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| title | chunk | source | category | tags | date_saved | instance |
|---|---|---|---|---|---|---|
| Baltimore classification | 6/7 | https://en.wikipedia.org/wiki/Baltimore_classification | reference | science, encyclopedia | 2026-05-05T09:06:57.533227+00:00 | kb-cron |
Non-canonical translation initiation: Viral initiation of translation: some viruses have evolved mechanisms to initiate translation. Methods include having internal ribosomal entry sites to allow cap-independent initiation, having downstream hairpin loops that allow for cap-dependent translation without an eIF2 initiation factor, and initiating translation at a CUG codon or other start codon with a leucine amino acid. These methods are used by various +ssRNA and ssRNA-RT viruses. Ribosomal shunting, also called nonlinear scanning: ribosomes start scanning from a 5′-cap structure then bypass a leader region in the mRNA and initiate translation downstream from the leader sequence. Ribosomal shunting is used by various dsDNA, +ssRNA, –ssRNA, and RT viruses. Termination-reinitiation, also called stop-start: after termination of translation of an ORF, a proportion of 40S subunits of the ribosome remain attached to the mRNA as a way to reinitiate translation of a subsequent ORF. This is used by various dsRNA and +ssRNA viruses.
Non-canonical elongation and termination of translation: Ribosomal frameshifting: ribosomes slip one nucleobase forward or backward during translation. This is used by various dsDNA, dsRNA, +ssRNA, and ssRNA-RT viruses to produce merged proteins from overlapping ORFs. Suppression of termination, also called stop codon read-through: certain viruses contain codons in their mRNA that would normally signal for termination of translation upon being recognized by a release factor but are instead partially recognized by tRNA during translation, which allows for continued translation up to the next stop codon to produce extended polypeptides at the end of the amino acid sequence. This is used by various dsRNA, +ssRNA, and ssRNA-RT viruses, often to express replicase enzymes. Ribosomal skipping, also called stop-carry on and stop-go: a viral peptide may prevent a ribosome from covalently linking a newly inserted amino acid, which blocks further translation. The amino acid sequence is then co-translationally cleaved, and a new amino acid sequence is started, which leads to the production of two proteins from one ORF. This is used by various dsRNA and +ssRNA viruses.
== Evolutionary origins and relations ==
Excluding ribozyvirians, RNA viruses of groups III–V are believed to share common ancestry. +ssRNA viruses form the basal, ancestral lineage of these viruses from which dsRNA viruses and –ssRNA viruses appear to have evolved from on multiple occasions. The two orders of RT viruses in the class Revtraviricetes, Blubervirales and Ortervirales, are believed by virologists to have evolved from two different families of retrotransposons on separate occasions. ssRNA-RT viruses all belong to Ortervirales and thus share common ancestry. dsDNA-RT viruses, on the other hand, are found in both orders and therefore represent two separate lineages of dsDNA-RT viruses. Ribozyvirians constitute a lineage of –ssRNA viruses unrelated to other RNA viruses. Most ssDNA viruses likely originate from plasmids that, on multiple occasions, recombined with other genomes to obtain the structural proteins needed to form virions. The evolutionary history of dsDNA viruses is the most complex as they appear to have emerged independently on numerous occasions. Two major lineages of dsDNA viruses exist: the realm Duplodnaviria and the realm Varidnaviria, the latter of which also contains ssDNA viruses that are descended from dsDNA viruses. The opposite is true in the realm Floreoviria, which contains dsDNA viruses descended from ssDNA viruses. There are also two minor realms, Adnaviria and Singelaviria, that exclusively contain dsDNA viruses. Lastly, there are dsDNA virus families unassigned to higher taxa that are unique from existing realms and which likely constitute small realms. Of the replication-expression systems used by viruses, only Baltimore group I (dsDNA) is used by cells. The other groups may be remnants of the primordial stage of life before the emergence of modern-like cells, during which the dsDNA system used by extant cells had not yet become uniform. The ancestors of RNA viruses in particular may have emerged during the time of the RNA world. And although virus realms are evolutionarily independent from each other, the replicative proteins encoded by viruses in the four major realms (Duplodnaviria, Floreoviria, Riboviria, and Varidnaviria) are built on the core RNA recognition motif, one of the most common nucleic acid-binding domains in nature. Therefore, the replication-expression cycles most likely diversified before the separation of large dsDNA replicators, which became the ancestors of cellular life, from other types of replicators, which became selfish genetic elements and gave rise to viruses.
== History ==