Genome complexity: retroviruses are a real part of us (Introduction)

by David Turell , Monday, April 13, 2020, 01:21 (1686 days ago) @ David Turell

And play major roles in evolution:

https://inference-review.com/article/the-yin-and-yang-of-the-genome#endnote-7

"Humans are, all of us, part retrovirus. Roughly 8% of the DNA in human cells is retroviral in origin: the relics of ancient infections in the germ line of our ancestors. This compares to the figure of 1.5% of the genome that encodes all the proteins that function to keep us alive. It is sobering to think that the double helix is really their world, these little parasites. We are just living in it.

***

"Viruses composed of RNA and relying on reverse transcriptase and a proviral DNA sequence intermediately became known as retroviruses....Three major enzymes comprise the pol: reverse transcriptase (RT), retroviral integrase (IN), and retroviral protease (PR). RT, of course, copies RNA to DNA. IN integrates the resulting DNA provirus into the host. PR is a protein that cuts long viral amino acid chains at precise locations.

***

"By the 1980s, the basic life cycle of the retrovirus was finally understood. A retrovirus attaches to a host cell by way of spikes on its surface: membranes fuse, the viral core is dumped into the cell, and reverse transcription occurs. The DNA provirus is then integrated, proviral promoter sequences hijack cellular transcription proteins, and mRNAs are produced and processed. Most mRNAs are translated into long amino acid chains; the requisite components self-assemble and bud off from the cell. After budding, PR cuts some of the long amino acid chains at the right spots; the freshly cut proteins condense, and the lifecycle is completed.

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"Viruses are nefarious and well-made. No invasion is haphazard. A retrovirus has just the right sequence of molecular keys fitting just the right sequence of cellular locks at just the right times. Half of a virus, or half of its proteins, would never make it. Where did viruses and retroviruses come from?

"Skalka notes that “no clear explanation for the origin of all viruses exists.”

***

"Skalka turns her attention to the dual nature of the retrovirus. The virus as poison needs no defense: it is obvious. But how could a retrovirus ever be a gift useful to an organism? In several ways, actually. The first is evolutionary. Retroviruses and ERVs increase the pool of available genetic variation. The richer the variation, the better the evolvability.

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"If it were not for retroviruses, humanity might still be primitive hunter-gatherers without civilization; our immune systems would be weaker; we would be hatching from eggs. How so? A regulatory segment in an ERV controls a copy of the enzyme amylase, which allowed humans to incorporate starch into their diets. Control of amylase opened the potential for the species to become farmers instead of hunter-gatherers. Similarly, HERVs in the major histocompatibility complex have shaped the evolution of the immune system. And certain ERV genes were recruited during the evolution of the mammalian placenta: specifically those assisting with cell fusion and immune suppression, which is co-opted for the protection of the fetus. (my bold)

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"Viruses want a sure thing, and so tend to target stable host genes unlikely to change; in response, the host is forced to change them, but in noncritical regions that may help repel the virus while doing minimal damage. In humans, roughly 5% of codon changes in mundane housekeeping genes are due to the arms race with viruses. In other mammals, it is an astounding 30%. (my bold)

***

"By using retroviruses as vectors in conjunction with the remarkable CRISPR-Cas system, which is a defense system against viruses in some prokaryotic organisms, virtually any DNA segment in any cell type can be targeted and replaced. This has massive potential for treating genetic diseases. However, it also involves ethical issues, as the system could be used to sculpt the genetic architecture of human embryos and make them into designer children. This again returns to the recurring theme of the book: the dual nature of retroviruses. Viruses deform and kill millions, but also provide opportunities to help millions. The principle is illustrated with no greater irony than in the case of HIV. Humans are now using genetically modified HIV particles as vectors to treat HIV symptoms, as well as other genetic diseases."

Comment: Note my bolds. The first shows that retroviruses are part of God's armamentarium in managing evolution. And note that allows us to manage problems. Is that a purposeful gift from God? The second shows another major difference in humans from other primates, creating more of our specialness. This is taken from a book review.