Quantitative Analysis of RNA Polymerase Slippages for Production of P3N-PIPO Trans-frame Fusion Proteins in Potyvirids

Choi, Dongjin; Hahn, Yoonsoo

doi:10.1007/s12275-023-00083-z

Cited by 3 publications

(1 citation statement)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to a conserved open reading frame (ORF), the genus Potyvirus has another ORF that produce a protein known as P3N/PIPO (the N-terminal half of P3 fused to the Pretty Interesting Potyvirus open reading frame). P3N-PIPO production requires an adenine insertion caused by RNA-dependent RNA-polymerase slippage at a conserved GAAAAAA sequence [69] (Figure 4).…”

Section: Proteolytic Activity Of Hc-promentioning

confidence: 99%

Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins

Hýsková,

Bělonožníková,

Chmelík

et al. 2024

Plants

View full text Add to dashboard Cite

The best-characterized functional motifs of the potyviral Helper-Component protease (HC-Pro) responding for aphid transmission, RNA silencing suppression, movement, symptom development, and replication are gathered in this review. The potential cellular protein targets of plant virus proteases remain largely unknown despite their multifunctionality. The HC-Pro catalytic domain, as a cysteine protease, autoproteolytically cleaves the potyviral polyproteins in the sequence motif YXVG/G and is not expected to act on host targets; however, 146 plant proteins in the Viridiplantae clade containing this motif were searched in the UniProtKB database and are discussed. On the other hand, more than 20 interactions within the entire HC-Pro structure are known. Most of these interactions with host targets (such as the 20S proteasome, methyltransferase, transcription factor eIF4E, and microtubule-associated protein HIP2) modulate the cellular environments for the benefit of virus accumulation or contribute to symptom severity (interactions with MinD, Rubisco, ferredoxin) or participate in the suppression of RNA silencing (host protein VARICOSE, calmodulin-like protein). On the contrary, the interaction of HC-Pro with triacylglycerol lipase, calreticulin, and violaxanthin deepoxidase seems to be beneficial for the host plant. The strength of these interactions between HC-Pro and the corresponding host protein vary with the plant species. Therefore, these interactions may explain the species-specific sensitivity to potyviruses.

show abstract

Section: Proteolytic Activity Of Hc-promentioning

confidence: 99%

Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins

Hýsková,

Bělonožníková,

Chmelík

et al. 2024

Plants

View full text Add to dashboard Cite

show abstract

Reconceptualizing programmed transcriptional slippage in RNA viruses

Valli,

Domingo-Calap,

González de Prádena

et al. 2024

Preprint

View full text Add to dashboard Cite

RNA viruses have evolved sophisticated strategies to exploit the limited encoded information within their typically compact genomes. One of such, named programmed transcriptional slippage (PTS), is defined by the insertion of an additional A at Anmotifs (n ≥ 6) of newly synthetized viral transcripts to get access to overlapping open reading frames (ORFs). Although key proteins from Ebolavirus and potyvirids (members of thePotyviridaefamily) are expressed via PTS, available information about this phenomenon is very scarce. Here, by using diverse experimental approaches and a collection of plant/virus combinations, we discover cases in which PTS does not fit with its current definition. In summary, we observe (i) high rate of single nucleotide deletions at slippage motifs, (ii) overlapping ORFs acceded by slippage at an U8stretch, and (iii) significant changes in slippage rates induced by factors not related to cognate viruses. Moreover, a survey of full-genome sequences from potyvirids shows a widespread occurrence of species-specific An/Un(n ≥ 6) motifs. Even though many of them, but not all, lead to the production of truncated proteins rather than access to overlapping ORFs, these results suggest that slippage motifs appear more frequently than expected and play relevant roles during virus evolution. In conclusion, our data prompt to broaden PTS definition in RNA viruses. Considering the potential of this phenomenon to expand the viral proteome by acceding to overlapping ORFs and/or producing truncated proteins, a revaluation of PTS significance during infections of RNA viruses is required.IMPORTANCEProgrammed transcriptional slippage (PTS) is used by RNA viruses as another strategy to maximise the coding information in their genomes. This phenomenon is based on a peculiar feature of viral replicases: they insert an untemplated A in An motifs (n ≥ 6) in a small fraction of newly synthesised viral RNAs. As a consequence, ribosomes can get access to overlapping open reading frames (ORFs) when translating those particular transcripts. Here, using plant-infecting RNA viruses as models, we discover cases challenging the previously stablished definition of viral PTS, prompting us to reconsider and redefine this expression strategy. An interesting conclusion from our study is that PTS might be more relevant during RNA virus evolution and infection processes than previously assumed.

show abstract

Reconceptualizing transcriptional slippage in plant RNA viruses

Valli,

Domingo-Calap,

González de Prádena

et al. 2024

mBio

View full text Add to dashboard Cite

RNA viruses have evolved sophisticated strategies to exploit the limited encoded information within their typically compact genomes. One of them, named transcriptional slippage (TS), is characterized by the appearance of indels in nascent viral RNAs, leading to changes in the open reading frame (ORF). Although members of unrelated viral families express key proteins via TS, the available information about this phenomenon is still limited. In potyvirids (members of the Potyviridae family), TS has been defined by the insertion of an additional A at A n motifs ( n ≥ 6) in newly synthesized transcripts at a low frequency, modulated by nucleotides flanking the A-rich motif. Here, by using diverse experimental approaches and a collection of plant/virus combinations, we discover cases not following this definition. In summary, we observe (i) a high rate of single-nucleotide deletions at slippage motifs, (ii) overlapping ORFs acceded by slippage at an U 8 stretch, and (iii) changes in slippage rates induced by factors not related to cognate viruses. Moreover, a survey of whole-genome sequences from potyvirids shows a widespread occurrence of species-specific A n /U n ( n ≥ 6) motifs. Even though many of them, but not all, lead to the production of truncated proteins rather than access to overlapping ORFs, these results suggest that slippage motifs appear more frequently than expected and play relevant roles during virus evolution. Considering the potential of this phenomenon to expand the viral proteome by acceding to overlapping ORFs and/or producing truncated proteins, a re-evaluation of TS significance during infections of RNA viruses is required. IMPORTANCE Transcriptional slippage (TS) is used by RNA viruses as another strategy to maximize the coding information in their genomes. This phenomenon is based on a peculiar feature of viral replicases: they may produce indels in a small fraction of newly synthesized viral RNAs when transcribing certain motifs and then produce alternative proteins due to a change of the reading frame or truncated products by premature termination. Here, using plant-infecting RNA viruses as models, we discover cases expanding on previously established features of plant virus TS, prompting us to reconsider and redefine this expression strategy. An interesting conclusion from our study is that TS might be more relevant during RNA virus evolution and infection processes than previously assumed.

show abstract

Quantitative Analysis of RNA Polymerase Slippages for Production of P3N-PIPO Trans-frame Fusion Proteins in Potyvirids

Cited by 3 publications

References 42 publications

Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins

Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins

Reconceptualizing programmed transcriptional slippage in RNA viruses

Reconceptualizing transcriptional slippage in plant RNA viruses

Contact Info

Product

Resources

About