RNA Interference Explained Silent Messengers in Plants: Small RNAs

Plant cells can silence certain genes – even in far distance. This so called RNA interference is known for a while, but it was not yet proven what messenger substance “transmits” RNA interference. Now, ETH researchers have definitively shown that these messengers in plants are short double-stranded RNA fragments.

Zurich/Switzerland – In most organisms, small bits of RNA play a key role in gene regulation by silencing gene expression. They do this by targeting and docking onto complementary sequences of gene transcripts (also RNA molecules), which stops the cell machinery from using them to make proteins. This mechanism is called RNA interference (RNAi), and it is critically important in biology.

Remarkably, the RNAi phenomenon is not necessarily confined to single cells; it can also manifest in other tissues and organs far away from the cell of origin. Researchers have been able to observe it mostly in plants, but also in “lower” animals such as the nematode worm C. elegans.

Searching for the Messenger Substance

Still, one key question had so far gone unanswered: Which messenger substance traverses cells and tissues? “We were able to rule out proteins 20 years ago, once it was discovered that RNAi can travel in plants,” says Olivier Voinnet, Professor of RNA Biology at ETH Zurich.

RNAi requires that the messenger docks to a complementary sequence of the gene transcript to be silenced. “Proteins alone don’t have this capability. DNA leaving the cell nucleus is also unlikely”, Voinnet continues. “The most likely candidate has always been an RNA molecule.” What has been unclear until now is which precise type and form of RNA – long, short, single- or double-stranded, bound to proteins or not.

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Plants Modulate Gene Expression at a Distance

But now, the ETH researchers are shedding light on this process in a new study. They are the first to demonstrate unequivocally that these distant messengers in plants are short double stranded RNA molecules. These consist of pairs (or double-strands) of just 21 to 24 nucleotides (the building blocks of RNA) called small interfering RNAs, or siRNAs for short.

siRNAs usually emerge as large and complex populations from the genomes of viruses that have infected a cell. But a cell’s own genes can also serve as blueprints for these molecules. As a result, cells can use RNAi to silence not only invading viruses but also their own genes.

Because RNAi moves, plants have the amazing capacity to modulate gene expression at a distance. This might be particularly important for them to constantly adapt their new growth, enabling what is called “phenotypic plasticity”.

siRNA: Sacrifice to Silence

In their new study, the researchers ruled out the possibility that other types of nucleic acids or complexes composed of RNA and proteins move across plant cells. “We can definitively show that double stranded siRNAs are necessary and sufficient to induce RNAi in distant cells and tissues of plants”, Voinnet says.

Not only did the ETH researchers identify the elusive long-distance messengers, they also show how siRNAs move and carry out their function. They found that, as long as an siRNA molecule exists as a free double-strand, it is mobile because it cannot bind to a matching RNA transcript. To bind, it first has to be “uploaded” to a specific Argonaute (AGO) effector protein. Only once bound to the correct AGO protein can the siRNA silence the target transcript; the process eventually destroys the fragment itself.

The model plant used for the study has ten different AGO proteins, several of which recognise matching siRNA fragments with specific signatures. These signatures are not homogeneous among the large cohorts of mobile siRNAs produced from viruses or the plant’s own genes.