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Forename: Yuta Surname: Sato

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Module: LZ036 Assignment: 2

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Virus

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Virus

In general terms, the question of whether or not viruses are alive is entirely dependenton the suitability of the definition of virus in the kingdom of life. It has been argued thatviruses are not alive because they do not fit into any of the accepted definitions of life(Moreira and Lpez-Garca, 2009).Conversely, It has been argued that viruses are soimportant in evolutionary terms that life should be re-defined to include them (Brssow,2009). However, this essay focuses upon appropriate consideration of what constitutes as avirus, may lead to the conclusion that viruses are in fact alive under current definitions, andthat appreciation of this may provide clarity to a functional definition of life (Forterre, 2010).

There has been a plethora of answers to the question What is Life (Luisi, 2010;Moreira and Lpez-Garca, 2009; Schrodinger, 2012) with a rough consensus recentlyemerging. In 2002, a living organism was proposed to be an organized unit, which carriesout metabolic reactions, generate its own quantity of ATP, defends itself against injury,responds to stimuli and contains the ability to reproduce itself (Ruiz-Saenz and Rodas, 2010,

p87). This is widely accepted as an appropriate definition (Ruiz-Saenz and Rodas, 2010).However, the answer to the question of whether viruses are or is not alive could provide extradefinitional clarity, as viruses are mainly situated on the boundary between life and noneliving life.

The heated debate regarding the origin of virus has been stimulated by molecular biologists. Majority of molecular biologists are in favour of hypothesis that virus originatedfrom nucleic acid, moving from one cell to another. (Knipe and Howley, 2007; Reece et al.,

2010) The evolution of genes provides the infection of un- injured cells. Original sources of viral genomes contain plasmids and transposons. Plasmids are usually small, it is circular DNA molecules included in the bacteria and in the eukaryotes called yeasts. Plasmids arefound in a part of the cell`s genome. It has capability to self-replicate from genome andtransfer from cell to cell with in a cell`s genome( Moreira and Lpez-Garca, 2009; 2010;Witzany, 2012). Therefore, Plasmids, transposons and viruses all share commoncharacteristics of mobile elements.

As an aside to this view, there is also a mode of thought that views life in terms of a

universal connected system: the tree of life. All members of the universal tree of life, asconstituted by the Bacteria, Eukaryota and Archaea domains - are connected to each other viaa common ancestor termed the last universal cellular ancestor of life (LUCA). The cellular nature of this common ancestor excludes viruses from the universal tree of life by definition.However, emerging evidence suggests that viruses are in fact connected to the evolutionarysystem of life. Furthermore, viruses may have been instrumental to the evolution of cellular organisms. This has led to a push to re-define life so that viruses can be included.

Following the crystallisation of tumour mosaic virus by Wendell Stanley in 1935,virions were postulated as the missing link between none living organisms and unicellular organisms (Kay, 1986; Zaitlin, 1998). Virology was placed at the borderline betweenchemistry and biology (Zaitlin, 1998). As a field it concentrated on describing the structural

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and chemical properties of virions, an example of this being the expression of polio virus as achemical formula (Wimmer, 2006).

Viruses are still popularly considered through the prism of the virion, for example inthe media, a spikey virion cartoon is used to represent influenza (BBC, 2013). There is a

possibility to think of micro-organisms, including viruses, as objects independent from thecell, for example when comparing the mass of microbes in the body to that of the brain(Eisen, 2012; 2012)

Viewed from the perspective of the virion, viruses are not alive by any currentlyaccepted definition of life ( Moreira and Lpez-Garca, 2009). Virions are inert and lack ametabolism, cannot replicate itself or generate its own supply of APT (Knipe and Howley,2007; Reece et al., 2010). Furthermore, virions cannot replicate outside a cellular environment (Moreira and Lpez-Garca, 2009; 2010; Witzany, 2012). As it was recentlyclaimed, it is a matter of logic that viruses are not alive (Moreira and Lpez-Garca,2009).Nevertheless, there has recently been an attempt to re-define life to include viruses.

This attempt stems from a growing appreciation of the important role played by virusesduring the evolution of life, and their potential evolutionary connection to cellular organisms(Bamford, 2003; Forterre, 2006a).

There is emerging evidence that viruses may have emerged from now extinct cellular lineages that existed in parallel to LUCA (Bamford, 2003; File et al., 2002; Forterre, 2006a;Forterre and Gribaldo, 2007). This places viruses in an evolutionary tree beside that of theother domains of life. From this perspective, there is a considerable argument for classifyingviruses as new domain, and redefining LUCA to mean the last common ancestor (Brssow,2009).

A number of viral genes are shared by a diverse groups of viruses. These viralhallmark genes include those encoding DNA replication proteins (Bradley et al., 2009;Koonin et al., 2006). This suggests that viruses share a common ancestor, that probablyoriginated at the time of, and independently to, LUCA (Bamford, 2003). In fact, there mayhave been three major viral lineages that emerged at this time corresponding to the threegroups of virus that we observe today (Bamford, 2003; Prangishvili et al., 2006).

