Virusoids
Virusoids are satellite circular RNAs. In virology, the term ‘satellite’ is used to describe infectious particles which require a helper virus in order to replicate after infecting the host. Thus, you usually cannot get infected by a virusoid alone if you aren’t infected by the right helper virus, and even if the virusoid manages to get into your cell, it won’t have the necessary equipment to replicate and thus spread in your body. The ‘equipment’ that virusoids need from their helper virus is the RNA polymerase. Virusoids are very similar to viroids but virusoids require the RNA polymerase from a helper virus instead of how viroids just use the RNA polymerase that the host cell uses.
Virusoids are usually 220 to 338 nucleotides long, so they are still very short circular RNAs. The virusoids contain ribozymes, which is like what the avsunviroidae use for self-splicing their concatemers during replication. The helper virus that virusoids need is a sobemovirus (a genus of virus which infects plants). One other difference between virusoids and viroids is that virusoids are encapsidated (packaged) by the coat protein of their helper virus, while viroids are just naked RNA. However, a similarity is that the majority of virusoids also have no coding capacity due to their small size.
Some examples of virusoids are the Lucerne transient streak virus satellite RNA (virusoid with LTSV as the helper virus), and the Subterranean clover mottle virus satellite RNA. Usually the trend is to prefix the name of the helper virus and then add ‘satellite RNA’ to the end to describe the virusoid. In Professor AbouHaidar’s lab, they discovered the smallest and only known exogenous coding and replicating circular RNA, the Rice Yellow Mottle Virus satellite RNA. This is a virusoid that is 220 nucleotides in length which also has coding capacity in the genome.
Ribozymes
Virusoids self-splice during replication with their own ribozymes. These are sections of their RNA that splice themselves out of the RNA chain and then go around and keep on cutting out more copies of the virusoid. Since replication of single stranded RNA needs to go from plus-sense to minus-sense to plus-sense again, there are both plus and minus-sense ribozymes. The particular ribozymes used for virusoids is called a hammerhead ribozyme, because it has a central box-like area with no base pairing and three stems of base-pairing RNA coming out of it. The stems are positioned so that one stem is the ‘handle’ of the hammer and the other two stems are roughly opposite to each other so they represent the face and claw of the hammer. These hammerhead ribozymes need magnesium (2+) ions in order to self-splice.
2 Magnesium (2+) ions are required for the ribozyme to perform its functions. No proteins or ATP is required for the ribozyme to do its thing, so even if you shut down the cellular translation or energy-producing functions, these virusoids can still replicate as long as there are magnesium ions. The ribozyme performs self-splicing by having one of the magnesium ions attack the hydroxyl group of the ribose, and then the other magnesium ion receives the charge from the phosphate backbone, which ends up severing the phosphate backbone link between the next RNA. The reverse of that reaction can also be catalyzed by the hammerhead ribozyme, and the result of that is self-ligation (re-joining the ends of the cut-off strands into a circle).
Apart from the hammerhead ribozymes which are present in many plant virusoids and viroids, there are also other types of ribozymes. Group I Introns are a type of self-splicing intron (introns are sequences of RNA that are removed during splicing. Only exons make it into the final RNA) which is present in pre-ribosomal RNA. Usually, introns wait for a spliceosome to come and cut them out, but these self-splicing introns can cut themselves out of the sequence. Then there are Group II Introns, which are also self-splicing introns that have been found in bacteria and the organelle genes of eukaryotic cells. This ties into how we suspect that eukaryotes originally might have evolved from swallowing prokaryotic bacteria which then became the organelles.
Another ribozyme is called RNase P. Ribonuclease P catalyzes site-specific hydrolysis of precursor tRNA which is essential for the formation of tRNA. What this means is that the RNase P cuts up immature tRNA (when we make new tRNA) at certain places, and that helps it to become fully functional mature tRNA.
Then we have the Hepatitis Delta Virus Ribozyme. This is the ribozyme that the HDV virus uses, and it is a noncoding RNA that is thought to be the only catalytic RNA known to be required for viability of a human pathogen. I.e. the HDV virus cannot function without its HDV Ribozyme. Remember that the virusoids and viroids which also use their own ribozymes all infect plants, so that is why the HDV Ribozyme can carry the title of the only one in humans.
Lastly, ribosomes are also a ribozyme, since fundamentally ribosomes are made of RNA and they catalyze the reactions of joining amino acids together to make protein. Remember that ribozymes are just RNA that can catalyze reactions (i.e. act as an enzyme without being a protein), so catalyzing the joining of amino acids also counts! Most of these other examples focus on catalyzing splicing of RNA so it’s good to remember that ribozymes can do more than just that.
