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Tide Bite: The virus that changed the tree of life

By Victoria Foe

Originally posted in Friday Harbor Labs Tide Bite

I came to FHL in 2000 to study cell division, to take advantage of sea urchins, starfish and sand dollars whose huge, transparent, permeable and easy-to-handle eggs make them ideal subjects for this work. Local species have eggs that ripen at different times, providing an almost year-round source of perfect research material. For marine cell experiments, FHL’s floating groundwater are the “lab benches” that landlocked cell scientists can only dream of.

Then in 2013, the Seaver Institute gave me the opportunity to address a question that haunted me since my graduate studies: does DNA replication activate the expression of new genes? If so, it would provide an elegant mechanism forcing embryonic development to take place at the same time as cell division. To answer it, you had to look directly at DNA and RNA under an electron microscope, and thousands of hours of searching for DNA tangles for the rare cases where DNA and RNA synthesis had collided. . I will write a future Tide Bite on what I discovered. But this bite is taken from a related review that I just finished. In this time of the COVID-19 pandemic, it is also a reminder that it is great disasters that can lead to great transformations.

This story is about another virus that turned the world upside down. Like coronaviruses, this transformer used RNA, not DNA, as genetic material. The events in question happened about two billion years ago, when life was simpler. At that time, Earth was home to only two of the three domains of life: bacteria and ever more sophisticated archaea. Organisms in these two domains are single-celled beings, with small DNA genomes, no discrete nucleus, and limited possibilities. At that time, there were no beautiful diatoms, no slippery amoebae, no captive algae, no starfish, no octopus, no grasses, no trees, no tree frogs, no birds, no mammals.

The genes that a bacterial or Archean cell uses to conduct its small affairs are short enough and few in number that they all fit like beads on a circular chromosome. These wired together information units are individually activated as needed and transcribed into messenger RNAs (mRNAs) – transportable cassettes – each of which directs the synthesis of a specific protein.

We do not know which species fell prey to the virus. Or even if the disease has attacked one or more species. But we are fairly sure that the pathogen was a group II retro-transposon (Rogozin et al. 2012, Lambowitz and Zimmerly 2004). When it infects its victim, a retrotransposon presents its mRNA-like genome for translation and the host innocently translates it, mistaking it for one of their own. This malicious piece of code contains instructions for doing reverse transcriptase and integrase. Reverse transcriptase makes a reverse copy of viral RNA into DNA. Integrase inserts viral DNA transparently into the host’s gene collar. Unlike coronaviruses, retrotransposon infections are usually permanent, as viral DNA – once integrated – is rarely lost from the host chromosome. As a result, the host and its offspring must now repair, replicate, and transcribe the parasite’s DNA with their own, much like a lark feeds the cuckoo chick in its nest, but in perpetuity. To ensure that newly transcribed copies of itself are released to infect other cells and other sites on the host’s chromosome, the retrotransposon RNA contains two special sequences: the first is molecular scissor folds capable of cutting RNA molecules at specific sites. The second, formed by bringing the two ends of the viral RNA into contact, creates the sequence that these scissors recognize. Thus, the vicious and infectious virus dissects itself from the host’s mRNA. In the process, the host’s own transcripts are left in fragments.

The mutation would ultimately reduce its virulence, but not before the virus has inserted itself into its victim’s chromosome. But in doing so, it definitely changed the way the host’s offspring could regulate their genes. In the Eucarya – the third realm of life, which includes ourselves and the life forms we see all around us – the genes are enormously longer than in bacteria and archaea and are arranged in a very strange way. . And in that strangeness, the fingerprints indicative of the virus remain. Eukaryotic genes exist as many discontinuous fragments of protein coding sequences interrupted by long stretches of non-coding “junk” DNA. RNA polymerases transcribe the short sequences of coding DNA as well as the long sequences of unwanted sequences into a long, continuous piece of RNA. The production of mRNA therefore requires cutting the waste and suturing the coding sequences together. The boundaries between waste and encoding RNA are encoded by the same sequence that even current group II bacterial retrotransposons use to mark the boundaries between viral and host sequences. In eukaryotes, splicing is now done by an RNA / protein complex called a spliceosome. But the RNA fraction at the heart of the spliceosome is the same self-folding sequence that retrotransposons use as scissors (Lambowitz and Zimmerly 2004, Rogers 1990). What has changed, however, is that eukaryotes have taken over the scissors: now the pieces of coding RNA are stitched together to form the eukaryotic mRNA, and these are the stranded relics of DNA. viral – long void of contagion and slowly mutated into non-coding waste – which is cut up, broken down and recycled. Under my electron microscope, I often see this size of RNA going on.

