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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 dependent
on the suitability of the definition of virus in the kingdom of life. It has been argued that
viruses 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 so
important 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 a
virus, may lead to the conclusion that viruses are in fact alive under current definitions, and
that 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 recently
emerging. In 2002, a living organism was proposed to be an organized unit, which carries
out 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 extra
definitional clarity, as viruses are mainly situated on the boundary between life and none
living 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 originated
from 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 are
found in a part of the cell`s genome. It has capability to self-replicate from genome and
transfer 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 common
characteristics 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, as
constituted by the Bacteria, Eukaryota and Archaea domains - are connected to each other via
a 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 evolutionary
system 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 between
chemistry and biology (Zaitlin, 1998). As a field it concentrated on describing the structural
and chemical properties of virions, an example of this being the expression of polio virus as a
chemical formula (Wimmer, 2006).
Viruses are still popularly considered through the prism of the virion, for example in
the 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 the
cell, 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 currently
accepted definition of life ( Moreira and Lpez-Garca, 2009). Virions are inert and lack a
metabolism, 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 recently
claimed, 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 viruses
during 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 the
other domains of life. From this perspective, there is a considerable argument for classifying
viruses 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 viral
hallmark genes include those encoding DNA replication proteins (Bradley et al., 2009;
Koonin et al., 2006). This suggests that viruses share a common ancestor, that probably
originated at the time of, and independently to, LUCA (Bamford, 2003). In fact, there may
have been three major viral lineages that emerged at this time corresponding to the three
groups 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 and
enzymes for DNA replication into the LUCA lineage. Prior to this, RNA was the heredity
molecule 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 DNA
replication enzymes of orthologous Bacteria and Archaea, the explanation being that the
DNA 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
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 groups
may 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 are
included. 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 debate
regarding whether viruses are alive should therefore concentrate on whether the sophisticated,
virus dependent processes that occur in virus-infected cells, constitute an independent living
identity 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). Phage
infection 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 becomes
more viral than host. Furthermore, infection of cells with a lytic virus results in host genome
degradation. Potentially, the only genes expressed in a virus-infected cell are viral (Bize et
al., 2009; Forterre, 2010). Viruses even encode their own metabolic structures, for example
the photo-synthetic protein encoded by cyanophages (Bragg and Chisholm, 2008). It is
therefore possible to view part of a virus life cycle as the assumption of the identity of the
infected 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, a
virus 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 that
counter-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 the
sputnik 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 reproducing
itself, 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 are
appropriately understood, viruses can be considered as alive under the currently agreed
definition of life. There is no need to resort or to re-defining life to include them, although
the emerging importance of viruses during cellular evolution is interesting in itself. The
answer to the question of whether viruses are considered as living organisms is slightly less
clear. There is certainly a persistent body of thought that resists the idea of considering
viruses as alive (Moreira and Lpez-Garca, 2009). However, careful examination of the
arguments reveals that this resistance is still grounded in the persistent restriction of the
concept 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

Bamford, D.H. (2003). Do viruses form lineages across different domains of life? Res.
Microbiol. 154, 231236.

Bell, P.J. (2001). Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA
virus? J. Mol. Evol. 53, 251256.

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 mechanism
in 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-throughput
sequence analysis of variants of human cytomegalovirus strains Towne and AD169. J. Gen.
Virol. 90, 23752380.

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

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

Eisen, J. (2012). Jonathan Eisen: Meet your microbes | Video on TED.com.

File, J., Forterre, P., Sen-Lin, T., and Laurent, J. (2002). Evolution of DNA polymerase
families: evidences for multiple gene exchange between cellular and viral proteins. J. Mol.
Evol. 54, 763773.

Forterre, P. (2006a). Three RNA cells for ribosomal lineages and three DNA viruses to
replicate their genomes: A hypothesis for the origin of cellular domain. Proc. Natl. Acad. Sci.
U. S. A. 103, 36693674.

Forterre, P. (2006b). The origin of viruses and their possible roles in major evolutionary
transitions. Virus Res. 117, 516.

