Viruses : Where did they come from?

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Since viruses have no ribosomes of their own, they have no rRNA and can't be included in the rRNA-based 'Universal tree'. However, there are 3 general views of how viruses may have originated:

  1. As genetic offshoots ('satellites') of their hosts genome
  2. As remnants of precellular life
  3. As highly reduced (degenerate) remnants of originally cellular parasites

Keep in mind that viruses are a collection of various very different kinds of 'organisms',and there is no reason to believe that viruses are generally related to one another geneologically - different groups of viruses presumably had different origins. Some viruses are probably genetic offshoots of their hosts, some may represent remnants of precellular life, and other may be degenerate cellular parasites. Others may have other origins that we haven't yet considered.

Viruses as genetic offshoots of their hosts

Although viruses lack ribosomal RNAs, it is possible to use other genes present in any particular virus for phylogenetic analysis if they are sifficiently conserved for good alignment. Many genes are very different in viruses than other organisms because of their specialization and rapid evolutionary rate, and therefore are not useful in phylogenetic analysis. Others are OK, for example the tRNA genesfound in bacteriophage T4 (and other T-even phage). In most of these cases, the virus is clearly found to be related to the host-group, i.e. these viruses are almost certainly off-shoots of the hosts genome. But it is certainly possible that only some of the genes are from the host (viruses gather bits of their host DNA all the time), and that the 'core' of the virus predates the host & acquired some genes from the host recently.

Another reason to believe that many (perhaps most) viruses are derived from their host genomes is that they are, without exception, fundamentally dependent on their hosts for cellular processes for replication.

An evolutionary continuum between bacterial genomes and bacteriophage

Plasmids are secondary chromosomes. Some "megaplasmids" are not meaningfully distinct from regular chromosomes; the usual distinction used is that if a DNA molecules contains essential genes, it is considered a chromosome, if not then it's a plasmid. But as a general rule, plasmids carry important genes, whether they're essential under any specific living conditions or not. Many plasmids (e.g. the "fertility" or "F" plasmid) can be transferred from cell to cell by "conjugation", a sort of sexual exchange of DNA not usually associated directly with reproduction. Viruses are similar to conjugative plasmids, except that they are transfered via an encapsidated intermediate rather than by direct contact between cells. These plasmids carry a series of genes that direct replication & conjugative transfer of the plasmid DNA.

F plasmid exchange

Many viruses do not kill the host; they are essentially transmissible plasmids that are transfered to their new host via an encapsidated form rather than directy via conjugation. If the plasmid is replicated to hiogh copy-numbers, it can slow the growth of the host somewhat; the result is that these viruses form cloudy phaques on plates. An example of this is filamentous bacteriophage M13 (and related bacteriophage such as IF1 and fd):

M13

M13, then, is a lot like a conjugative plasmid except that the transfer mechanism doesn't involve direct donor-recipient contact. This is a fairly clear case of a virus as a genetic offshoot of the host.

Some viruses seem to have derived from transposons (mobile genetic elements). Retroviruses are essentially transmissible retroposons (transposons with reverse transcriptase genes, e.g. Ty in yeast, Copia and P-element in flys, HIV in humans). Bacteriophage Mu is essentially a transmissible out-of-control transposon.

Mu
Bacteriophage Mu. M.S. Inman Virology 1976 72:393

Mu

Some viruses, then, are the ultimate 'selfish genes'.

Viruses as remnants of precellular life

Many believe in an "RNA World" before the evolutionary invention of DN or protein, or probably even lipid membranes. This is reasonable because:

  • DNA functions only through RNA intermediates.
  • Protein synthesis is fundamentally an RNA-driven process (tRNAs, ribosomes, mRNAs).
  • RNA can perform the functions both of DNA (genome) and protein (catalysis).

The complexity of this RNA World, presuming it existed, is a matter of wildly speculative and largely uninformed debate.

Many RNA viruses (especially virus "satellites", such as plant virusoids, but also hepatitus delta virus) seem similar to what these pre-biotic RNAs might have been like, in that they direct their own replication process without DNA intermediates and preform at least some of their own replication functions (self-cleavage & ligation of replication forms by ribozymes). About all these viruses need from their host to replicate is a primase, RNA polymerase, NTPs, and a decent physical/chemical environment. And so, some beleive that these viruses may have originated deep in time, and persist today as remnants of the pre-biotic RNA world.

RYMV
The Rice Yellow Mottle Virus-associated viroid - not it's genome, the whole thing. Rick Collins, Virology 1998 241:269

For my money, it's hard to imagine that these RNAs, which are functional only in cytoplasm (that of it's host) could be directly descended from independent RNAs that lived in the precellular RNA world that may or may not have existed. If these viruses are remnants of precellular life, they must have originally had mechanisms for replication independent of cytoplasm. It seems unlikely that only parasitic remnants persist, but it is possible that free-living 'viruses' have yet to be discovered. After all, how would you look for them, or even detect their presence?

TSRV
Tobacco Ringspot Virus Satellite RNA-S replication (JWBrown)

Viruses as degenerate parasites

Some viruses may be the simplified remnant of microbial intracellular parasites, similar to Bdellovibrio, Chlamydia, or Rickettsia. It is certainly true that parasites often become extremely simplified, shedding anything unneeded. Starting with an obligate intracellular energy parasite such as Chlamydia, all that need happen to become a virus is the fusion of the cytoplasms of the host and parasite, so that the virus can use the translational apparatus and perhaps even the hosts transcription and/or DNA replication machinery. The genome of the parasite could then become even more drastically simplified. Smallpox virus, at 0.2 x 0.3um, is as big as small bacteria, with a genome nearly as large (ca. 0.2Mbp) and the smallest parasitic microbes (N. equitans is less than 0.5Mbp).

The best potential example of this, however, might be Mimivirus, a virus of amoeba, which has a capsid 0.4um in diameter (as big as Nanoarchaeum or Opitutus) and a genome of 1.2Mbp, as big as many prokaryotic genomes and bigger than many. The genome encoded a slew of translational proteins, such as EF-Tu, release factor 1, tRNA-synthetase (tRNA charging emzymes), IF-1, topoisomerases, etc. However, this organism lacks genes for ribosomal RNAs or proteins, as well as genes for central metabolism.

Mimivirus
Mimivirus : SciencePhotoLibrary

Interestingly, Mimiviruses (there are several known) carry out their replication and assembly of the core in the nucleus, then assembly of the large virus particle in specific regions of the host cytoplasm; "virus factories". And so even though the virus fuses with the host, and hijacks it ribosomes and other components, it retains some ditinction between "self" and "host" during replication.

mimivirus-enfected amoeba
Mimivirus-infected amoeba. Note the "virus factory" (VF), from which assembled virus particles emerge. Nature Rev. Microbiol 6:315 D. Raout

Mimivirus was disovered accidently during investigation of Legionella in amoebas, and is large enough that it was first seen in Gram stains, and thought to be a Gram-positive bacterium! A larger "species", Mamavirus, is infected by a smaller satellite virus, the sputnik virophage.