Published: October 9, 2015
Science & Tech Staff Writer
The classification of viruses has been the subject of intense debate within the field of evolutionary biology for quite some time. Viruses are small intracellular parasites containing either DNA or RNA surrounded by a protective protein coating. In order to reproduce, viruses infect host cells and use the cells’ metabolic and biosynthetic contents for propagation. Because viruses cannot reproduce on their own, and because their evolutionary origins are ambiguous, classification of viruses becomes convoluted. A new study published Sept. 25 in Science Advances used the genomic and structural formations for viruses in order to analyze viral origins and evolution.
Arshan Nasir, Ph.D., and Gustavo Caetano-Anollés, Ph.D., the authors of this research study, focused on the protein structures encoded in the genomes of cells and viruses called folds. During the analysis of 5080 completely sequenced proteomes from cells and viruses, Nasir and Caetano-Anollés assigned different folding domains to the proteins. Though highly diverse, the viral proteomes retained ancient evolutionary history that could be extracted using methods of bioinformatics. “Their high mutation rates can obscure deep evolutionary signals. Protein folds are better markers of ancient events, because their 3D structures can be maintained even as the sequences that code for them begin to change,” stated Caetano-Anollés.
Nasir and Caetano- Anollés’s data suggest that viruses originated from multiple ancient cells that coexisted with ancestors of modern cells. Therefore, there is a common ancient cellular linage for both cells and viruses. Virocells, the cells infected by the virus that then reproduce that virus, experienced gradual reduction in genome and particle size. This reduction resulted in the existence of modern viruses, which lack their original cellular make-up. When in the presence of cellular contents -upon entering a host cell, for instance- the virus’s cellular nature is restored.
After infection of the host cells, viruses form “factories.” or virocells that begin to compartmentalize and utilize the metabolic machinery of the cell in order to propogate. Because of the similarities found between the cell and the virus, Nasir and Caetano-Anollés were able to formulate a tree of life no longer excluding viruses. They note that despite vast similarities, viruses do contain some genetic sequences divergent from those found in the cell, which indicates that viruses are genetic designers in their own right.
Nasir and Caetano-Anollés compare viruses to intracellular parasitic bacteria that are also dependent upon host cells. Nasir and Caetano-Anollés identified 66 unique proteins in viruses; the identification of unique proteins suggests that viruses should be reclassified as living organisms. Nasir says, “The argument that viruses do not replicate or evolve independently of cells and hence should not be deemed worthy of living status has been toned down because each species replicates and evolves in nature and requires coexistence with other life forms.”
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