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Other Double-Stranded DNA Viruses
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
As reviewed by Claverie and Abergel (2018), the Mimiviridae family exhibited the broadest distribution of genome sizes, from 370 kb for Aureococcus anophagefferens virus (AaV) to 1.51 Mb for Tupanvirus deep Ocean (TupanDO, or TPV-DO), as well as of particle sizes (from 750–140 nm for icosahedral virions, up to 2.3 µm for the tailed tupanviruses). About tupanviruses and the proposed genus Tupanvirus see Rodrigues et al. (2019). Despite these huge differences, all members of the family demonstrated similar architecture of particles, including an internal lipid membrane. Figure 5.6. demonstrates a portrait of Acanthamoeba polyphaga mimivirus (APMV), a reference strain of the Mimivirus genus. However, the technical barriers have prevented high-resolution reconstructions of APMV (Xiao et al. 2009).
Clinical and Laboratory Diagnosis of Human Respiratory Viral Infections
Published in Sunit K. Singh, Human Respiratory Viral Infections, 2014
Cristina Costa, Francesca Sidoti, Rossana Cavallo
Different molecular assays employing a variety of amplification targets have been described for the detection of hMPV, bocavirus, parvovirus types 4 and 5, and mimivirus. In particular, parvovirus types 4 and 5 genomes have been detected by conventional or nested PCR targeting the nonstructural (NS-1) gene. At present, no commercial tests are available for parvovirus types 4 and 5 or mimivirus.66–69
Consequences and repair of radiation-induced DNA damage: fifty years of fun questions and answers
Published in International Journal of Radiation Biology, 2022
Unlike cellular organisms, DNA repair proteins are not very well-conserved in viruses, presumably due to their small genomes. However, the Mimivirus (short for mimicking microbe), a double stranded DNA virus that infects Acanthamoeba polyphaga, has a genome size of 1.2 megabases with six genes that code for DNA repair enzymes. Vishy Bandaru, a post-doc in my lab, cloned, expressed and purified two of these, MvNei1 and MvNei2, homologs of the human NEIL proteins (Bandaru et al. 2007). Both recognize oxidized pyrimidines in duplex DNA and in bubble structures and MvNei2 also removes lesions from single stranded DNA. The lyase activity of MvNei1 cleaves the DNA by ß,δ-elimination while MvNei2 lyase cleaves the DNA by ß-elimination. Like NEIL1, MvNei1 contains an anti-parallel ß-hairpin ‘zincless finger’ motif while MvNei2 contains a zinc finger motif like human NEIL2. Also, MvNei2 resembles human NEIL3 at the N-terminus and NEIL2 at the C-terminus.
Mass spectrometric analysis of glycosylated viral proteins
Published in Expert Review of Proteomics, 2018
O-linked glycans generally have much simpler structures but lack the single biosynthetic pathways found with the N-glycans. They are usually classified according to their core structures with for example core 1 consisting of Galβ-1→3-GlcNAc-Ser/Thr and core 2 being Galβ-1→3-(β1→6-GlcNAc)GlcNAc-Ser/Thr. Their significance appears to be less than that of the N-linked glycans for functions such as cell–cell adhesion. As with the N-glycans, the giant viruses can synthesize other types of O-glycan; for example, the large mimivirus, Acanthamoeba polyphaga, synthesizes O-glycans previously thought to be exclusive to cellular life [12].
The gut virome in Irritable Bowel Syndrome differs from that of controls
Published in Gut Microbes, 2021
S. Coughlan, A. Das, E. O’Herlihy, F. Shanahan, P.W. O’Toole, I.B. Jeffery
Of classified clusters, the most abundant families were those of the tailed bacteriophage viruses Siphoviridae (27.7%), Myoviridae (13%), and Podoviridae (8.9%) respectively, which are all in the Caudovirales order, in agreement with previous studies of the gut virome in healthy and disease cohorts (Table S3).17–21,24,26,27 The 4th most abundant family (6%) was the Mimiviridae family, whose members infect amoebae and protists, and whose member Mimivirus has been previously noted as a potentially dubious taxonomic classification in a study of the gut virome in ulcerative colitis.24,28 This led us to examine the confidence of the taxonomic classifications in more detail. Examination of the percentage identity and percentage coverage for each protein sequence aligned to the hit protein used for taxonomic assignment (percentage query cover) revealed a wide distribution of both scores for each family indicating that many of the classifications (Figure 1 and Figure S4) were based on low scores. While families in the Caudovirales order had high-scoring hits present, scores for most other families, including Mimiviridae were low indicating that the family-level classification was not reliable. Except for Mimiviridae, all other families with low scoring hits had very low abundances (<0.2% of total abundance at VC level and <0.6% at contig level; Tables S3 & S4, Figure 1). Ascoviridae, Iridoviridae, Marseilleviridae, Pithoviridae, and Poxviridae, all families of nucleocytoplasmic large dsDNA viruses (NCLDVs; proposed order Megavirales29) of eukaryotes had mainly low scoring hits (Figure 1) and were present in very low abundances (Figure 1; Table S1). Furthermore, Pithoviridae viruses have a diameter of 500 nm, which is larger than the 450 nm filter used to remove non-viral material in this study (Methods), and so would not be expected in our sequence data.30 Some Mimivirdae genomes are less than 450 nm and so could legitimately be present in our data. However, taxonomic assignments to families without the presence of high scoring hits or with low abundance are likely not as reliable as those for Caudovirales.