A rogue’s gallery of the genome

The notion of harmful and beneficial bacteria, viruses, etc., greatly oversimplifies the reality of what is going on at a molecular level. The following excerpts introduce the themes of natural genetic engineering, viral transmission of genetic material and symbiotic relationships which include such players as endogenous viruses (originating in the host). 

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Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual’s genome but are neutral or harmful to the individual as a whole.  

The SGE model is a more *ecological* view that considers the genome as a set of genetic elements with potentially different kinds of interactions, ranging from cooperative (mutualistic), to neutral (commensal), to selfish (parasitic)

An increasing number of genetic studies began to uncover non-Mendelian and other elements within diverse organisms that appeared to have *self-promoting* features that cannot simply be explained as adaptations for the organism.  

Mobile elements include plasmids, endogenous viruses, and transposable elements (TEs). TEs have the ability to copy and move to new locations within the genome; as a consequence, they can accumulate. 

Selfish genetic elements, genetic conflict, and evolutionary innovation
John H. Werren. Department of Biology, University of Rochester, Rochester, NY 14627
PNAS | June 28, 2011 | vol. 108 | suppl. 2 | 10863–10870

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As short DNA sequences, TEs possess the capability to migrate between diverse sites within the genome, a capacity that enables them to promote genomic mutations in a number of ways, ranging from the most limited regulatory mutations to the most extensive rearrangements of the genome. Scientists who pioneered the original discovery of TEs announced their potential roles in genomic adaptation, which was sharply contested by other theorists. Such was the misunderstanding of the beneficial roles of TEs that for over two decades they were regarded almost exclusively in a negative light as genome-damaging intragenomic parasites. 

A major watershed in TE research came when the Drosophila melanogaster genome was sequenced, which unleashed unprecedented analysis of TEs. This path breaking investigation resulted in the initial identification of TE-produced adaptations in Drosophila melanogaster. Subsequent studies illuminated the fundamental contributions of TEs in the processes of adaptive evolution. This important inference was the product of a methodical search of the entire genome that focused on adaptive insertions that resulted from TEs.

Endogenous retroviruses heavily colonize vertebrate genomes, which share approximately 50% of their genomic DNA. These Endogenous retroviruses have emerged from host cell retroviral infections via evolutionary progression, which permits the permanent integration of viral genomes into host DNAs and facilitates multigenerational transmission. Endogenous retroviruses obstruct replication cycles of exogenous pathogenic retroviruses that are transmitted horizontally.

All through evolution an obvious fact is always glaring us on the face is that every time a new system of defense emerges, it is always the result of accommodation and coexistence. The great radiation of the single-celled life forms most likely was the result of accommodating the parasitic retrotransposons and eventually co-opting them to preserve the species. As a result over 50% of the man’s DNA is made of retroelements and 8% is retroviral in origin. Similarly, over 90% of bacteria and other microorganisms that inhabits our bodies are *beneficial* life forms co-opted to protect us from the harmful pathogenic ones.

Back to the Soil: Retroviruses and Transposons
Omar Bagasra and D. Gene Pace, in:
Biocommunication in Soil Microorganisms, Soil Biology 23
Springer-Verlag Berlin Heidelberg 2011

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