Research from Prof. Shraga Schwartz's lab at the Weizmann Institute of Science reveals how hyperthermophiles add hundreds of editing modifications to ribosomal RNA – methylation and acetylation that work together to stabilize the structure – and offers new explanations for the effectiveness of RNA-based drugs and technologies.
To survive, you have to change, and those who have already cracked this billions of years ago are single-celled organisms that live in high temperatures. In recent decades, research into their adaptive mechanisms has yielded revolutionary technologies such as rapid DNA replication (PCR), the production of heat-resistant proteins, and even the production of fuels and chemicals. The most impressive of all are hyperthermophiles – creatures whose home is volcanic craters, underwater volcanic fissures, and hot springs, places where the temperature is higher than 80 degrees Celsius. A new research method developed by scientists at the Weizmann Institute of Science has revealed how hyperthermophiles re-edit the RNA molecules at the core of their ribosomes – the cellular protein-production factories – in order to survive at high temperatures. The findings from Prof. Shraga Schwartz, ThatPublished in the scientific journal Cell, undermine the notion that basic life processes are uniform across species and across the lifespan. These findings may allow for improved RNA-based medical and industrial technologies, and they solve some of the mysteries surrounding a long-standing mystery in the field of drug development.
The ribosome is one of the most ancient and basic biological structures and is common to all kingdoms of life – archaea, bacteria and eukaryotes. More than 60 years ago, it was discovered that ribosomal RNA molecules undergo chemical "editing" (modifications) after they are produced in the cell. However, due to the difficulty of measuring these changes, it was not known to what extent they vary between species or depending on environmental conditions. "Until recently, mainly based on studies in yeast and humans, it was believed that RNA editing was uniform in ribosomes of different individuals of the same species and did not vary depending on the environment," explains Prof. Schwartz from the Department of Molecular Genetics at the Institute. "However, in recent years, evidence has accumulated in a handful of species that editing can sometimes be dynamic and allow the ribosome structure to adapt to the environment. The difficulty in conducting a large-scale study to confirm this concept stemmed from the large number of types of repairs, the difficulty in identifying them, and the limitations of existing methods, which usually allowed testing a single type of repair in one sample at a time."
"It turned out that the warmer a creature's natural environment, the more editing it does."
A new method developed in Prof. Schwartz's laboratory, led by Dr. Miguel A. Garcia Campos, allows for the simultaneous examination of 16 different types of editing modifications in dozens of RNA samples and is propelling the study of RNA editing forward. Using it, the scientists mapped the editing modifications in 10 single-celled species for the first time and compared them to four previously studied. They specifically selected species that survive in extreme environmental conditions, including three hyperthermophilic species, with the idea that if the ribosome has an adaptation mechanism to the environment, it would be found in them. "While most bacteria and archaea are content with a few dozen modifications in ribosomal RNA, in the hyperthermophilic species we found hundreds of editing modifications," describes Prof. Schwartz. "In fact, it turned out that the warmer an organism's natural environment, the more editing modifications it performs."
After finding a difference between species with different habitats, the scientists tested whether the same species was able to re-edit its ribosomal RNA – and thus change the structure of the ribosome – in response to changes in the environment during its life. To do this, each species was grown in three to five different environmental conditions. In unicellular organisms living at normal temperatures, most of the editing changes were constant and did not depend on the growth conditions. In contrast, almost half of the modifications in hyperthermophiles were dynamic and occurred at more sites in the RNA molecules as the temperature increased. The scientists concluded that changes in the structure of the ribosome are not only possible – they are an important adaptive mechanism.
The scientists identified three types of modifications that increased in frequency systematically and widely with increasing temperature. "A particularly surprising discovery was that one of these modifications – the addition of a methyl group (methylation) – appeared in hyperthermophilic species almost always with another modification – the addition of an acetyl group (acetylation)," says Prof. Schwartz. "This raised the hypothesis that the modifications work together. We joined the group of Prof. Sebastian Glatt from the Jagiellonian University in Krakow, and examined the stability of an RNA molecule without modifications, after the addition of one chemical group, methyl or acetyl, and after the addition of both. Both methylation and acetylation have been found to have a stabilizing effect on RNA, but when they work together, the whole is greater than the sum of its parts."
What was not yet clear was how the editing changes the structure of the ribosome. To test this, the team of researchers joined Prof. Moran Shalu Ben-Ami from the Department of Structural and Chemical Biology at the Institute, who performed cryo-EM single-particle electron microscopy and mapped a ribosome from a hyperthermophilic archaea. The scientists mapped the structure in two states – when the enzyme that performs methylation at high temperatures is active and when it is silenced. The scientists discovered that the methyl groups that are added at high temperatures are distributed throughout the ribosome and form a variety of weak bonds with surrounding molecules, which together strengthen the structure. They also identified that in areas where editing corrections were made, there are fewer spaces in the ribosome, so that “holes” in the structure have been filled.
The new findings reveal a sophisticated mechanism by which subtle chemical changes to an RNA molecule can dramatically improve its structural stability and enable it to function in a changing environment. In doing so, they provide a possible solution to the mystery of the “magic methyl” – the unexplained more than 100-fold improvement in the efficacy of some drugs observed when a methyl group is added.
"It is now becoming possible that at least some of the editing changes along an RNA molecule – such as methylation and acetylation – are not isolated from each other, and that we should try to decipher them as a continuous code," says Prof. Schwartz. "Our research on ribosomal RNA contributes to understanding the relationship between different editing changes, and the method we have developed will accelerate and expand the study of many types of changes and new species."
“Many RNA-based technologies are currently on the market or in development – from vaccines against epidemics, to cancer tests and treatments, to tools for gene editing in the biotechnology and medical industries,” he adds. “The natural RNA editing process has undergone billions of years of refinement, and unlocking its secrets could enable the development of more reliable and efficient RNA-based technologies.”
Also participating in the study were Joe Georgeson, Dr. Ronit Nir, Dr. Vinitra Iyer and Dr. Anatoly Kostanovich from the Institute's Department of Molecular Genetics; Dr. Robert Reichelt, Dr. Felix Grunberger, Nicholas Alexander, Prof. Sebastian Pereira-Serka and Prof. Dina Grohmann from the University of Regensburg, Germany; Dr. Kristin A. Flock, Prof. Brett W. Burkhardt and Prof. Thomas J. Santangelo from Colorado State University; Dr. Donna Matsov from the Institute's Department of Structural and Chemical Biology; Dr. Lauren Lowy from Lawrence Berkeley National Laboratory, California; Dr. Sophoni Thallah Gamage, Dr. Sherin A. The authors are: H. O. H. Manage and Dr. Jordan L. Meyer of the National Cancer Institute, Frederick, Maryland; Dr. Milan Jerobeck and Prof. Jörg Vogel of the University of Würzburg, Germany; Dr. Yoko Nobi and Prof. Masato Touka of Tokyo Metropolitan University (TMU), Japan; Jakub S. Nowak of the Jagiellonian University, Krakow, Poland; Manoj Ferreira, Alexander Apostel and Dr. Shiyu Fang of Michigan Technological University (MTU), Houghton, Michigan; Dr. Gil Yona of the Institute's Department of Life Sciences Research Infrastructures; and Prof. Eric Westhoff of the Institute of Molecular and Cellular Biology (IBMC), Strasbourg, France.
More of the topic in Hayadan:
