Algal Viruses with Distinct Intraspecies Host Specificities Include Identical Intein Elements

Abstract

Heterosigma akashiwo virus (HaV) is a large double-stranded DNA virus infecting the single-cell bloomforming raphidophyte (golden brown alga) H. akashiwo. A molecular phylogenetic sequence analysis of HaV DNA polymerase showed that it forms a sister group with Phycodnaviridae algal viruses. All 10 examined HaV strains, which had distinct intraspecies host specificities, included an intein (protein intron) in their DNA polymerase genes. The 232-amino-acid inteins differed from each other by no more than a single nucleotide change. All inteins were present at the same conserved position, coding for an active-site motif, which also includes inteins in mimivirus (a very large double-stranded DNA virus of amoebae) and in several archaeal DNA polymerase genes. The HaV intein is closely related to the mimivirus intein, and both are apparently monophyletic to the archaeal inteins. These observations suggest the occurrence of horizontal transfers of inteins between viruses of different families and between archaea and viruses and reveal that viruses might be reservoirs and intermediates in horizontal transmissions of inteins. The homing endonuclease domain of the HaV intein alleles is mostly deleted. The mechanism keeping their sequences basically identical in HaV strains specific for different hosts is yet unknown. One possibility is that rapid and local changes in the HaV genome change its host specificity. This is the first report of inteins found in viruses infecting eukaryotic algae.

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

“…The detection of inteins from all of our samples in this study, the presence of a variety of putative inteins from every station from the Global Ocean Survey data set (Yooseph et al, 2007) and the presence of DNA polymerase I motif C inteins in the phycodnavirus isolates HaV (Nagasaki et al, 2005) and CeV (Monier et al, 2008) all suggest that inteins are common among marine viruses. This raises the question of how DNA polymerase I motif C inteins are acquired by phycodnaviruses.…”

“…However, we found that prasinovirus-like phylotypes (and KBvp-8 in particular) dominated both the winter 2006 sample, which was prefiltered, and the summer samples, which were not. Some PCR bias does seem likely, as it has been reported that the AVS primers do not amplify the DNA polymerase gene of several representative members of genera within the family (Sandaa et al, 2001;Nagasaki et al, 2005). Different approaches, such as quantitative PCR assays targeting specific viral groups, will be needed to determine the actual in situ abundance of prasino-like viruses relative to other genera within the family Phycodnaviridae.…”

“…Inteins appear to be most common in Archaea, but have been identified in all three domains of life and in viruses (Perler, 2002). Among the phycodnaviruses, inteins have been identified in the DNA polymerase I of H. akashiwo virus (HaV; Nagasaki et al, 2005) and Chrysochromulina ercina virus (CeV; Larsen et al, 2008) and in the helicase and ribonucleotide reductase of the PBCV (NY-2A; Fitzgerald et al, 2007). Little is known about the prevalence or diversity of inteins among the large number of marine phycodnaviruses that have not been cultivated.…”

Co-occurrence of DNA- and RNA-viruses infecting the bloom-forming dinoflagellate, Heterocapsa circularisquama, on the Japan coast

“…The genome size of HcV was estimated using pulsed-field gel electrophoresis (PFGE); and partial genome sequencing of HcRNAV and HcV were conducted according to the methods described by Nagasaki et al (2005a) and Nagasaki et al (2005b), respectively.…”

Genetic Optimization of Artificial Neural Networks to Forecast Virioplankton Abundance from Cytometric Data

“…It has also been proposed on several occasions that sediments can constitute a potentially important reservoir of infectious bacteriophages [67], cyanophages [68] or algal viruses [69]. However, no processes involving the recruitment of viruses into or their release from sediments had so far been clearly demonstrated.…”