A new study by CSIR-Centre for Cellular and Molecular Biology indicates that minor mistakes while synthesising proteins can be advantageous for cells under stress by enabling them to sense and react to toxic molecules. This establishes how nature achieves precision and yet remains flexible, enabling cells to evolve and modify themselves even in very adverse conditions by way of precision-tuned molecular mechanisms.
About 3.5 billion years ago, when the first living cells formed on earth, the weather conditions were far from pleasant. The ancient earth was bombarded with ultraviolet radiation and faced extreme temperatures. Such conditions are known to produce molecules broadly categorised as Reactive Oxygen Species (ROS) in cells. They help cells survive the stressful conditions successfully. However, their overproduction can also damage cells in various ways. One such adverse outcome is disruption of protein synthesis in cells.
A new study from Rajan Sankaranarayanan’s lab at CSIR-Centre for Cellular and Molecular Biology, Hyderabad, suggests that minor errors in protein synthesis under stress might benefit cells. These mistakes might help cells detect the overproduction of ROS in cells and activate protective mechanisms in response.
Sankaranarayanan’s team looked at the functioning of enzymes called aminoacyl-tRNA synthetase (aaRS), which help in protein synthesis. Proteins are made of twenty different amino acids, one attached to the other in specific sequences. And for each amino acid, there is a corresponding aaRS that carries the specific amino acid and catalyses its addition to a protein being formed in a cell. Sometimes, aaRSs can pick the wrong amino acids. However, these enzymes have in-built editing domains that identify such mistakes and correct them.
In this study, the scientists studied functions of editing domains of two structurally very similar aminoacyl synthetases — one that picks amino acid alanine (called AlaRS) and the other for threonine (called ThrRS). Among proteins, similar structures generally suggest similar functions. However, these two enzymes exhibited discrepancies in their editing functions. In presence of ROS, ThrRS is more prone to attach the wrong amino acid than AlaRS.
The scientists sought reasons for this discrepancy in the structures of the two enzymes. The atomic images of their structures revealed that the editing domain of AlaRS binds to a zinc ion.
The zinc ion in the editing domain of AlaRS is universally conserved, i.e., the AlaRS of all life forms on earth, from bacteria to humans, binds a zinc ion at this spot. Yet, it was surprising to note that such a ubiquitous zinc ion in AlaRS could not be ascribed to any of the functions that a metal ion in a protein are generally known for, such as in supporting the structure, or a role in catalytic activity,”
said Jotin Gogoi, first author of the study.
Instead, the study found that the zinc ion protects the catalytic function of AlaRS from ROS in cells under stress. That is, despite stressful conditions in a cell, AlaRS consistently selects alanine and no other amino acid.
This is where ThrRS differs. The scientists found that the editing domain of ThrRS does not bind to a zinc ion even though it carries a pocket structurally similar to AlaRS. They found a critical difference in one position in the protein that subtly influences the structure of the ThrRS preventing the zinc ion to bind anymore. The scientists propose that the absence of zinc ion compromises the editing abilities of ThrRS under stress. This means that when ThrRS binds a wrong amino acid, the error goes unnoticed by its editing domain leading to the incorporation of an incorrect amino acid into the newly formed protein.
Sankaranarayanan said,
It is clear that the editing functions of both AlaRS and ThrRS have existed at least since LUCA, with their discrepancy in binding to zinc ion.” LUCA refers to the Last Universal Common Ancestor, a hypothetical ancestor of all life forms today.
Not only that, the scientists also suggested that the mistakes made by ThrRS in protein translation help in making a more statistical proteome in cells. Sankaranarayanan explained, “Stochastic errors in protein translation processes give rise to more variety in the same proteins. These variants are called statistical proteins. Higher number of statistical proteins increases the chances of survival under differing environmental stresses albeit with slower growth. But too many of them can also cause cell death.”
Such mechanisms help cells to operate on a lean model within a range of stable structures of proteins. Every time a protein is made, there is a possibility that subtle changes are brought about in their composition and structure. These changes often preserve structural stability of the protein, and some may alter the functions of proteins. If the changes prove to be beneficial, they subsequently dictate necessary changes in genes to make them more permanent.
Deepak Nair, Professor at Regional Centre of Biotechnology, Faridabad, an expert in the study of enzymes and not associated with the study, substantiated this point. He noted, “The study sheds light on how the protein synthesis apparatus balances the conflicting needs of high-fidelity and a limited amount of error to enable evolution in the presence of stress. The observed differences in the two synthetases also represents a good example of how, even with the same core structure, changes in a few key amino acids in proteins can result in new chemical attributes that have considerable impact on their function in biology.”