In addition, it suggested that viruses are responsible for various aspects of cell biology (Forterre, 2010). In one model, viruses were responsible for introducing DNA andenzymes for DNA replication into the LUCA lineage. Prior to this, RNA was the hereditymolecule of the cell (File et al., 2002; Forterre, 2006a, 2006b; Villarreal and DeFilippis,2000). This model is supported by the lack of homology observed between the DNAreplication enzymes of orthologous Bacteria and Archaea, the explanation being that theDNA dependent enzymes of Bacteria and Archaea were introduced by distinct viral lineages(Bamford, 2003; File et al., 2002; Prangishvili et al., 2006).

Therefore, it is argued that viruses were of central importance during the evolution of cellular organisms and have themselves evolved from a biological entity similar to that of

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LUCA. This presents a reasonable case for re-classifying life to include viruses. However,defenders of the status quo point out that the genetic homology between diverse viral groupsmay be the result of horizontal gene transfer (HGT) (Moreira and Brochier-Armanet, 2008).This is widely accepted as a method of viral evolution (Moreira and Lpez-Garca,2009).Moreover, viruses often capture and mimic cellular genes for the purpose of immune

evasion. In fact, it is still the majority view that viruses are merely the by-products of cellular life and similarities between viruses and cells are a result of the fact that viruses are the

product of escaped cellular genes. From this point of few viruses should still be considered as biological entities without life.

Viruses are alive

It is not yet possible to justify re-defining our concept of life such that viruses areincluded. However, as we begin to appreciate viruses as entities beyond that of virions, it may

be possible to justify defining viruses as alive under the current definitions of life.

It is widely accepted as outdated to think of viruses primarily in terms of the virion

(Knipe and Howley, 2007). The virion constitutes only part of the virus as a biological entity,the relationship of it to the virus being analogous to that of a seed to a plant. The debateregarding whether viruses are alive should therefore concentrate on whether the sophisticated,virus dependent processes that occur in virus-infected cells, constitute an independent livingidentity to that of the host (Forterre, 2010).

Virus infection of a eukaryotic cell results in the formation of viral intracellular super-structures (Bell, 2001; Claverie, 2006; Miller and Krijnse-Locker, 2008; Novoa et al., 2005;Suzan-Monti et al., 2007; Takemura, 2001). These become factories for virion production.The viral factories of the mimi-virus are particularly large (Suzan-Monti et al., 2007). Phageinfection of a bacterium can result in the bacterium being entirely transformed into a virus

factory (Forterre, 2010). It could be argued in these cases that the bacterium or cell becomesmore viral than host. Furthermore, infection of cells with a lytic virus results in host genomedegradation. Potentially, the only genes expressed in a virus-infected cell are viral (Bize etal., 2009; Forterre, 2010). Viruses even encode their own metabolic structures, for examplethe photo-synthetic protein encoded by cyanophages (Bragg and Chisholm, 2008). It istherefore possible to view part of a virus life cycle as the assumption of the identity of theinfected cell. From this point of view, if you view a cell as alive, viruses are also alive.

The above position is attractive. Returning to the definition of life described above, avirus infected cell is organised to maximise virion production (Rice and Davido, 2013). Also,within the context of the infected cell a whole array of viral proteins are produced thatcounter-act the potentially damaging effect of host immune cell proteins on viral replication,for example the HCMV protein IE1 protects viral infected cells from apoptosis (Kim et al.,2003) . There is also evidence that viruses can get ill from other viruses, for example thesputnik satellite virus grows solely in mimi-virus infected amoeba, decreases the yield of mimi-virus and causes production of morphological aberrant mimivirus virions (Pearson,2008; La Scola et al., 2008). Finally, a virus infected cell is clearly capable of reproducingitself, by the release of virions and infection of other cells the equivalent to the dispersal of seeds.

To conclude, this essay has clearly illustrated evidences that when viruses areappropriately understood, viruses can be considered as alive under the currently agreeddefinition of life. There is no need to resort or to re-defining life to include them, althoughthe emerging importance of viruses during cellular evolution is interesting in itself. The

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answer to the question of whether viruses are considered as living organisms is slightly lessclear. There is certainly a persistent body of thought that resists the idea of consideringviruses as alive (Moreira and Lpez-Garca, 2009). However, careful examination of thearguments reveals that this resistance is still grounded in the persistent restriction of theconcept of virus to the virion, and there is growing appreciation that this is fundamentally

misleading to the question of whether viruses deserve a place in the kingdom of life.

Reference

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Bell, P.J. (2001). Viral eukaryogenesis: was the ancestor of the nucleus a complex DNAvirus? J. Mol. Evol. 53 , 251 256.

Bize, A., Karlsson, E.A., Ekefjrd, K., Quax, T.E.F., Pina, M., Prevost, M.-C., Forterre, P.,Tenaillon, O., Bernander, R., and Prangishvili, D. (2009). A unique virus release mechanismin the Archaea. Proc. Natl. Acad. Sci.

Bradley, A.J., Lurain, N.S., Ghazal, P., Trivedi, U., Cunningham, C., Baluchova, K.,Gatherer, D., Wilkinson, G.W.G., Dargan, D.J., and Davison, A.J. (2009). High-throughputsequence analysis of variants of human cytomegalovirus strains Towne and AD169. J. Gen.Virol. 90 , 2375 2380.

Bragg, J.G., and Chisholm, S.W. (2008). Modeling the fitness consequences of acyanophage-encoded photosynthesis gene. Plos One 3 , e3550.

Claverie, J.-M. (2006). Viruses take center stage in cellular evolution. Genome Biol. 7 , 110.

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