Knockdown of capsid protein encoding novel ATPase domain inhibits genome packaging in potato leafroll virus

The curious case of genome packaging and assembly in RNA viruses infecting plants

“…Interestingly, apart from RNA viruses, the same ATPase fold consisting of Walker A, Walker B, sensors, and arginine fingers was also found to be present on the polypeptide chain of CPs of DNA viruses infecting plants, such as members of Nanoviridae and Geminiviridae families. Intriguingly, the presence of very rare patterns of a novel ATPase domain with multiple Walker A, sensor motifs, Walker B, and arginine motifs fetched during our thorough comprehensive analysis has indicated a variation within the ATPase superfamily ( Figure 1A ) ( Ranjan et al, 2021 ; Kumar et al, 2022 ; Mohanty et al, 2023 ). Such variations could be responsible for the evolution of different architectures of an ATPase domain with a single function of ATP hydrolysis during evolution time ( Iyer et al, 2004 ; Chelikani et al, 2014b ).…”

“…In our previous study, an attempt was made to expand and sub-classify type I packaging machinery for several plant RNA viruses, viz., Polerovirus and Potexvirus. These smaller RNA viruses infecting plants fall under an ATP-dependent sub-type IA packaging system, which possess a classical P-loop containing an ATPase domain situated over linear polypeptide chains of CPs ( Ranjan et al, 2021 ; Kumar et al, 2022 ; Mohanty et al, 2023 ). The viral encoded CP recognizes the genomic end, nucleates over the viral genome in the presence of ATP, and ultimately, encapsidates them to a mature virion ( Ranjan et al, 2021 ; Mohanty et al, 2023 ).…”

“…The type IB virus takes the help of viral- or host-encoded ATPase, whereas the type IC virus prefers an ATP-independent fashion to package their genome inside capsid coats ( Ranjan et al, 2021 ). The role of packaging ATPase in genome packaging is well-known for viruses of type II and III systems, but our recent discovery of the presence of novel ATPase domains on polypeptide chains of CPs has completely changed our perception of genome packaging in plant RNA viruses and raised many interesting facts ( Ranjan et al, 2021 ; Kumar et al, 2022 ; Mohanty et al, 2023 ). An ATPase domain comprising different motifs responsible for ATP hydrolysis is situated on the linear primary structure of the CP of almost all plant RNA viruses ( Figures 1A, B ).…”

“…Genome packaging and assembly is a crucial step during the life cycle of RNA viruses infecting plants ( Rao, 2006 ; Ranjan et al, 2021 ; Kumar et al, 2022 ; Mohanty et al, 2023 ). Three different approaches have been reported by which viruses condense their genome inside the empty prohead ( Chelikani et al, 2014a ; Ranjan et al, 2021 ; Mohanty et al, 2023 ).…”

“…The plant RNA virus replicates within a cytoplasmic compartment, which is heavily populated by cellular RNAs ( Burd and Dreyfuss, 1994 ; Rao, 2006 ). Thus, CPs, the RNA-binding proteins, exhibit a remarkable degree of packaging specificity, despite their probability of co-packaging cellular RNAs ( Burd and Dreyfuss, 1994 ; Ranjan et al, 2021 ; Kumar et al, 2022 ).…”