Evolution: bacteriophages weird genome (Evolution)

by David Turell , Wednesday, May 05, 2021, 23:13 (1296 days ago) @ David Turell

A new paper on how Z appeared:

https://www.sciencenews.org/article/virus-dna-z-bacteriophage-genetic-alphabet-bond-life

"More than 40 years ago, scientists in Russia reported that a type of bacteriophage called cyanophage S-2L replaces the DNA building block adenine, commonly known as A, with 2-aminoadenine, designated Z. But no one knew how the phage went from A to Z, or why.

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"In the 1990s, Philippe Marlière, a xenobiologist then at the Pasteur Institute in Paris, was “looking for examples divergent from life as we know it,” when he came across the 1977 Russian study describing the cyanophage with the unusual DNA. After getting a sample of the virus, Marlière and colleagues deciphered the phage’s complete set of genetic instructions, or genome.

"In the virus’s genome, the researchers found instructions for building an enzyme, called PurZ, that could carry out the first step in making Z — also known as diaminopurine. The Pasteur Institute filed a patent on the enzyme in Marlière’s name in 2003.

"With the enzyme in hand, “it became crystal clear how Z was made, but we didn’t [do] any experiments to prove that we were right,” says Marlière,

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"Indeed, this phage’s polymerase isn’t what he was looking for. Marlière’s collaborator Pierre Alexandre Kaminski and colleagues found that cyanophage S-2L’s polymerase isn’t picky about using A or Z. Instead, another viral enzyme called DatZ degrades adenine building blocks, leaving the polymerase no choice but to use Z, Kaminski, a biochemist at the Pasteur Institute,

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"The Siphoviridae bacteriophages that infect a wide variety of bacteria all have versions of the polymerase, called DpoZ, that preferentially insert Z instead of A into the viruses’ DNA, the researchers report. Marlière has filed a patent on the enzyme.

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"Just because the phages have the enzymes, they don’t necessarily use Z in their DNA. So Zhao and colleagues in China chose a phage called SH-Ab 15497 that infects Acinetobacter bacteria, and confirmed that its DNA alphabet also has Z in place of A, his team reports.

"Why phages would bother with the unconventional DNA was still unknown. One hypothesis is that replacing A with Z is a countermeasure against bacterial defense enzymes, known as restriction enzymes, that chop up DNA from invading phages. Such enzymes have a hard time recognizing and cutting DNA containing Z bases, Zhao and colleagues found. “The phage is trying to avoid being destroyed by the host,” he says. “This is really a protection mechanism for the phage.”

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"It’s debatable whether Z-containing phages are new forms of life (not to mention the ongoing debate about whether viruses are alive), says Floyd Romesberg, a synthetic biologist at the global pharmaceutical and biotechnology company Sanofi’s site in La Jolla, Calif. But it does open up new possibilities, he says, for what life is, was, and could become.

“'Life isn’t exactly what we thought it was. Life doesn’t have to be GTAC,” he says, referring to the four letters of the standard DNA alphabet. “What it says is that life can be more diverse.'”

Comment: This is all part of the ecosystem between bacteria and bacteriophages. In my view all ecosystems are important in the natural balances they create. That is why I point out their importance and ow they fit into the giant evolved bush of life. This is another discovery like Archaea. It makes one wonder, how many strange forms of life are still out there to uncover.