Shapiro redux: bacteria make giant proteins (Introduction)

by David Turell , Monday, December 11, 2023, 21:16 (346 days ago) @ David Turell

To fight all:

https://www.nature.com/articles/d41586-023-03937-z?utm_source=Live+Audience&utm_cam...

"Jacob West-Roberts, a computational biologist at the University of California (UC) Berkeley, was scouring microbial DNA sequences for giant genes and discovered what he thought was a whopper: a gene encoding a protein made up of 1,800 amino acids. The average protein has a few hundred.

“'Wait till you see this,” responded his PhD adviser, UC Berkeley environmental microbiologist Jillian Banfield, and pointed out proteins longer than 30,000 amino acids, already known from sequencing data.

"Their team has now found dozens of even bigger proteins, including what might be the longest ever: an 85,000-amino-acid behemoth. The mega-molecules could help an enigmatic group of environmental microorganisms to feed on other microbial cells, the researchers propose. They describe their findings in a preprint posted on bioRxiv1 last month.

“It’s a good study,” says Brian Hedlund, a microbiologist at the University of Nevada, Las Vegas. “They essentially doubled the size of the largest known predicted proteins from 40,000 to 85,000 amino acids, which are all insane.”

***

"Giant proteins were especially common in Omnitrophota, a bacterial phylum first discovered in Yellowstone National Park in the northern United States in the 1990s and now commonly found in environmental samples. In total, the researchers found 46 Omnitrophota genes encoding proteins longer than 30,000 amino acids, including the 85,804-amino-acid-colossus, which turned up in waste water. “They were just absolutely everywhere,” says West-Roberts.

***

"Genome sequencing identified a gene predicted to encode a protein nearly 40,000 amino acids long, and matching protein fragments turned up in a biochemical assay. Harder’s team might even have caught a glimpse of the giant in electron micrographs of the Omnitrophota cells, which seemed to show them attacking and devouring other bacteria and microbes called archaea.

***

"The AI predictions of the proteins’ structures revealed more cell-wall-binding regions, but also a big surprise: a very long tube-like apparatus unlike anything researchers have ever seen. This structure could be involved in delivering molecules to prey, or could attach to other cells before the host microbe devours them.

***

"The fact that giant proteins are so common in Omnitrophota is especially surprising because of the microbes’ tiny physical size, says Oleg Reva, a bioinformatician at the University of Pretoria in South Africa. The study shows that giant proteins are “sophisticated weapons wielded by the diminutive microbial hunters in their pursuit of bacterial and archaeal prey”, he adds.

"The discovery of genes encoding proteins as longer than 85,000 amino acids does not mean that the molecules exist in this state in cells, researchers say. One possibility is that the protein is chopped into smaller pieces after it’s made, and these portions take on a range of functions in cells. That could explain why Harder’s team was able to find only pieces of its giant protein. “Currently I don’t see experimental evidence that these large proteins exist,” Harder says.

"Many of the giant proteins contain protein-breaking enzymes called peptidases, which could chop the Goliaths down into Davids, West-Roberts and his team say. Firm answers might require researchers to grow Omnitrophota cells, something that only Harder’s team has managed to do so far. “All the others, they’re just imaginary,” says Harder. “There’s a lot of mystery to solve.'”

Comment: I carefully looked for a reference to Shapiro in all the references. None. A shame. I assume God helped with the DNA editing as the molecules are so large.