Prior to this, people had always believed that RNA and protein only interacted briefly during cellular processes. In a new study, researchers from the Max Planck Institute of Land Microbiology in Germany found that this is not the case: bacterial viruses, also known as bacteriophages, “bind” specific RNA to host proteins during the developmental cycle. This chemical modification, called RNAylation, may open up new avenues for phage therapy or drug development. The relevant research results were published in Nature, with the title “A viral ADP-ribosyltransferase attaches RNA chains to host proteins”.
Famous American biologist Linus Pauling once wrote, “Life is a relationship between molecules. The interactions between proteins and RNA affect translation, repair of genetic information, and transportation of cellular building blocks. These interactions are instantaneous contacts between RNA and RNA binding proteins based on specific RNA structures or sequences.” Now, these authors have discovered that Proteins and RNA can also be tightly bound together through so-called covalent bonds.
Phages are “fast killers”
This new study investigates bacterial and bacteriophage systems. Phages attack specific bacteria, such as T4 phages that infect Escherichia coli. T4 is a “fast killer”: bacterial cells are destroyed 20 to 30 minutes after the start of infection. This is faster than the action of antibiotics. With the increase in antibiotic resistance, bacteriophage therapy is being seen as a potential alternative therapy for treating bacterial infections.
In order to infect bacteria, bacteriophage T4 has evolved a fascinating strategy. After the invasion, it used three different ADP ribosyltransferase (ART) as biocatalysts. By connecting some of the coenzyme nicotinamide adenine dinucleotides (NAD) to proteins, these ARTs can modify over 30 host proteins. This allows bacteriophages to reprogram bacteria and kill them.
Study on NAD RNA Linking Host Proteins and Phages
Katharina Höfer, the co-author of the paper and the Max Planck Institute of Terrestrial Microbiology, has been studying the function of RNA for some time. She is particularly interested in NAD-RNA (RNA-carrying NAD). Eight years ago, she and colleagues at Heidelberg University discovered the presence of this type of RNA in bacteria. Since then, NAD-RNA has appeared in various forms and sizes in different biological populations, but their biological significance remains unclear.
Höfer wants to know if ART, used by bacteriophages like T4, can not only bind NAD but also bind NAD-RNA to proteins. In order to answer this question, these authors had to develop many methods themselves. But later it became clear that the ART ModB of T4 phage not only accepted NAD, but also NAD-RNA as a substrate – whether in vitro or in the living system. They referred to this novel reaction – the entire RNA protein binding – as RNA acylation. This is a completely new concept of natural RNA protein interaction.
RNAylation may be a mechanism for controlling cellular resources
But why do T4 bacteriophages use RNAylation? Obviously, this process is crucial for efficient infection of bacteriophages, as the T4 bacteriophage mutant lacking ModB kills bacteria much slower.
These authors can confirm that ModB can specifically bind different RNAs to bacterial proteins involved in translation in living cells.
The first author of the paper, Maik Wolfram Schauerte, said, “RNAylation may be part of the bacteriophage strategy. Attaching bacterial RNA to the ribosome may prevent the translation of bacterial proteins, allowing the bacteriophage to regulate its own protein biosynthesis.”
RNAylation as a potential new tool in synthetic biology
In order to study the molecular mechanism of RNAylation, Höfer began collaborating with researchers from the University of Heidelberg and the Max Planck Institute for Multidisciplinary Science in Göttingen.
Höfer explained, “Our research findings not only extend the previous description of the developmental cycle of bacteriophages, but also point out a novel biological role for bacteriophages. They point to a novel biological role for NAD-modified RNA, which activates RNA, allowing enzymes to transfer RNA to proteins. This also opens up new research avenues.”
For example, RNAylation may become a tool for synthetic biology in the future. As a ‘molecular glue’, it may be used to form specific RNA-protein conjugates, thereby combining the characteristics of proteins and nucleic acids.
However, there are still many unsolved mysteries. Höfer explained, “Some ARTs accept NAD-RNA, while others do not, which raises the question of the exact mechanism. The difficulty lies in the considerable size and complexity of this modification. RNAylation is relatively easy to detect in vitro, but in vivo, the diversity of target proteins and RNA makes research challenging. To elucidate the function of RNAylation, we need to develop new methods to study our specific problems in vivo.”
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Reference
Maik Wolfram-Schauerte et al. A viral ADP-ribosyltransferase attaches RNA chains to host proteins. Nature, 2023, doi:10.1038/s41586-023-06429-2.