A New Connection between Metabolism and Regulation

In cells, ribonucleic acids (RNAs) are most commonly known as messengers or scaffold molecules, but they can also accelerate key biochemical reactions and regulate metabolic pathways. These regulatory RNAs were discovered just a few years ago. In studies on bacteria, scientists from Heidelberg University have now found previously unknown modifications in the RNAs that contribute to their stability against the degradation mechanisms of the cell. Among other things, regulatory RNAs are associated with cancer development and bacterial infections. The findings of the research at the Institute of Pharmacy and Molecular Biotechnology were published in the journal “Nature”.

In bacteria, most of these regulatory RNAs act by binding other RNA molecules, e.g. messenger RNAs, thereby triggering the degradation of the resulting complexes. As a consequence, the bound RNAs are no longer available for the biosynthesis of proteins, Prof. Dr. Andres Jäschke of the Institute of Pharmacy and Molecular Biotechnology explains. “So far, regulatory RNAs had been assumed to be composed of the four standard building blocks, the nucleotides A, C, G and U. We were now able to show that some regulatory RNAs in the gut bacterium Escherichia coli carry a particular modification at their ends that confers increased stability against the cell’s degradation machinery.” Furthermore, the team headed by Prof. Jäschke found an enzyme that can remove this modifying cap and release the previously protected RNA for degradation. According to Prof. Jäschke, the modifier is an “old acquaintance”, i.e. nicotinamide adenine dinucleotide (NAD), which assumes a key role in the metabolism of both bacteria and higher organisms.

These NAD-modified regulatory RNAs can be isolated by a novel method that was developed by chemist Dr. Hana Cahová and biotechnologist Dr. Marie-Luise Winz. In their approach, an enzyme from a marine mollusc and a technique known as “click chemistry” were used to label only the NAD-modified RNA molecules contained in a total RNA sample, while all others remained unaltered. The labelled RNAs can thus be selectively isolated and identified by high-throughput sequencing and comparison with databases. “For many of the modified RNAs we identified, no biological function is known to date. Interestingly, others have been described in the context of cellular metabolism or associated with the bacterial response to ‘stress’ caused by extreme environmental conditions,” Andres Jäschke notes.

The scientists have now looked into the question why a bacterium modifies some of its regulatory RNAs with NAD. “As the chemical nature of the ends was known to be a key factor in the degradation of RNA by cellular enzymes, we assumed that the NAD modification might stabilize the RNA,” says biotechnologist Katharina Höfer. Together with biochemist Gabriele Nübel, she thus investigated several known degradation pathways. The researchers could indeed demonstrate a significantly increased stabilisation against two modification and degradation enzymes. As it would be useful for the cell to cleave off the protective cap once its purpose is fulfilled, the scientists tested further enzymes and discovered what they were looking for yet again: one of the enzymes was able to remove NAD and thus initiate RNA degradation.

Andres Jäschke’s team suspect the attached NAD to have additional functions. “The nicotinamide adenine dinucleotide interacts with many proteins in a specific manner, so the NAD-RNAs might form protein complexes as well, which, in turn, might regulate various processes in the bacterium. In addition, NAD can occur in the cell in two different forms, namely in an oxidised and in a reduced one. The equilibrium between these two states may influence and modulate the biological function of NAD-RNAs,” Prof. Jäschke explains.

While protective caps at the ends of RNA have been known for decades in higher organisms, this is the first study to report a cap-like – but chemically different – structure in bacteria, according to the scientists. These investigations open up a new research area, as the biological functions and the mechanisms of this new modification now need to be clarified. “We are particularly interested to find out whether these NAD modifications are present in bacteria only or in higher organisms as well,” comments Andres Jäschke. “If this were a phenomenon specific to bacteria, it might provide clues for new antibacterial treatments.”

The research work was supported by fellowships from the Alexander von Humboldt Foundation and the Hartmut Hoffmann-Berling International Graduate School for Molecular and Cellular Biology (HBIGS) of Heidelberg University.

Original Publication:
Cahová, H., Winz, M.-L., Höfer, K., Nübel, K. & Jäschke, A.: NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature (22 December 2014), DOI 10.1038/nature14020