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KSU Study Suggests Not All Nematodes Capable of Robust RNAi

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Although RNAi is an extremely effective gene-silencing tool in Caenorhabditis elegans, not all nematodes experience robust gene silencing with the introduction of double-stranded RNA, according to researchers from Kansas State University.

As a result, outcomes in RNAi knockdown experiments in non-Caenorhabditis nematodes “should be interpreted cautiously,” the investigators wrote in The Journal of Nematology.

Given the ease with which dsRNA can be introduced into C. elegans to induce RNAi — either by injection or feeding — there has been much interest in establishing RNAi systems in other nematodes, according to the paper. However, work from a number of research groups has shown that not all nematode species are amenable to RNAi.

As part of a broader interest in soil processes, the KSU team was interested in uncovering the genes involved in nematode metabolism and defense, Michael Herman, the study’s senior author, told Gene Silencing News.

Specifically, the scientists were interested in Oscheius sp. FVV-2., Rhabditis sp., Mesorhabditis sp., and Acrobeloides sp. — four bacterivore nematodes found in soil sampled from the Konza Prairie Biological Station near Manhattan, Kansas.

“We were looking to see whether we could use RNAi as a way to test candidate gene functions,” Herman explained. “At the same time, [we were] looking to see how widespread RNAi ability … was … extended throughout the nematode phylogeny.”

To do so, the researchers isolated genes with easily observed phenotypes related to morphology and viability, and attempted to inhibit them by either injecting the worms with dsRNA or by feeding them the RNAi triggers.

They found that neither approach resulted in a “robust knockdown phenotype in three species of Rhabditidae and a single species from Cephalobidae,” they wrote in their study.

“Although qRT-PCR assays detected a decrease in Mesorhabditis sp. and Oscheius sp. FVV-2 expression following dsRNA microinjection, this effect was between 10- to 70-fold less potent than that observed in C. elegans,” they added.

“Some people assume all nematodes can do RNAi,” Herman noted. “That is certainly not true.”

In speculating why a strong RNAi effect was not observed in the nematodes as compared with C. elegans, the researcher wrote that it was possible that the genes selected are “either not transcribed, or do not have similar knock-down phenotypes.”

However, Herman said that they believe the cause has more to do with the different functioning of systemic RNAi in the worms.

The transmembrane protein SID-1 has previously been identified as key to the transport of RNAi silencing signals between cells in C. elegans, and the team was unable to amplify SID-1 sequences from any of the grassland nematodes.

“Our current hypothesis is that those nematodes that have a SID-1 function that is closely related to the one in C. elegans are RNAi-able, but those that don’t, don’t have that response,” Herman said.

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