RNA polymerases fall off chromosomes as cells divide, so at the start of each new cell cycle, they must re-load at the start of a gene and begin the journey again along its length (Shermoen and O’Farrell 1991) . Therefore, the inclusion of unwanted DNA lengths in genes acts as a time fuse, determining when the first mRNA of each gene (hence the protein) appears. Some genes take less than a minute to transcribe, some take hours, some are so long they take days. In different genes and species, natural selection has altered the lengths of unwanted DNA inserted between splice sites, sometimes by orders of magnitude. Bacteria, Archeans and eukaryotes turn all genes on and off through regulatory molecules that manage the loading of RNA polymerase. But the added tool of using unwanted DNA transcription as a retarder has allowed eukaryotes to create much more complex genetic circuits. One such example is the self-inhibiting feedback circuit with a long delay defined by unwanted DNA, which produces the oscillations that result in the formation of segments in vertebrate embryos (Takashima et al. 2011). The resulting activation of the oscillatory gene establishes the cell blocks that produce vertebrae, ribs, muscles, etc. along the axis of the body, sequentially.

Additionally, by selectively using alternative splice sites, eukaryotes can make multiple variants of a protein from a single gene. The Down syndrome cell adhesion gene (Dscam) takes this to the extreme. Dscam encodes cell surface receptors used for the identity and guidance of axons during nervous system development in organisms as diverse as fruit flies and humans. By virtue of the combinatorial use of many alternative splice sites, the single Dscam gene can potentially generate over 38,000 slightly different versions of the DSCAM protein (Schmucker et al. 2000)!

In summary, a catastrophic viral invasion of the ancestor of all eukaryotes has introduced a radical new tool for gene regulation, which would facilitate the development of more complex life forms. Much of this regulation is based on gene length and is independent of base sequence, explaining why so much of what was once thought to be unwanted DNA is now an integral part of eukaryotic genomes. In humans, for example, over 80% of the genome is transcribed into RNA, but only about 1% encodes messenger RNAs. No crisis has ever been more spectacularly exploited than this confrontation two billion years ago between a primitive cell and its virus. A tiny cell rearranged its calamity and gave birth to a world populated by what Darwin called “the most beautiful and wonderful endless forms.”

Dr Foe is Emeritus Professor and Researcher at the University of Washington. She has been a full-time member of the Friday Harbor Labs research community for 20 years, was a founding member of the FHL Center for Cell Dynamics, and was a Guggenheim and MacArthur Fellow.

The references: Lambowitz AM and S. Zimmerly. 2004. Introns of the mobile group II. Annu Rev Genet: 38 (1-35); Rogers JH 1990. The role of introns in evolution. FEBS letters: 268/2 (339-343); Rogozin IB, Carmel L., Csuros M. and EV Koonin. 2012. Origin and evolution of spliceosomal introns. Direct Biology: 7/1 (11-28); Schmucker D., Clemens JC, Shu H., Worby CA, Xiao J., Muda M., Dixon JE, and SL Zipursky. 2000. Drosophila Dscam is an axon guiding receptor exhibiting extraordinary molecular diversity. Cellular: 101/6 (671-684); Shermoen AW and PH O’Farrell. 1991. The progression of the cell cycle through mitosis leads to the abortion of nascent transcripts. Cellular: 67/2 (303-310); Takashima Y., Toshiyuku O., Gonzalez A., Miyachi H. and R. Kageyama. 2011. Intronic delay is essential for oscillatory expression in the segmentation clock. PNAS: 108/8 (3300-3305).

The electron microscope makes it possible to examine the workings of life. Here, a gene is transcribed into RNA. The direction of the transcription is from left to right; transcripts lengthen as RNA polymerases move through the gene, until spliceosomes begin to cut unwanted sequences and shorten transcripts. Unwanted RNA can be thought of as lariats, with a spliceosome holding the ends together for cutting. At the distal (right) end of the gene, the spliceosomes remain bound to the now fully pruned mRNA. Electron micrograph by V. Foe. (Photo provided)