Genome complexity: bacteria have histones (Introduction)

by David Turell , Thursday, February 16, 2023, 02:05 (437 days ago) @ David Turell

Now definite:

https://www.the-scientist.com/news-opinion/bacteria-have-histones-after-all-study-70951

"With the exception of two known proteins, bacteria are generally thought to lack histones, having evolved an independent set of DNA-folding histonelike proteins instead. As evolutionary biologist Tobias Warnecke at the LMS London Institute of Medical Sciences explains, bacterial DNA-packaging proteins have 3D structures that are “clearly distinct.” Still, the general absence of histones in bacteria is puzzling given that bacteria exchange genes with archaea and eukaryotes—a process called horizontal gene transfer—and could have adopted more histones in this way.

"Now, Warnecke and colleagues are challenging the idea that these space-saving proteins are not commonplace in bacteria. In a preprint uploaded to bioRxiv this January that has yet to undergo peer review, the team describes hundreds of potential histone proteins in bacteria, including one that they predict interacts with DNA in an unusual way.

***

"The team detected a histone fold in an uncharacterized B. bacteriovorus’ protein called Bd0055 and wondered if this protein could help orchestrate DNA packaging. By observing that, in the presence of the protein, DNA moved much slower through pores in a gel, they confirmed that Bd0055 binds DNA. Deleting the gene turned out to be lethal in B. bacteriovorus cells both inside and outside prey bacteria, indicating that the protein is essential throughout the lifecycle.

"With all evidence thus far suggesting Bd0055 could be a typical histone protein, the team set out to determine if Bd0055 forms spools for DNA to wrap around. Computer simulations carried out by Shawn Laursen at the University of Colorado Boulder revealed that the protein-protein interactions that are needed to form spools would be unstable for this protein. Instead, the simulations revealed that Bd0055 might bind to the outer edges of DNA strands. Warnecke has never seen other histones behave this way. “There’s really nothing like the edge-on binding,” he says.

"Rather than packaging the DNA to occupy less space, the authors argue that the edge-on binding could straighten the strands and protect the DNA from over-compression during division into smaller cells. Indeed, straightened DNA spirals have been observed in this bacterium. Nessa Carey, a molecular biologist who works on histones and was not involved with the study, agrees, noting that “it’s a possible interpretation” but also wonders if the protein may have a shielding action against bacteriophages or arsenal in the prey bacterium. The protein could be “making DNA harder to get at and attack.”

"While Dame is intrigued by the findings, he notes that the function of the protein needs to be confirmed inside cells. Carey says that it’s “incredibly thorough structural work” but mentions that the lethal outcome of deleting the histone is unfortunate: “If all you get is a lethal phenotype, it tells you it’s important, but it doesn’t tell you why.” She proposes that more sophisticated genetic variants will be needed to build on these findings.

"B. bacteriovorus is known to have exchanged genes with a distant relative, Leptospira interrogans, in the past, and the researchers found a similar histone protein in this species. Laursen says he plans to investigate this histone next. His supervisor, Karolin Luger, tells The Scientist in an email that because Leptospira histones share many features with Bd0055, the team suspects they might bind DNA “in the same unorthodox manner,” but there are also “intriguing differences.”

Comment: histones are found but too early for a full story. Since bacteria don't store DNA in a nucleus it must be a different mechanism= for DNA control.