“Adapt or perish, now as ever, is nature’s inexorable imperative,” wrote H. G. Wells. This principle – that survival requires change – was mastered billions of years ago by single-celled organisms living in extreme heat. Over the past few decades, studies of these organisms’ adaptive mechanisms have yielded revolutionary technologies – from rapid DNA replication (PCR) and the production of heat-resistant proteins to the generation of fuels and chemicals.
The most remarkable of these organisms are hyperthermophiles, which inhabit volcanic craters, hydrothermal vents and hot springs – environments where temperatures exceed 80 degrees Celsius. A new method developed by Weizmann Institute of Science researchers reveals how hyperthermophiles modify the RNA molecules at the core of their ribosome – the cell’s protein production factory – to survive in extremely hot environments. Findings from Prof. Schraga Schwartz’s lab, recently published in Cell, challenge the assumption that fundamental life processes are uniform across species and throughout life. These findings may lead to improved RNA-based medical and industrial technologies and shed light on a long-standing mystery in drug development.
“”In fact, we saw that the hotter an organism’s natural environment, the more modifications its ribosome undergoes”
The ribosome is one of the earliest and most basic biological structures, shared by all three domains of life: Archaea, Bacteria and Eukaryotes. In the late 1950s, researchers discovered that ribosomal RNA molecules undergo “chemical editing” (modification) after they are produced in the cell. Yet, because such changes were difficult to measure, it remained unclear how much they varied between species or in response to environmental conditions.
“Until recently, it was widely assumed, mainly based on research in yeast and humans, that RNA modification in the ribosome was uniform among all members of a given species and did not change with the environment,” explains Schwartz, of Weizmann’s Molecular Genetics Department. “However, in recent years, evidence has emerged in a few species suggesting that modification can sometimes be dynamic, allowing the ribosomal structure to adapt to the environment. Still, confirming this on a large scale was difficult due to the sheer number of modification types, the challenge of identifying them and the limitations of existing methods, which typically allowed researchers to examine only one modification type per sample and only one sample at a time.”
The new system, developed in Schwartz’s lab under the leadership of Dr. Miguel A. Garcia-Campos, enables scientists to examine 16 modification types across dozens of RNA samples – a major leap forward for RNA editing research. Using this system, the researchers mapped modification patterns in 10 single-celled organisms and compared them with four previously studied species. They deliberately prioritized extremophiles – organisms that thrive in various harsh environments – including three hyperthermophiles, hypothesizing that ribosomal environmental adaptation mechanisms were more likely to have emerged in these organisms.
“While most bacteria and archaea manage with only a few dozen ribosomal RNA modifications, we found hundreds in hyperthermophilic species,” Schwartz notes. “In fact, we saw that the hotter an organism’s natural environment, the more modifications its ribosome undergoes.”
Having observed differences between species from different environments, the researchers next asked whether a species could re-edit its ribosomal RNA – thus altering the structure of its ribosome – in response to environmental changes during its lifetime. To test this, they grew each species under three to five different conditions. For mesophiles, microorganisms that thrive in moderate temperatures, most modifications were permanent and did not vary with the environment. In contrast, nearly half of the modifications in hyperthermophiles were dynamic, occurring at more sites on the RNA molecules as the temperature rose. The researchers concluded that changes in ribosomal structure are not only possible but constitute an important adaptive mechanism.
Specifically, three modification types were found to consistently become more frequent as temperature increased. “One particularly surprising finding was that one of these modifications – the addition of a methyl group, or methylation – almost always appeared in hyperthermophilic species together with another modification: the addition of an acetyl group, or acetylation,” says Schwartz. “This suggested that the two work in concert. We teamed up with Prof. Sebastian Glatt’s group at Jagiellonian University in Kraków to test the stability of RNA molecules with neither addition, with one or the other, and with both. Both methylation and acetylation had a stabilizing effect on RNA, but when combined, the effect was greater than the sum of its parts.”
What remained unclear was how this chemical editing changes the ribosome’s structure. To find out, the researchers joined forces with Prof. Moran Shalev-Benami’s team in Weizmann’s Chemical and Structural Biology Department, which used cryo-electron microscopy to map the ribosome of a hyperthermophilic archaeon. They mapped the structure in two states: when the enzyme responsible for methylation at high temperatures was active, and when it was silenced. The methyl groups added at high temperatures were found to be distributed across the ribosome, forming weak bonds with surrounding molecules that together strengthened the overall structure. Likewise, regions where editing occurred contained fewer gaps, effectively “plugging holes” in the ribosome.
These findings reveal a sophisticated mechanism in which subtle chemical changes to RNA molecules can markedly enhance the ribosome’s stability, allowing it to function in changing environments. They may also help explain the long-standing “magic methyl” phenomenon – an unexplained more-than-hundredfold increase in the potency of some drugs after the addition of a methyl group. “It now seems likely that at least some modifications along an RNA molecule – such as methylation and acetylation – don’t act independently, and need to be deciphered as a combinatorial code,” Schwartz says. “Our study of ribosomal RNA helps clarify the interplay among different modifications, and the method we developed could accelerate and expand the study of many modification types and new species.”
“There are now many RNA-based technologies on the market or in development – from vaccines against pandemics and cancer diagnostics and therapies to gene-editing tools used in biotechnology and medicine,” he adds. “The natural RNA-editing process has undergone billions of years of refinement, and uncovering its secrets could pave the way for more reliable and efficient RNA-based technologies.”