Ace Lake was formed at the end of the Quaternary, ∼   12,000 years ago, and was initially fresh. Seawater invaded the lake basin during an early Holocene sea level highstand (∼   7000 years), and the lake was reformed after subsequent sea-level fall after ∼   5000 years. This lake system is of special interest because the capture of marine-derived biota allows the study of the short-term evolution of species and ecosystem function. Metagenomics and metaproteomics studies have provided genetic and functional information about the microbial communities in Ace Lake (Lauro et al., 2011). The upper, oxygen-rich layer is dominated by phycodnaviruses, whereas the bottom anoxic layer is dominated by bacteriophages (siphovirus, myovirus, podovirus).

Studies in Ace Lake and the nearby Organic Lake identified the presence of virophages, associated with phycodnaviruses that may play an important role in aquatic ecosystems (Lauro et al., 2011; Yau et al., 2011). Virophages use the replicative cytoplasmic virion factory of giant viruses for their own replication (Fischer and Suttle, 2011). Metaproteomics in samples from Deep Lake, also located in the Vestfold Hills (Fig. 1E), showed the presence of several archeal viruses, consistent with a dominance of haloarchaea in this hypersaline lake, and mapped repetitions and spacers of the CRISPR defense system in haloarchaea conferring host immunity against viruses (Tschitschko et al., 2015). This study also showed that viruses may contribute to the generation of host surface protein variants, by mutating and shuffling the host genes. The virus supplying the variant host gene may benefit from reduced competition by more destructive and virulent viruses that do not efficiently infect through these surface protein variants.

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Geminiviridae

In Virus Taxonomy, 2012

Genome organization and replication

Viruses in the genera Mastrevirus, Curtovirus and Topocuvirus have a single genomic component, whereas those in the genus Begomovirus have either one or two components. Replication occurs through double stranded replicative intermediates by a rolling circle mechanism. Complementary-sense DNA synthesis on the virion-sense (encapsidated) strand to produce dsDNA depends solely on host factors. Virus ssDNA synthesis is initiated by cleavage of the virion-sense strand by the virus-encoded replication-associated protein (Rep) immediately downstream of the 3′ thymidine residue in an absolutely conserved TAATATT/AC sequence located in the loop of a potential stem-loop structure within the intergenic region. Geminiviruses do not encode a DNA polymerase, and consequently are heavily dependent on host factors that must be recruited during early stages of replication. In all cases, coding regions in both virion-sense and complementary-sense strands diverge from an intergenic region, and transcription is bi-directional, with independently controlled transcripts initiating within the intergenic region. Viruses in the genus Mastrevirus use transcript splicing for gene expression, those in other genera use multiple overlapping transcripts.

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