New & Noteworthy

Message in a Bubble

February 18, 2015

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If you’re shipwrecked on a desert island, writing a message on a scrap of paper, sealing it in a bottle, and flinging it into the ocean could be your only chance at communication. As the song goes (see below), the message in a bottle is an S.O.S. to the world.

It turns out that cells may do something very similar. But instead of using a bottle, they enclose their messages in membrane-bound bubbles.

Many different mammalian cell types have been seen to form these extracellular vesicles (EVs). In mammalian cells, it’s known that EVs are used for cell-to-cell communication. They contain signals that allow cells to influence their neighbors, both for good (for example, regulating the immune response) and for bad (transmitting viruses or toxic peptides). In most cases these signals aren’t well-characterized, but the EVs may include DNAs and proteins, and they’re rich in RNAs.

Fungi have been found to produce EVs too, but they’ve been much less studied. In a new paper in Scientific Reports, da Silva and colleagues looked at the extracellular vesicles (EVs) produced by four different fungal species, including S. cerevisiae, and found that among other things, the vesicles actually include at least parts of many RNAs, both protein-coding and non-coding.

The scientists decided to look at S. cerevisiae and three species of fungal pathogens that infect humans: Cryptococcus neoformans, Paracoccidioides brasiliensis, and Candida albicans. (S. cerevisiae can be pathogenic too, but isn’t as virulent as any of those species.) They isolated EVs from each and treated the unbroken EVs with RNase to get rid of any RNA that might be contaminating their surfaces.

Then they broke open the vesicles to see what was inside. They found that the EVs contained many small RNAs, most less than 250 nucleotides in length. The scientists used RNA-seq analysis to determine the sequences of these small RNAs, and compared them to the genomic sequences that were already known for these organisms.

Many of the sequences corresponded to noncoding RNAs. For S. cerevisiae, the RNA sequences identified included the mitochondrial small and large ribosomal RNAs, RNA components of RNase enzyme complexes, a variety of small nuclear and small nucleolar RNAs, and tRNAs.

Sequences corresponding to several dozen S. cerevisiae mRNAs were also detected. There wasn’t much rhyme or reason to the kinds of proteins they encoded.  But the set of mRNA fragments didn’t correspond simply to the set of most abundant mRNAs in the cell. So it seemed like the vesicles didn’t just contain random samples of the cytoplasm, but instead had been loaded selectively with particular mRNAs.

This study raises as many questions as it answers, and there is a lot of work to be done before fungal EVs will be understood. The intriguing discovery of RNA in EVs suggests the possibility that the RNAs could influence gene expression in cells that take up the EVs, either by regulating processes like splicing or translation, or even by encoding a protein that gets translated in the recipient cell.

Being able to influence neighboring fungal cells via EVs could be an advantage for fungi in the fierce competition for biological resources. Or perhaps EVs are used to subvert gene expression in host tissues during a fungal infection. Far from being an S.O.S., these messages could be threatening.

These speculations all need much more research. Fungi are an integral part of our world, and we need to pay careful attention to the messages that they send us!

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

“Message in a Bottle,” The Police, 1979