Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes

Abstract

Human hepatitis delta virus (HDV) is a unique infectious agent whose genome is composed of a small circular RNA. Recent data, however, have reported the existence of highly divergent HDV-like circRNAs in the transcriptomes of diverse vertebrate and invertebrate species. The HDV-like RNAs described in amniotes such as birds and reptiles encode self-cleaving RNA motifs or ribozymes similar to the ones present in the human HDV, whereas no catalytic RNA domains have been reported for the HDV-like circRNAs detected in metagenomic data from some amphibians, fish, and invertebrates. Herein, we describe the self-cleaving motifs of the HDV-like genomes reported in newts and fish, which belong to the characteristic class of HDV ribozymes. Surprisingly, HDV-like circRNAs from a toad and a termite show conserved type-III hammerhead ribozymes, which belong to an unrelated class of catalytic RNAs characteristic of plant genomes and plant subviral circRNAs, such as some viral satellites and viroids. Sequence analyses revealed the presence of very similar HDV-like hammerhead ribozymes encoded in two termite genomes, but also in the genomes of several dipteran species. In vitro transcriptions confirmed the cleaving activity for these motifs, with moderate rates of self-cleavage. These data indicate that all described HDV-like agents contain self-cleaving motifs from either the HDV or the hammerhead class. Autocatalytic ribozymes in HDV-like genomes could be regarded as interchangeable domains and may have arisen from cellular transcriptomes, although we still cannot rule out some other evolutionary explanations.

HDV-Like Viruses

“…All characterized deltaviruses have a negative-sense self-complementary circular RNA genome folded into the classical unbranched rod-like structure, including ribozymes [ 22 , 25 , 26 , 27 ]. While the presence of ribozymes has not been reported in the four metazoan HDV-like genomes identified by [ 24 ], a more recent study confirmed the presence of self-cleaving motifs in these HDV-like genomes [ 29 ]. HDV-like ribozymes have been recently mapped in the newt and fish HDV-like sequences [ 29 ].…”

“…While the presence of ribozymes has not been reported in the four metazoan HDV-like genomes identified by [ 24 ], a more recent study confirmed the presence of self-cleaving motifs in these HDV-like genomes [ 29 ]. HDV-like ribozymes have been recently mapped in the newt and fish HDV-like sequences [ 29 ]. Contrastingly, the toad and termite HDV-like genomes lacked analogous HDV-like ribozymes and instead showed the presence of conserved type III hammerhead ribozymes, which belong to an unrelated class of catalytic RNAs characteristic of plant genomes and plant subviral circular RNAs, such as some viral satellites and viroids [ 29 ].…”

“…HDV-like ribozymes have been recently mapped in the newt and fish HDV-like sequences [ 29 ]. Contrastingly, the toad and termite HDV-like genomes lacked analogous HDV-like ribozymes and instead showed the presence of conserved type III hammerhead ribozymes, which belong to an unrelated class of catalytic RNAs characteristic of plant genomes and plant subviral circular RNAs, such as some viral satellites and viroids [ 29 ].…”

“…A ribozyme, a self-cleaving RNA sequence, resides in the viroid-like sequence of the HDV genome that cleaves a linear form of multiple-copy length of the viral genome or antigenome into monomeric units that are then circularized to complete the replication cycle. All described HDV-like agents contain self-cleaving motifs from either the HDV or the hammerhead class [ 22 , 23 , 26 , 27 , 29 ]. In vitro transcription and self-cleavage analysis confirmed the cleaving activity for these motifs in the newt, fish, toad, and termite HDV-like RNAs [ 29 ].…”

“…All described HDV-like agents contain self-cleaving motifs from either the HDV or the hammerhead class [ 22 , 23 , 26 , 27 , 29 ]. In vitro transcription and self-cleavage analysis confirmed the cleaving activity for these motifs in the newt, fish, toad, and termite HDV-like RNAs [ 29 ]. The cleaving activity for the other identified ribozymes has not yet been tested.…”