A removable and cosmopolitan dsRNA Toti-like virus causes latent infection in a model diatom strain

Abstract

AbstractDiatoms contribute to 20% of global primary productivity. Although some diatom viruses have been identified, the molecular mechanisms underlying their interactions with the host remain poorly understood. In this study, we report the discovery of an RNA molecule in the DNA extracts of thePhaeodactylum tricornutumstrain Pt1, which possesses a well-annotated genome and has been used as a diatom model system since 1956. We confirmed this molecule to be a double-stranded linear RNA molecule and, through sequencing, demonstrated it to be a virus in theTotiviridaefamily that is prevalent among marine stramenopiles. We also detected this virus inPhaeodactylum tricornutumstrain Pt3, which was collected in 1930s from a similar geographic location to Pt1, suggesting its prevalence within the region. By employing various inhibitors of the viral RNA-dependent RNA polymerase, we successfully generated a virus-free line isogenic to Pt1, establishing a model system to investigate the impact of RNA viruses on diatom physiology. The virus-free lines did not display obvious growth advantages or defects, indicating a tendency of the virus towards latent infection. Furthermore, we generated a robust antibody against the coat protein of this virus. By performing immunoprecipitation coupled with mass spectrometry, we found that translation-related proteins are enriched as potential interacting partners of the coat protein. Our results suggest that potential viral impacts in molecular research should be considered when Pt1 and Pt3 are used for studying translation-related processes. Additionally, our study unveiled a temperate mode of interaction between viruses and marine algal hosts that differs from the commonly-reported virulent, lytic infections.Highlightsprevalent dsRNA virus belonging to theTotiviridaefamily was discovered in the Pt1 and Pt3 strains of the model diatomPhaeodactylum tricornutum.virus is absent in eight other strains ofP. tricornutum, highlighting the importance of studying multiple accessions.virus can be eliminated using a nucleotide analogue, resulting in a virus-free isogenic strain that allows us to investigate how viruses may affect diatom physiology.robust antibody against the coat protein of this virus was developed to assist mechanistic studies of diatom-virus interactions.