Viruses are essential agents within the roots and stem of the tree of life

Villarreal, Luis P.; Witzany, Guenther

doi:10.1016/j.jtbi.2009.10.014

Cited by 167 publications

(107 citation statements)

References 161 publications

Supporting

Mentioning

106

Contrasting

Order By: Relevance

“…Applied to the virosphere, we outlined this in detail as a reply to outdated opinions concerning the role of virus within the tree of life (Villarreal and Witzany 2010). One crucial question therefore is Is really new sequence space the result of selection of an abundance of replication errors (Eigen 1971), or in contrary, is it the result of the practical competence of living agents to generate new sequences?…”

Section: Introductionmentioning

confidence: 99%

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

Villarreal

Witzany

2015

J Mol Evol

Self Cite

View full text Add to dashboard Cite

In the early 1970s, Manfred Eigen and colleagues developed the quasispecies model (qs) for the population-based origin of RNAs representing the early genetic code. The Eigen idea is basically that a halo of mutants is generated by error-prone replication around the master fittest type which will behave similarly as a biological population. But almost from the start, very interesting and unexpected observations were made regarding competition versus co-operation which suggested more complex interactions. It thus became increasingly clear that although viruses functioned similar to biological species, their behavior was much more complex than the original theory could explain, especially adaptation without changing the consensus involving minority populations. With respect to the origin of natural codes, meaning, and code-use in interactions (communication), it also became clear that individual fittest type-based mechanisms were likewise unable to explain the origin of natural codes such as the genetic code with their context-and consortia-dependence (pragmatic nature). This, instead, required the participation of groups of agents competent in the code and able to edit code because natural codes do not code themselves. Three lines of inquiry, experimental virology, quasispecies theory, and the study of natural codes converged to indicate that consortia of cooperative RNA agents such as viruses must be involved in the fitness of RNA and its involvement in communication, i.e., code-competent interactions. We called this co-operative form quasispecies consortia (qs-c). They are the essential agents that constitute the possibility of evolution of biological group identity. Finally, the basic interactional motifs for the emergence of group identity, communication, and cooperation-together with its opposing functions-are explained by the ''Gangen'' hypothesis.

show abstract

Section: Introductionmentioning

confidence: 99%

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

Villarreal

Witzany

2015

J Mol Evol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mimiviridae | DNA virus phylogeny | girus | viral translation | tree of life T he discovery of the viral nature of Acanthamoeba polyphaga Mimivirus (1), followed by the determination of its outstanding genome sequence (1,182 kb) (2) led to an irreversible change in the way microbiologists looked at viruses (3)(4)(5)(6), even reviving the debate on their classification as living microorganisms (7,8). After Mimivirus, no obvious limit could be set anymore on the expected size of a viral particle, or the complexity of its gene content, both of them now largely overlapping with that of the simplest cellular organisms, such as parasitic bacteria (9).…”

mentioning

confidence: 99%

Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae

Arslan

Legendre

Seltzer

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

312

334

View full text Add to dashboard Cite

Mimivirus, a DNA virus infecting acanthamoeba, was for a long time the largest known virus both in terms of particle size and gene content. Its genome encodes 979 proteins, including the first four aminoacyl tRNA synthetases (ArgRS, CysRS, MetRS, and TyrRS) ever found outside of cellular organisms. The discovery that Mimivirus encoded trademark cellular functions prompted a wealth of theoretical studies revisiting the concept of virus and associated large DNA viruses with the emergence of early eukaryotes. However, the evolutionary significance of these unique features remained impossible to assess in absence of a Mimivirus relative exhibiting a suitable evolutionary divergence. Here, we present Megavirus chilensis, a giant virus isolated off the coast of Chile, but capable of replicating in fresh water acanthamoeba. Its 1,259,197-bp genome is the largest viral genome fully sequenced so far. It encodes 1,120 putative proteins, of which 258 (23%) have no Mimivirus homologs. The 594 Megavirus/Mimivirus orthologs share an average of 50% of identical residues. Despite this divergence, Megavirus retained all of the genomic features characteristic of Mimivirus, including its cellular-like genes. Moreover, Megavirus exhibits three additional aminoacyl-tRNA synthetase genes (IleRS, TrpRS, and AsnRS) adding strong support to the previous suggestion that the Mimivirus/Megavirus lineage evolved from an ancestral cellular genome by reductive evolution. The main differences in gene content between Mimivirus and Megavirus genomes are due to (i) lineages specific gains or losses of genes, (ii) lineage specific gene family expansion or deletion, and (iii) the insertion/migration of mobile elements (intron, intein).Mimiviridae | DNA virus phylogeny | girus | viral translation | tree of life

show abstract

“…has been raised repeatedly throughout the history of Scola et al, 2008), had the potential to radically modify our views about the living or nonliving status of viruses (mainly because it has become very difficult to draw a boundary between some cellular organisms strongly dependent on their host and harbouring less than a minimal genome and the giant viruses that encode many genes and exhibit some degree of autonomy (Claverie & Abergel, 2010; this special issue)) and/or the role viruses could have played in the origins of life (Forterre, 2010b;Raoult & Forterre, 2008). These views have been met with scepticism by many other virologists (López-García, 2012; López-García & Moreira, 2012;Moreira & López-García, 2009), giving rise to a strong controversy (see, e.g., (Villarreal, 2004), (Villarreal & Witzany, 2010); see also Claverie and Abergel, Forterre, as well as van Regenmortel, this special issue).…”

Section: What Is the Place Of Viruses In The Biological World?mentioning

confidence: 99%