The genetic code: Now 5 letters instead of 4

[The_J]

It's April, and this might already be the scientific breakthrough of the year!

https://www.the-scientist.com/news-opinion/some-viruses-use-an-alternative-genetic-alphabet-68726

Some Viruses Use an Alternative Genetic Alphabet
In a trio of studies, researchers follow up on a 40-year-old finding that certain bacteriophages replace adenine with so-called diaminopurine, perhaps to avoid host degradation.

In 1977, scientists showed that a virus called S-2L that infects cyanobacteria has no adenine in its genome. Instead, S-2L uses a nucleotide known as diaminopurine or 2-aminoadenine, shortened to Z, that makes three hydrogen bonds—rather than the two that adenine (A) makes—when paired with thymine (T). In three papers published today (April 29) in Science, researchers show that the use of Z by phages, those viruses that infect bacteria, is more widespread than previously believed, and they describe the pathways by which the alternative nucleotide is made and incorporated into phage genomes.

[...]

This opens up various questions like:
- is on this planet additional life, which we cannot detect?
- Is evolution as happening here really universal?
- Aliens could be a lot more different than we think


This is awesome, and I'm excited!

 

[Kyriakos]

Do those still use a 4-letter alphabet in their own genome? (just replacing one with another)
Also, even if they do, can both letters co-exist in a genome?

 

[Sarin]

Do those still use a 4-letter alphabet in their own genome? (just replacing one with another)
Also, even if they do, can both letters co-exist in a genome?

From the snippet, Z replaces A (adenine).

Quite an interesting find, though not as groundbreaking as the OP might suggest. Alternative genetic alphabets exist-in fact, our own cells use two, TACG for DNA, and UACG for RNA. But unlike U-T swap in our own cells, this stands out because Z actually binds differently than adenine it replaces. Which creates interesting compatibility issues and opportunities, as viruses hijack their host's cellular machinery for their own reproduction.

I believe that what we see here is interesting window to the "what if" of evolution. Evolution works by trying out stuff, and while most of it doesn't work, things that work well are retained. It's almost a certainty that in the primordial "soup", many variations on the genetic alphabets had arisen, but the UACG-later upgraded to TACG for stability-was most successful and overtook the others. But in these viruses, perhaps by combination of luck and advantage under certain conditions, one of these alternatives survived. It's quite analogous to how placental mammals overtook and pushed monotremes and marsupials to extinction on most continents, but they survived in and around Australia and in case of marsupials, also Americas.

 

[The_J]

There have been engineering attempts to add additional bases to a genome, and I know of one paper, where they managed to get a single base stably into a plasmid, but that is it so far for additional codes, from my knowledge. The DNA/RNA comparison cuts it only partially, since nearly all organisms use both (I forgot how exactly replication in positive-strand RNA viruses works , so maybe all).
But this is basically another system, and while comparable, is running in parallel.
I work with metagenomics, and there we always thought we'd get all the info from everything above a certain abundance threshold. Now we have no idea what we're missing. This is for me, work-wise, actually also a bit scary .
I'm still excited. I'll read the 3 papers over the weekend, I'm curious how this stuff would show up in our sequencing data, and if I could do something with it.

 

[Sarin]

There have been engineering attempts to add additional bases to a genome, and I know of one paper, where they managed to get a single base stably into a plasmid, but that is it so far for additional codes, from my knowledge. The DNA/RNA comparison cuts it only partially, since nearly all organisms use both (I forgot how exactly replication in positive-strand RNA viruses works , so maybe all).
But this is basically another system, and while comparable, is running in parallel.
I work with metagenomics, and there we always thought we'd get all the info from everything above a certain abundance threshold. Now we have no idea what we're missing. This is for me, work-wise, actually also a bit scary .
I'm still excited. I'll read the 3 papers over the weekend, I'm curious how this stuff would show up in our sequencing data, and if I could do something with it.

Code is one thing, how it's translated is another. Between DNA methylation, alternative translations and so on, even one code in one organism can be expressed in several ways. Prokaryotes and eukaryotes will "read" and express the same DNA sequence differently.

Here, we see different thing. A transcription/translation apparatus within host cells that can accommodate more than one code. I'd like to know how much do these phages bend the host's metabolism to produce and integrate into DNA synthesis the Z base and whether the flexibility they exploit is a vestigial remnant of times when their ancestors used a different code.