Potato Spindle Tuber Viroid Modulates Its Replication through a Direct Interaction with a Splicing Regulator

Abstract

Viroids are circular noncoding RNAs (ncRNAs) that infect plants. Despite differences in the genetic make-up and biogenesis, viroids and various long ncRNAs all rely on RNA structure-based interactions with cellular factors for function. Viroids replicating in the nucleus utilize DNA-dependent RNA polymerase II (Pol II) for transcription, a process that involves a unique splicing form of transcription factor IIIA (TFIIIA-7ZF). Here, we provide evidence showing that potato spindle tuber viroid (PSTVd) interacts with a TFIIIA splicing regulator (ribosomal protein L5; RPL5) and PSTVd infection compromises the regulatory role of RPL5 over splicing of transcripts, while ectopic expression of RPL5 reduces TFIIIA-7ZF expression and attenuates PSTVd accumulation. Furthermore, we illustrate that the RPL5 binding site on the PSTVd genome resides in the central conserved region critical for replication. Together, our data suggest that viroids can modulate specific regulatory factors leading to splicing changes in only one or a few genes. This study also has implications for understanding the functional mechanisms of ncRNAs and elucidating the global splicing changes in various host-pathogen interactions.Viroids are the smallest replicons among all living entities. As circular noncoding RNAs, viroids can replicate and spread in plants often resulting in disease. Potato spindle tuber viroid (PSTVd), the type species of nuclear-replicating viroids, requires a unique splicing form of transcription factor IIIA (TFIIIA-7ZF) for its propagation. Here, we provide evidence showing that PSTVd directly interacts with a splicing regulator, RPL5, to favor the expression of TFIIIA-7ZF, thereby promoting viroid replication. This finding provides new insights to better understand viroid biology and sheds light on the noncoding RNA-based regulation of splicing. Our discovery also establishes RPL5 as a novel negative factor regulating viroid replication in the nucleus and highlights a potential means for viroid control.

Role of Protein Glycosylation in Host-Pathogen Interaction

“…This process is normally accomplished by manipulating the host cellular machinery in different ways. The acellular pathogens, like a virus, viroid or prion, usually utilize nucleic acid or host protein synthesis pathways to replicate itself [66,67]; while cellular pathogens, such as fungi, bacteria, protozoon or nematodes, gain only nutrients from hosts but utilize their own cellular machinery for proliferation [58,68]. In this scenario, they need to secrete effectors into hosts, altering the host energy metabolism pathway or transferring nutrients to the infection site.…”

Evidence Supporting That RNA Polymerase II Catalyzes De Novo Transcription Using Potato Spindle Tuber Viroid Circular RNA Templates

“…We recently established an in vitro transcription (IVT) system for studying the Pol II-catalyzed replication of potato spindle tuber viroid (PSTVd), the type species of nuclear-replicating viroids [40]. We identified the eukaryotic transcription factor TFIIIA-7ZF as a critical factor facilitating Pol II-catalyzed transcription using the (+)-strand PSTVd RNA template [40,41]. We also mapped the TFIIIA-7ZF binding site [40], which is next to the transcription initiation site of (−)-strand intermediates [42] and is shown vital for Pol II binding [43] and PSTVd replication [44].…”

Symptomatic plant viroid infections in phytopathogenic fungi

“…Their RNAs form rod-shaped secondary structures but likely lack ribozyme activities (2,16). Potato spindle tuber viroid (PSTVd) requires a unique splicing variant of transcription factor IIIA (TFIIIA-7ZF) to replicate by Pol II (17) and optimizes expression of TFIIIA-7ZF through a direct interaction with a TFIIIA splicing regulator (ribosomal protein L5, a negative regulator of viroid replication) (18). The molecular basis of viroid pathogenicity is not fully understood, although some mechanisms have been suggested, including the down-regulation of host gene expression via RNA silencing-mediated degradation guided by viroid-derived small RNAs (19)(20)(21).…”