When bacteria die, their bodies rupture and spill a buffet of nutrients for neighboring microbes. The live cells feast on molecules served by their dead counterparts and in turn become a meal for others when they die, continuing the nutrient recycling process.1
However, bacteria are picky eaters: They cannot take up large molecules such as proteins, which must be broken down into amino acids and smaller peptides by protease enzymes. Given this, scientists have been trying to better understand how microbes scavenge and process nutrients from their dead neighbors.
Now, researchers have shown that Escherichia coli encode an enzyme that helps break down their protein content when they die so neighboring bacterial cells can dine on the remains.2 The results, published in Nature Communications, highlight a novel postmortem biochemical mechanism and offer deeper insights into nutrient recycling.
“We sort of think of death as being the end,” said Martin Cann, a biochemist at Durham University and a study author. “What this demonstrates, at least in this bacterium, is that…it's been genetically encoded that after death there is at least one enzyme that still has a functional role to play in an ecosystem.”
Initially, Cann’s work focused on carbon dioxide sensing in microbes and other organisms. In 2019, he attended a talk by Wilson Poon, a theoretical physicist at the University of Edinburgh and study coauthor, about the physics of death, which inspired Cann to venture into a new area of nutrient recycling research. Poon presented a hypothesis about the optimal way for an organism to die for it to be used by other organisms. Intrigued by the theory and lack of experimental evidence supporting it, Cann joined forces with Poon soon after to investigate the phenomenon in bacteria.
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Bacterial death is necessary in nutrient recycling, a widespread occurrence among bacteria. To explore its underlying mechanism, the researchers selected E. coli. They examined the effect of E. coli-derived dead cell material—lysate—on live E. coli cells. Live cells treated with the lysate showed enhanced growth compared to water-treated controls.
Cann and his team hypothesized that proteins released by dead cells were a feast that encouraged live cell growth. Since bacteria cannot take up entire proteins, the researchers investigated how enzymes sliced up proteins into a usable nutrient source for living bacteria. The next question they faced was whether these enzymes came from living cells or the dead ones.
From Poon’s hypothesis, Cann thought that the source of enzymes came from dead cells. They used an E. coli strain lacking the two important proteases: Lon and outer membrane protease T (OmpT). This cell lysate did not enhance live wild type cell growth, confirming the role of these enzymes in nutrient recycling.
To pinpoint the enzyme responsible, Cann and his team used the lysate of an E. coli strain lacking each of the proteases to feed live cells. While dead cells lacking OmpT enhanced live cell growth, the lysate obtained from Lon-null cells did not, suggesting that Lon protease degrades proteins released after death, making them accessible to other live bacteria.
Next, the researchers treated E. coli lacking Lon protease with the lysate of wild type E. coli. This enhanced growth of live cells, indicating that live cells do not require Lon protease for nutrient recycling; the enzyme plays a postmortem role.
This was a major paradigm shift, noted Cann. “We’ve moved from thinking about live organisms degrading the dead ones to dead organisms encoding [their] own breakdown after death.”
Cann and his team next investigated whether the Lon system comes at a cost to the cell when it is still alive. They observed that wild type cells with the Lon system grew more slowly, indicating a fitness cost, while Lon-null cells grew to a higher density. This prompted the researchers to investigate whether the enzyme offered any benefit to live cells.
Since Lon protease helps degrade harmful unfolded proteins produced under stressed conditions, the researchers subjected the cells to a heat shock.3 Heat-shocked wild type cells grew better than Lon-null cells, suggesting that in addition to a postmortem benefit, the enzyme provides a private benefit to the cells that produce it.
However, when Cann and his team cocultured Lon-producing cells with a small proportion of Lon-null cells, the latter population increased significantly, demonstrating that other cells can exploit Lon producers. Although the exploitation reduced under stressed conditions, the Lon system’s benefits to producers did not outweigh the costs.
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This prompted Cann and his team to question why such a system would evolve. “If we think about evolution, we think about evolution acting on organisms and their fitness that makes them better able to reproduce,” said Cann. “If we have a phenotype that manifests after death, how can something such as that arise through evolution?”
In their quest to find an answer, the researchers turned to Stuart West, an evolutionary biologist at the University of Oxford and study coauthor. West previously showed that natural selection favors a trait if it has positive effects on the success of an organism’s relatives, even if it incurs a high cost to the organism.4 Based on this, Cann and his team concluded that Lon protease production is a social adaptation that is likely to be partially explained by this theory of kin selection.
“This is a very well-rounded study,” said Sunil Laxman, a biochemist at the Institute for Stem Cell Science and Regenerative Medicine, who was not involved in the study. He noted that microbial culture media contain broken down proteins because cells cannot utilize whole ones. While he anticipated a protease’s role in postmortem nutrient recycling, he remarked that this study offers the first experimental evidence of this phenomenon.
The experiments were carried out under controlled lab settings, but Laxman believes that such a system would most likely operate in the natural environment as well. The next steps would be to expand the study to more enzymes and microbes, he said. “Various other microbes have various other proteases that are quite abundant, and presumably will be releasing those as their cells die.”
“Moving forward, we have to understand the extent of this mechanism in biology,” agreed Cann. His team hopes to manipulate such postmortem enzymes to enhance nutrient cycling in industrial bioreactors to improve recombinant protein yield.