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The faults in our RNA

DNA has long been in the spotlight. Faulty genes are responsible for diseases that continue to evade the best that medicine can throw at them. But less attention is paid to problems with its final products, the proteins that are produced in huge numbers after genetic instructions are read and acted on. When protein production goes wrong, the consequences can be as devastating as faulty genes. To tackle this our cells have a sophisticated quality control process that kicks into action to clear up the mess. Yet we know little about how this works. The answers not only offer insights into one of the most fundamental processes of life, but could help to reveal the connections with a growing list of diseases.

The genomic revolution has led to enormous advances in understanding DNA, the instruction manual for life that’s found in every cell in our body. Home genetic-testing kits promise to tell us everything from our chances of developing deadly diseases, to the secrets of our ancestry and even the lifestyle we should adopt to stay healthy. Yet learning to read our genetic code is only part of the story. 

Whilst DNA is the blueprint for life, these instructions must be read and converted into biological action. The finished products, called proteins, are the workhorses that carry out the huge range of functions needed for life. Proteins make up the structures in our muscles and bones, the hormones that send signals around our body, the enzymes that help us digest food and the antibodies that defend against invading viruses.

Protein Production

RNA glass art: RNA World exhibition, Royal Botanic Garden Edinburgh
RNA glass art: RNA World exhibition, Royal Botanic Garden Edinburgh

To build proteins, long strands of DNA code must first be copied into another molecule called messenger RNA. This process, called transcription, allows genetic information to be transported from the centre of the cell, where it is kept safe from damage, to outer reaches of the cell where proteins are made. During this process RNA strands can be rearranged to make an enormous catalogue of protein products, whose numbers far exceed our library of genes.

In the next stage, called translation, RNA strands are read and decoded by molecular factories called the ribosomes. Ribosomes slide along the RNA and build proteins from smaller building blocks, called amino acids, adding one at a time depending on the RNA’s instructions. The processes involved in protein production are central to the functioning of all life and have serious consequences if they go wrong. Mistakes during translation, or in the creation of ribosomes, cause a number of rare and incurable hereditary diseases, ranging from anaemias to growth retardation syndromes.

Ribosome Stalling

Our work, published in Nature Communications, explores one particular problem encountered during translation. Occasionally ribosomes get stuck on messenger RNA strands, for example when they are damaged. If this fault, called ribosome stalling, is not detected and corrected then it becomes dangerous in several ways. 

Like a robot working in a factory, the ribosome operates on a production line. If it is stalled on one strand of RNA it cannot make any other proteins. To make matters worse, if the ribosome stalls before it has finished translating the strand of RNA, it creates shorter protein fragments. These proteins may not work properly and can be toxic to the cell. Short, faulty pieces of protein can form aggregates, similar to those that cause Alzheimer’s or Parkinson’s disease. 

Quality Control Process

To prevent this, cells have developed ways to detect and remove stalled ribosome-RNA complexes. This quality control process is vital and found in many living things from simple yeast cells, to humans. It detects and recycles stalled ribosomes and destroys the damaged RNA, as well as any potentially toxic protein products. 

This process is a recent discovery and we do not fully understand how it works. However, we do know that it is particularly important in neurons. Failure of the quality control process leads to neurodegeneration in mouse models, and we expect similar effects in humans, although more research is needed in this area. 

“The process of removing stalled proteins during production is found throughout nature, so we know that it is of fundamental importance to life. Greater knowledge of how this occurs could potentially aid progress in the understanding of many diseases.”

Marie-Luise WinzSchool of Biological Sciences

Yeast Study

In our study, we focused on a key player in this quality control mechanism, a protein called Hel2, which recognises stalled ribosomes and triggers the quality control process. We used common baker’s yeast - Saccharomyces cerevisiae – as a simple model organism to better understand this protein. 

Previous studies had found that Hel2 makes contact with RNA, but it was unknown where these interactions are located, or whether they are important. In our study, we used UV-light to freeze contact points between RNA and the protein. We found a region of Hel2 that directly interacts with messenger RNA strands, and identified the RNAs that are contacted. We also discovered that Hel2 forms physical contact points with ribosomes that helps to recognise when they have stalled.

What surprised us is that Hel2 had hardly any interactions with the beginning of messenger RNA strands, but had much more contact towards the end, where ribosomes should normally be released. The protein also seemed to act indiscriminately, moving between many different RNA strands. This suggests that Hel2 has many short-lived interactions with ribosome-RNA complexes to check for stalling. 

To find out if this was correct, we removed the part of Hel2 involved in making physical contact with RNA. This prevented both the destruction of faulty messenger RNA and its protein products - showing that Hel2 contact with RNA is crucial for the quality control process to function correctly.

The Future

Our study is an important step in understanding the starting point for this vital quality control mechanism but it still leaves many questions unanswered. We have more to learn about how recognition of stalled ribosome complexes is regulated, why Hel2 does not make contact with the early parts of messenger RNA strands and how stalled ribosomes are distinguished from non-stalled ones. The answers will not only provide insights into a fundamental process found throughout nature but could potentially aid understanding of many diseases.

 

Marie-Luise Winz, Postdoctoral Research Associate  
Tollervey Lab, Wellcome Centre for Cell Biology

 

Related Links

Press release: Protein study may aid understanding of diseases

Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control, Nature Communications

Tollervey lab website