It's a tough world for microbes. When resources grow limited and environments worsen, microbes have figured out ways to hunker down and go dormant until conditions improve.
However, scientists have discovered a tiny new protein that appears to play a significant role in allowing 'hibernating' yeast cells to resume normal metabolic operations when it's safe to do so, providing a new clue to organisms' adaptability.
In a recent study published in Nature, scientists from EMBL and the University of Virginia in the U.S. described their discovery of a protein, which they named SNOR because of its role in waking a dormant cell when environmental conditions improve. Thanks to advanced imaging and molecular biology techniques, scientists were able to identify a previously uncharacterised protein and determine its vital role in coping with inhospitable environments.
"Dormancy is much more common than you would think in microbial life, as microbes rarely have unlimited resources and nutrients to grow," said Simone Mattei, who heads EMBL Imaging Centre's Electron Microscopy Team. "This study is about how protein synthesis is regulated during dormancy, also known as cellular quiescence."
The research piggybacks on earlier findings related to how cells react to starvation. The researchers found that ribosomes in S. pombe yeast cells would surround the cell's mitochondria when faced with glucose deprivation. However, they still didn't understand the ribosomal regulation, nor what happened when glucose was available again, which caused cells to resume normal operations.
The new research sought to answer these questions. Normally, in structural biology, scientists purify macromolecular complexes to determine their structure with methods like X-ray crystallography or cryo-electron microscopy (cryo-EM). By introducing in situ cryo-ET, which can actually reconstruct a 3D-view of ribosomal structures inside cells, the scientists could see that, compared to the purified samples, ribosomes inside the cell were binding other factors, even if the resolution they could resolve the ribosome's structure was lower. So they knew there was something there, but could not see what it was. In other words, even at lower resolutions, they could tell that after purification, they weren't seeing everything that was there.
In the current study, using a much larger cryo-ET data set than previous studies, the researchers saw in significantly greater detail the ribosome structure within the cell. This pointed them towards a protein sitting at the "catalytic core of the ribosome", as Mattei describes it. By resolving the ribosome map at such high resolution, they could clearly identify this new protein – an approach called visual proteomics. Visual proteomics combines protein data with advanced imaging to show where proteins are located inside cells, often in 3D maps.
"The exciting part is this technical aspect," Jomaa said. "You can literally find new proteins bound to the ribosomes just by looking at them. At such high resolution, you identify their sequence from the map and then validate these findings with biochemical studies. In our case, we found this uncharacterised protein had not yet been described as being involved in synthesising proteins or metabolism. However, our experiments demonstrated its key role in cell dormancy. That's how we came to name it SNOR."
The scientists confirmed that SNOR was involved in slowing down protein synthesis by expressing SNOR in the midst of translation. While SNOR lowered translation efficiency, it didn't abruptly spark dormancy. Clearly, other proteins that are hibernation factors – in particular, eIF5A – were involved too.
The big surprise came when scientists provided glucose back to starved cells in which SNOR was knocked down and saw that ribosomes were unable to restart protein synthesis without it. SNOR presence was essential for ribosomes to promptly restart protein synthesis within 30 minutes of resuming glucose availability.
Next steps
Of course, with every discovery, new questions unfold. In this case, the researchers are eager to understand what first 'awakens' SNOR to signal the rest of the cell to restart protein synthesis.
"We have a few ideas about what might be at work, but the answer isn't clear," Mattei said. "Maybe it's a signalling pathway triggered by the change in glucose levels, but it's important to know not just that the mechanism exists, but how it is triggered naturally and if we can manipulate that trigger, such as preventing cancer cells from restarting their growth after a period of dormancy."
Additionally, with funding from the U.S. National Science Foundation and the German Research Foundation (DFG), the collaborators have also begun working to better understand the signalling pathways and mechanisms that drive cellular protein synthesis restarts. They are also returning to their earlier work to better understand why ribosomes swarm around the mitochondria in these same deprived states.
The bigger picture
While SNOR is only found in yeast and other fungi, Mattei notes that at this point, it would be interesting to explore other organisms and factor in evolutionary considerations.
"Certain plants produce spores and need to germinate at a precisely specified point in time. Organisms often use hibernation as a way to control their rate of development, waiting for the right environment," he said. "We may not find SNOR in these other organisms, but quite possibly other factors have the same function, where we could see how they too cope with stressful conditions, disease, or other challenging environments.
Scientists are increasingly interested in how organisms adapt to changing environments. The concept of lowering metabolic levels to a sustainably viable state in light of new conditions is not new, but according to Mattei, it's particularly relevant at this moment as climate changesrequire increasing levels of adaptation. They hope that these findings will shed light on how life adapts to extreme conditions, with broader implications for medicine, agriculture, and biotechnology.
"Hibernation is one clear example of how the self adapts and survives," Mattei said. "This is of fundamental relevance. After all, we are all here today because we survived."
