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. 2021 Dec 16;22(24):13492.
doi: 10.3390/ijms222413492.

Genome Features of a New Double-Stranded RNA Helper Virus (LBCbarr) from Wine Torulaspora delbrueckii Killer Strains

Manuel Ramírez  1 , Rocío Velázquez  1 , Antonio López-Piñeiro  2 , Alberto Martínez  1
Affiliations

Genome Features of a New Double-Stranded RNA Helper Virus (LBCbarr) from Wine Torulaspora delbrueckii Killer Strains

Manuel Ramírez et al. Int J Mol Sci. .

Abstract

The killer phenotype of Torulaspora delbrueckii (Td) and Saccharomyces cerevisiae (Sc) is encoded in the genome of medium-size dsRNA viruses (V-M). Killer strains also contain a helper large size (4.6 kb) dsRNA virus (V-LA) which is required for maintenance and replication of V-M. Another large-size (4.6 kb) dsRNA virus (V-LBC), without known helper activity to date, may join V-LA and V-M in the same yeast. T. delbrueckii Kbarr1 killer strain contains the killer virus Mbarr1 in addition to two L viruses, TdV-LAbarr1 and TdV-LBCbarr1. In contrast, the T. delbrueckii Kbarr2 killer strain contains two M killer viruses (Mbarr1 and M1) and a LBC virus (TdV-LBCbarr2), which has helper capability to maintain both M viruses. The genomes of TdV-LBCbarr1 and TdV-LBCbarr2 were characterized by high-throughput sequencing (HTS). Both RNA genomes share sequence identity and similar organization with their ScV-LBC counterparts. They contain all conserved motifs required for translation, packaging, and replication of viral RNA. Their Gag-Pol amino-acid sequences also contain the features required for cap-snatching and RNA polymerase activity. However, some of these motifs and features are similar to those of LA viruses, which may explain that at least TdV-LBCbarr2 has a helper ability to maintain M killer viruses. Newly sequenced ScV-LBC genomes contained the same motifs and features previously found in LBC viruses, with the same genome location and secondary structure. Sequence comparison showed that LBC viruses belong to two clusters related to each species of yeast. No evidence for associated co-evolution of specific LBC with specific M virus was found. The presence of the same M1 virus in S. cerevisiae and T. delbrueckii raises the possibility of cross-species transmission of M viruses.

