One of the most acclaimed theories on the nature of viruses was that these were particles that were generated when a cell or an organism developed an infection.  In addition, viruses were also perceived as entities that were mainly comprised of deoxyribonucleic acid (DNA) and incapable of performing any metabolic activity.  One feature that further supported this prokaryotic concept was that viruses were capable of undergoing crystallization, a process that has never been observed in any living organism.  A few decades later, viruses were perceived in a different light, as these were observed to increase in size in order to produce more copies of its self.  These virus factories were similar in size as that of the nucleus of a eukaryotic cell.  Since then, the origin and nature of viruses, as well as bacteria, have been under scrutiny by several biologists, microbiologists, biochemists and philosophers.

It has long been recognized that viruses and bacteria were organisms that did not have a nucleus.  Using such scheme, organisms can be generally divided into two major groups, wherein those that have a nucleus are called eukaryotes, while those without a nucleus are known as prokaryotes.  This scheme was rather simple to follow, as this would put viruses and bacteria under the classification of prokaryotes.  However, there has been recent conflict with this theory because current studies of viruses have shown that there is a wide range of viral types.  For example, viruses that are capable of invading prokaryotes were called bacteriophages, while there were also other virus types that had the capability of infecting other types eukaryotic cells were simply named viruses.  Such nomenclature needed further review and modification.

In addition to the wide variety of viruses that were isolated and classified, it has also been observed that viruses that were capable of infecting various hosts that were in turn, highly different from viruses, especially in terms of the protein production.  It was then apparent that viruses were capable of producing proteins that had no homologous counterparts in any other type of cell or organism.  Comparative nucleic and amino acid sequencing analyses showed that viruses carried hallmark proteins that were not present in any other living organism or eukaryotic cell (Koonin et al., 2006).  Given this new discovery, the classical theory of viruses originating from cells, or the prokaryotic concept, was thus abolished.

Another theory on the origin of viruses, as well as bacteria, is the trinity concept.  This theory recognizes that there are three primary lines that existed in the beginning of life.  These three lineages were comprised of two prokaryotic groups and one eukaryotic group.  Under the prokaryotic grouping, two categories were present, namely the eubacteria or the real bacterial species and the archaebacteria or the strange bacterial species.  The main differences related to such bacterial classification was based on the emergence of the bacteria, wherein archaebacteria were described to be the first species that arose and eubacteria were the modern bacteria that emerged later.  Despite such differences, investigations in biochemistry and genetics showed that the archaebacteria were similar in processes to ribosomes of eukaryotes.  In addition, there were certain ribosomal proteins that had no homologous counterparts in the eubacterial species.

An additional theory to the origin of bacteria and viruses is the Last Universal Common Ancestor (LUCA) theory (Forterre, 2010).  This concept, on the other hand, lays heavily on the principle that viruses have the capability to invade bacteria and thus, tracing the earliest ancestral bacterial will provide information on the actual origin of these organisms.  One feature that further strengthens the LUCA theory is the observation that viruses have the capability of infecting the three cellular domains that were identified in the trinity concept.  Given this fact, it is thus highly possible that before any of the three cellular domains of the trinity concept emerged, viruses were already existing.  It is also probable that the three cellular domains of the trinity concept were already prone to infection and invasion by viruses even during early times.

The LUCA theory also strengthens the concept that viruses were the first living organisms that existed, as this further explains that viruses emerged before the last universal ancestor of cells had arisen.  Given this scenario, another corollary could be presented, wherein the first nucleic acid that existed was ribonucleic acid (RNA) and not DNA.  For a number of decades, there has been intense debate and scrutiny on the first kind of nucleic acids that were created after the Big Bang explosion (Koonin, 2007).  Most classical biologists supported that idea that DNA was the first nucleic acid that emerged, as this was what is observed in most living organisms.  However, it should be understood that during earlier times, viruses were also not considered as living organisms but simply particles that were secreted by infected eukaryotic cells.

Given that viruses are capable of infecting the three cellular domains of the trinity concept and that viruses may have existed before the LUCA, then it is highly possible that RNA is indeed the first kind of nucleic acid that was produced after the Big Bang explosion (Koonin, 2007).  There has been significant questioning with regards to the RNA concept, as this scenario would require a number of molecular and ionic factors that would facilitate in the stabilization of a single-stranded macromolecule.  The DNA-first theory is thus more acceptable to biologists and theorists, as the double-stranded macromolecular scenario would not require any additional external factors to attain stability of the structure.

One of the strong arguments against the RNA-first theory is parallel to the DNA replication model.  In this model, a single strand of DNA is bound by single-stranded binding proteins to stabilize the structure.  It should be understood that before DNA replication could occur, at least one nick to the DNA helix is required for the relaxation of the duplex and consequent unwinding of the two DNA strands.  At the same time, short primers known as Okazaki fragments are annealed to one of the complementary DNA strands.  A DNA-dependent polymerase, an enzyme that is capable of utilizing free nucleotides for attachment to the Okazaki fragments is then produced, which in turn generates a growing DNA strand.  In the case of viruses, one strand of RNA is present, yet there is no need for the presence and binding of single-stranded binding proteins for stability.  It is thus apparent that such nucleic acid configuration is feasible in nature and that these viruses still have the capability of producing copies of its self and infect other cellular organisms.  

Another theory that is related to the origin of viruses and bacteria is that bacteria may have originated from viruses (Koonin and Wolf, 2009).  There are currently specific viruses that produce proteins that are also present in bacterial species.  Despite this similarity, it should be understood that viruses are capable of infecting bacteria, suggesting that the viruses are more advanced in terms of invasion and reproduction.  Bacteria, on the other hand, have no capability of infecting viruses, as these species are simply destroyed by viruses and their cellular machinery are controlled by viral proteins that are introduced during the invasion.

The accumulation of information from the fields of biochemistry, evolution and genetics has shown that viruses play a lead role in the transition from simple organisms to multi-cellular complex species.  Furthermore, these viruses have gained the capacity to produce nucleic acids that could adhere to each other, resulting in the current accepted double-stranded structure of DNA.  It has also been suggested that the production of the cell wall in plants, as well as the cell membrane in the eukaryotic species are mechanisms designed to prevent the entry of viruses into the cells.


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