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1. Repression of turnip crinkle virus replication by its replication protein p88

   https://doi.org/10.1016/j.virol.2018.10.024  

   Zhang, Shaoyan ; Sun, Rong ; Guo, Qin ; Zhang, Xiao-Feng ; Qu, Feng ( January 2019 , Virology)
2. Repression of turnip crinkle virus replication by its replication protein p88

   https://doi.org/doi.org/10.1016/j.virol.2018.10.024  

   Zhang, S. ; Sun, R. ; Guo, Q. ; Zhang, X.-F. ; Qu, F. ( January 2019 , Virology)

   We recently reported that p28, one of the two turnip crinkle virus (TCV) replication proteins, trans-complemented a defective TCV lacking p28, yet repressed the replication of another TCV replicon encoding wildtype p28 (Zhang et al., 2017). Here we show that p88, the TCV-encoded RNA-dependent RNA polymerase, likewise trans-complemented a p88-defective TCV replicon, but repressed one encoding wild-type p88. Surprisingly, lowering p88 protein levels enhanced trans-complementation, but weakened repression. Repression by p88 was not simply due to protein over-expression, as deletion mutants missing 127 or 224 N-terminal amino acids accumulated to higher levels but were poor repressors. Finally, both trans-complementation and repression by p88 were accompanied by preferential accumulation of subgenomic RNA2, and a novel class of small TCV RNAs. Our results suggest that repression of TCV replication by p88 may manifest a viral mechanism that regulates the ratio of genomic and subgenomic RNAs based on p88 abundance. 

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3. Repression of turnip crinkle virus replication by its replication protein p88

   Zhang, S ; Sun, R ; Guo, Q ; Zhang, X-F ; Qu, F ( January 2019 , Virology)

   We recently reported that p28, one of the two turnip crinkle virus (TCV) replication proteins, trans-complemented a defective TCV lacking p28, yet repressed the replication of another TCV replicon encoding wildtype p28 (Zhang et al., 2017). Here we show that p88, the TCV-encoded RNA-dependent RNA polymerase, likewise trans-complemented a p88-defective TCV replicon, but repressed one encoding wild-type p88. Surprisingly, lowering p88 protein levels enhanced trans-complementation, but weakened repression. Repression by p88 was not simply due to protein over-expression, as deletion mutants missing 127 or 224 N-terminal amino acids accumulated to higher levels but were poor repressors. Finally, both trans-complementation and repression by p88 were accompanied by preferential accumulation of subgenomic RNA2, and a novel class of small TCV RNAs. Our results suggest that repression of TCV replication by p88 may manifest a viral mechanism that regulates the ratio of genomic and subgenomic RNAs based on p88 abundance. 

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4. Single-cell mutation rate of turnip crinkle virus (-)-strand replication intermediates

   https://doi.org/10.1371/journal.ppat.1011395  

   Carvalho, Camila Perdoncini ; Han, Junping ; Khemsom, Khwannarin ; Ren, Ruifan ; Camargo, Luis Eduardo ; Miyashita, Shuhei ; Qu, Feng ( August 2023 , PLOS Pathogens)

   Pagán, Israel (Ed.)

   Viruses with single-stranded, positive-sense (+) RNA genomes incur high numbers of errors during replication, thereby creating diversified genome populations from which new, better adapted viral variants can emerge. However, a definitive error rate is known for a relatively few (+) RNA plant viruses, due to challenges to account for perturbations caused by natural selection and/or experimental set-ups. To address these challenges, we developed a new approach that exclusively profiled errors in the (-)-strand replication intermediates of turnip crinkle virus (TCV), in singly infected cells. A series of controls and safeguards were devised to ensure errors inherent to the experimental process were accounted for. This approach permitted the estimation of a TCV error rate of 8.47 X 10⁻⁵substitution per nucleotide site per cell infection. Importantly, the characteristic error distribution pattern among the 50 copies of 2,363-base-pair cDNA fragments predicted that nearly all TCV (-) strands were products of one replication cycle per cell. Furthermore, some of the errors probably elevated error frequencies by lowering the fidelity of TCV RNA-dependent RNA polymerase, and/or permitting occasional re-replication of progeny genomes. In summary, by profiling errors in TCV (-)-strand intermediates incurred during replication in single cells, this study provided strong support for a stamping machine mode of replication employed by a (+) RNA virus.

    

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5. Host Lipids in Positive-Strand RNA Virus Genome Replication

   https://doi.org/10.3389/fmicb.2019.00286  

   Zhang, Zhenlu ; He, Guijuan ; Filipowicz, Natalie A. ; Randall, Glenn ; Belov, George A. ; Kopek, Benjamin G. ; Wang, Xiaofeng ( February 2019 , Frontiers in Microbiology)