Back to Shapiro: how some bacteria handle DNA (Evolution)

by David Turell , Wednesday, February 08, 2023, 15:53 (444 days ago) @ David Turell
edited by David Turell, Wednesday, February 08, 2023, 15:59

Very differently using Histones:

https://www.nature.com/articles/d41586-023-00334-4

"A startling discovery in bacteria suggests that some species have a bizarre way of packaging chromosomes and regulating gene expression — using proteins that, until recently, weren’t thought to exist in bacteria at all.

"In a preprint posted on bioRxiv on 26 January, researchers report the characterization of proteins called histones that, in two bacterial species, seem to bind together to coat regions of the bacterial chromosome1. This is completely different from the arrangement of histones seen in other organisms. For example, in organisms called eukaryotes, whose cells have a membrane-bounded nucleus, DNA winds around histones, rather than being encased by them.

"Although histones are vital tools for maintaining chromosome structure and controlling gene activity in eukaryotes and microorganisms called archaea, for years it was widely assumed that they did not exist in bacteria.

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"Eukaryotic histones are remarkably uniform in their structure and function — a consistency that can be frustrating for researchers who want to study histone evolution, says biochemist Karolin Luger at the University of Colorado Boulder. “If you want to get at the evolutionary origin, you can’t go to a ‘primitive’ eukaryote,” she says. “It already has everything.”

"The lack of diversity also raises questions for synthetic biologists in search of new ways to control gene expression, says Tobias Warnecke, a molecular evolutionary biologist at Imperial College London. “The fundamental composition of the chromatin and how gene expression works is very similar across eukaryotes and then you start wondering, ‘is that a frozen accident?’” he says. “Is there something special about histones that makes them unique, or can we build systems in a different way?”

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"When the researchers isolated the histone protein from B. bacteriovorus and analysed its structure, both on its own and while it was interacting with DNA, they were surprised to find that it did not behave like any known histones from archaea or eukaryotes. The bacterial histones came together in pairs that surrounded the DNA strand. Long chains of these could act as a shield around the DNA, a marked difference from their function in eukaryotes, in which histones group together to form a spool around which the DNA winds. “I was blown away,” says Luger.

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"As part of their study, the researchers surveyed thousands of bacterial genomes. They found histone-like proteins in about 2% of the genomes, which suggests that there will be many other systems to study. “People got excited and said ‘oh, bacteria weren’t supposed to have histones’,” says Warnecke. “But if you work on microbial evolution, you know that if you look hard enough, you’ll find some.'”

Comment: the theory that eukaryotes and Archaea are directly related in early evolution now has to accept that bacteria may be more directly related than thought. Note that the article does not mention Shapiro's work. It depends upon how much he did with histones, if at all. At least we now know how active histones are in editing.