Keywords: LBC helper virus; Torulaspora delbrueckii; dsRNA genome; high-throughput sequencing; killer Kbarr.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Partial multiple sequence alignment between ScV-LBC1-original, ScV-LBClus4, and TdV-LBCbarr2 (+) strand nucleotide sequences (cDNA). The full sequence alignment is presented in Supplemental Material (Figure S1). 5′GAA(A/T)TT conserved motif (5′ conserved), translation initiation (start of Gag and Gag-Pol), termination (stop of Gag or Gag-Pol) codons, ribosome frameshifting site (−1 frameshift site), frameshifting associated sequence (stem-loop for frameshift), packaging signal (stem-loop for packaging), and replication signal (stem-loop for replication) are indicated, shaded and/or underlined in the nucleotide sequence. Different residue in LBCbarr2 with respect to LBCbarr1 virus is yellow shaded. formula image, ribosomal frameshift. Asterisks (*) indicate identical nucleotide positions. The secondary structures of the putative cis signals for frameshifting, packaging, and replication of TdV-LBCbarr2 are displayed at the right of the sequence panel.
Figure 2
Figure 2
Secondary structure representations of signals for frameshifting, encapsidation, and replication present in the (+)RNA strand of L and M viruses from killer yeasts: (A) S. cerevisiae K1 (original), (B) T. delbrueckii Kbarr1 (EX1180), and (C) T. delbrueckii Kbarr2 (EX1257). FR, frameshifting region. ES, encapsidation signal. RS, replication signal. formula image, ribosomal frameshift. Black arrow indicates the single nucleotide changes between ES of LBCbarr1 and LBCbarr2. Green dot-line arrow indicates equivalent ES for L and M viruses in the same yeast. Orange dot-line arrow indicates possible equivalent ES for LBCbarr1 and Mbarr1 in Kbarr1 EX1180 yeast. Red dot-line arrow indicates unknown equivalent ES in M viruses for the ES of ScV-LBC1-original.
Figure 3
Figure 3
Comparison between partial amino-acid sequences of Gag-Pol encoded by ScV-LBC1-original, ScV-LBClus4, and TdV-LBCbarr2 genomes. The full sequence alignment is presented in Supplemental Material (Figure S2). The separation between Gag and Pol is indicated (Gag◄►Pol). The H156 residue required for 5′cap-snatching is black shaded. The four crucial residues for cap recognition (Tyr-152, Asn-154, Tyr-452 and Trp-545) are grey shaded. The highly conserved central third of Pol (RdRp domain) is underlined, the five consensus motifs (3, A, B, C, and D) conserved in RNA-dependent RNA polymerases from Totiviruses are indicated above the sequence, and the conserved amino acids for each motif are grey shaded. Different residue in TdV-LBCbarr with respect to ScV-LBC is yellow shaded. Asterisks (*) indicate identical amino acids; colons (:) and single dots (.) indicate conserved and semi-conserved amino acids, respectively.
Figure 4
Figure 4
Conserved motifs in the Gag-Pol RdRp domain of L viruses from S. cerevisiae and T. delbrueclii. The extent of each domain is indicated in the top of the figure. The last amino acid of the stretch containing each motif is indicated to the right of the sequence. Asterisks (*) indicate identical amino acids; colons (:) and single dots (.) indicate conserved and semi-conserved amino acids, respectively. Conserved identical residues in all virus motifs are grey shaded. Different residues in LBC with respect to LA viruses are yellow shaded. Different residues for TdV-LBCbarr and ScV-LBC1-original are pink shaded. “Y” residue in motif A of TdV-LBCbarr that is coincident with LA viruses is indicated inside a square.
Figure 5
Figure 5
Phylogenetic relationship of yeast LBC viruses. (A) Percentage identity matrix between the complete amino acid sequences of the Gag-Pol proteins of LBC viruses. Each identity value was rounded to the nearest whole number. (B) Phylogram with evolutionary distances (given by the MUSCLE program) and geographical location at which each killer yeast strain was isolated. RG, Ribera del Guadiana region in Extremadura. ESP, Spain. Viruses included in each of the two main clusters, as well as their identity values, are shaded in red or green. The Tuber aestivum (Tav-1) totivirus was used as outgroup (GenBank accession number HQ158596.1).
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References

    1. Schmitt M.J., Breinig F. Yeast viral killer toxins: Lethality and self-protection. Nat. Rev. Microbiol. 2006;4:212–221. doi: 10.1038/nrmicro1347. - DOI - PubMed
    1. Wickner R.B., Fujimura T., Esteban R. Viruses and prions of Saccharomyces cerevisiae. Adv. Virus Res. 2013;86:1–36. doi: 10.1016/B978-0-12-394315-6.00001-5. - DOI - PMC - PubMed
    1. Ramírez M., Velázquez R., López-Pineiro A., Naranjo B., Roig F., Llorens C. New Insights into the genome organization of yeast killer viruses based on “atypical” killer strains characterized by high-throughput sequencing. Toxins. 2017;9:292. doi: 10.3390/toxins9090292. - DOI - PMC - PubMed
    1. Rodríguez-Cousiño N., Esteban R. Relationships and evolution of double-stranded RNA Totiviruses of yeasts inferred from analysis of L-A-2 and L-BC variants in wine yeast strain populations. Appl. Environ. Microbiol. 2017;83:e02991-16. doi: 10.1128/AEM.02991-16. - DOI - PMC - PubMed
    1. Rodríguez-Cousiño N., Maqueda M., Ambrona J., Zamora E., Esteban E., Ramírez M. A new wine Saccharomyces cerevisiae double-stranded RNA virus encoded killer toxin (Klus) with broad antifungal activity is evolutionarily related to a chromosomal host gene. Appl. Environ. Microbiol. 2011;77:1822–1832. doi: 10.1128/AEM.02501-10. - DOI - PMC - PubMed

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