The Characterization of a Novel Virus Discovered in the Yeast Pichia membranifaciens

Abstract

Mycoviruses are widely distributed across fungi, including the yeasts of the Saccharomycotina subphylum. This manuscript reports the first double-stranded RNA (dsRNA) virus isolated from Pichia membranifaciens. This novel virus has been named Pichia membranifaciens virus L-A (PmV-L-A) and is a member of the Totiviridae. PmV-L-A is 4579 bp in length, with RNA secondary structures similar to the packaging, replication, and frameshift signals of totiviruses that infect Saccharomycotina yeasts. PmV-L-A was found to be part of a monophyletic group within the I-A totiviruses, implying a shared ancestry between mycoviruses isolated from the Pichiaceae and Saccharomycetaceae yeasts. Energy-minimized AlphaFold2 molecular models of the PmV-L-A Gag protein revealed structural conservation with the Gag protein of Saccharomyces cerevisiae virus L-A (ScV-L-A). The predicted tertiary structure of the PmV-L-A Pol and other homologs provided a possible mechanism for totivirus RNA replication due to structural similarities with the RNA-dependent RNA polymerases of mammalian dsRNA viruses. Insights into the structure, function, and evolution of totiviruses gained from yeasts are essential because of their emerging role in animal disease and their parallels with mammalian viruses.

Identification and Genome Characterization of a Novel Virus within the Genus Totivirus from Chinese Bayberry (Myrica rubra)

“…As discussed in a paper published in the year 2023, the presence of highly diverse microbial communities comprising fungi, bacteria, archaea, and protists colonizing plants and forming symbiotic relationships emphasizes the need for careful examination of the origin of viruses detected in viromic studies [ 22 ]. The genus Totivirus contains viruses that initially infect fungi or protozoa [ 5 , 6 , 7 ]. For a long time, viruses within the genus Totivirus were believed to only infect fungi or protozoa.…”

“…The genus Totivirus comprises viruses with a non-segmented, double-stranded RNA (dsRNA) genome, generally containing two open reading frames (ORFs) responsible for encoding the putative capsid protein (CP) and the RNA-dependent RNA polymerase (RdRP) [ 4 , 5 ]. The genus Totivirus contains viruses that initially infect fungi or protozoa [ 6 , 7 ]. However, more and more totiviruses or totivirus-like viruses have been found in a series of other eukaryotic hosts, including, but not limited to: mosquitoes [ 8 ], ants [ 9 ], fish [ 10 ], crabs [ 11 ], and plants [ 5 , 12 ].…”

Infection of Nigrospora nonsegmented RNA Virus 1 Has Important Biological Impacts on a Fungal Host

“…NoNRV1 could not use the stop/restart mechanism since it lacks a typical stop/restart motif such as AUGA or UAAUG (underlined: ORF1 stop codon; italicized: ORF2 start codon) at the ORF1/ORF2 junction that has been illustrated well in the Helminthosporium victoriae virus 190S [75,76]. It has been reported that Totiviruses have a well characterized slippery sequence for ribosomal-1 frameshifting that causes a fusion event between gag and pol proteins [66,67,74]. Interestingly, NoNRV1 has a similar slippery sequence (CCC_UUU_C) to other unassigned mycoviruses (PlNV-1, UvNV-1, UvNV-2), just 5 nt ahead of the ORF1 stop codon (Figure 2C).…”

“…The 3 UTR sequence was folded into two hairpins with perfect base paring in their stems (Figure 2D). Such hairpin structures are common in the UTRs of other dsRNA mycoviruses [32,[43][44][45]66,67] and are presumed to play an important role in viral replication and assembly [32,46,47]. The IGR sequence between ORF1 and ORF2 is 58 nt long and forms two hairpins that are separated by a 9 nt stretch (Figure 2D).…”

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

“…Single-stranded RNA viruses of S. cerevisiae (from the family Narnaviridae) were discovered by the detection of dsRNA replication intermediates [13]. Contemporary RNA sequencing techniques have enabled the discovery of many more mycoviruses, either from individual strains of fungi or from environmental samples, including novel viruses from the Totiviridae and Narnaviridae virus families in yeasts of the Saccharomycotina subphylum [14][15][16][17][18]. Due to its short generation time, ease of genetic manipulation, and the large array of genetic tools and other resources, S. cerevisiae is an ideal model organism for studying viruses and other parasitic genetic elements.…”