Forterre, P., and Gribaldo, S. (2007). The origin of modern terrestrial life. Hfsp J. 1, 156168.

Kay, L.E. (1986). W. M. Stanleys Crystallization of the Tobacco Mosaic Virus, 1930-1940.
Isis 77, 450472.
Kim, J., Kwon, Y.J., Park, E.-S., Sung, B., Kim, J.H., Park, C.-G., Hwang, E.-S., and Cha,
C.-Y. (2003). Human cytomegalovirus (HCMV) IE1 plays role in resistance to apoptosis with
etoposide in cancer cell line by Cdk2 accumulation. Microbiol. Immunol. 47, 959967.

Knipe, D.M., and Howley, P.M. (2007). Fields Virology (Lippincott Williams & Wilkins).

Koonin, E.V., Landweber, L.F., and Lipman, D.J. (2006). A community experiment with
fully open and published peer review. Biol. Direct 1, 1.

Luisi, P.L. (2010). The Emergence of Life: From Chemical Origins to Synthetic Biology
(Cambridge University Press).

Miller, S., and Krijnse-Locker, J. (2008). Modification of intracellular membrane structures

for virus replication. Nat. Rev. Microbiol. 6, 363374.

Moreira, D., and Brochier-Armanet, C. (2008). Giant viruses, giant chimeras: The multiple
evolutionary histories of Mimivirus genes. Bmc Evol. Biol. 8, 12.

Moreira, D., and Lpez-Garca, P. (2009). Ten reasons to exclude viruses from the tree of
life. Nat. Rev. Microbiol. 7, 306311.

Novoa, R.R., Calderita, G., Arranz, R., Fontana, J., Granzow, H., and Risco, C. (2005). Virus
factories: associations of cell organelles for viral replication and morphogenesis. Biol. Cell
Auspices Eur. Cell Biol. Organ. 97, 147172.

Pearson, H. (2008). Virophage suggests viruses are alive. Nature 454, 677.

Prangishvili, D., Forterre, P., and Garrett, R.A. (2006). Viruses of the Archaea: a unifying
view. Nat. Rev. Microbiol. 4, 837848.

Reece, J.B., Urry, L.A., Cain, M.L., Wasserman, S.A., Minorsky, P.V., and Jackson, R.B.
(2010). Campbell Biology (Benjamin Cummings).

Rice, S.A., and Davido, D.J. (2013). HSV-1 ICP22: hijacking host nuclear functions to
enhance viral infection. Future Microbiol. 8, 311321.

Ruiz-Saenz, J., and Rodas, J.D. (2010). Viruses, virophages, and their living nature. Acta
Virol. 54, 8590.

Schrodinger, E. (2012). What is Life?: With Mind and Matter and Autobiographical Sketches
(Cambridge University Press).

La Scola, B., Desnues, C., Pagnier, I., Robert, C., Barrassi, L., Fournous, G., Merchat, M.,
Suzan-Monti, M., Forterre, P., Koonin, E., et al. (2008). The virophage as a unique parasite of
the giant mimivirus. Nature 455, 100104.

Suzan-Monti, M., Scola, B.L., Barrassi, L., Espinosa, L., and Raoult, D. (2007).
Ultrastructural Characterization of the Giant Volcano-like Virus Factory of Acanthamoeba
polyphaga Mimivirus. Plos One 2.

Takemura, M. (2001). Poxviruses and the origin of the eukaryotic nucleus. J. Mol. Evol. 52,
419425.
Villarreal, L.P., and DeFilippis, V.R. (2000). A Hypothesis for DNA Viruses as the Origin of
Eukaryotic Replication Proteins. J. Virol. 74, 70797084.

Wimmer, E. (2006). The test-tube synthesis of a chemical called poliovirus: The simple
synthesis of a virus has far-reaching societal implications. EMBO Rep. 7, S3S9.

Witzany, G. (2012). Viruses: Essential Agents of Life (Springer).

Zaitlin, M. (1998). The Discovery of the Causal Agent of teh Tobacco Mosaic Disease. In
Discoveries in Plant Biology, (USA: World Publishing Co.), pp. 105100.