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UCSD Team Reports on Role of microRNA in Fruit Growth


NEW YORK (GenomeWeb) – Newly published research out of the University of California, San Diego has identified a key role for a specific microRNA in the growth of fruit in the model plant Arabidopsis thaliana. The work uncovers a novel "regulatory hub" dependent on the small, non-coding RNAs for controlling plant development.

Fruit morphogenesis in Arabidopsis, as well as many other plant species, is generally divided into early and later, post-fertilization events. The former include differentiation and patterning, while the latter include cell growth and expansion, ripening, and senescence — a stage that includes seed dispersal.

The fruiting process, UCSD's Martin Yanofsky told GenomeWeb, represents a key evolutionary development, providing angiosperms the ability to protect and nourish seeds in a way that ancient plants could not.

In recent years, a number of groups have identified various genetic factors underlying fruit growth. In 1998, for instance, Yanofsky and collaborators at Cold Spring Harbor Laboratory published a paper on the discovery of a gene called FRUITFULL (FUL) that encodes a MADS-domain transcription factor required for normal fruit cell growth and differentiation.

When that gene was mutated in Arabidopsis, the researchers found, normal fruit development was disrupted.

"Like pretty much all flowering plants, fertilization of the ovules leads to growth of the fruit," Yanofsky explained this week. "The fruit normally grow to accommodate the growth of the seeds inside. In the FRUITFULL mutant we identified and characterized, even though fertilization of the ovules occurs and you get seeds, the fruit don't grow."

Others, meanwhile, have shown that the plant hormone auxin helps coordinate fruit growth and maturation, with auxin signaling directed by transcription factors called auxin response factors, or ARFs.

"However, in spite of the wealth of accumulated information, we are only beginning to understand how the coordination of fruit growth … is achieved mechanistically," Yanofsky and his team wrote in their latest paper, which appeared in Nature Plants.

With miRNAs emerging as key players in a variety of biological roles in both animals and plants, "we became interested in the possible role of microRNAs in the control of fruit development," he said.

In 2011, Yanofsky's lab reported on the discovery that the Arabidopsis gene APETALA2 (AP2), which was known to play a key role in floral organ identity, is also involved in fruiting.

Arabidopsis fruit is composed of the valves, which make up the majority of the fruit and are derived from the ovary walls; the replum, which separates the valves; and the valve margin, which comprises a narrow stripe of cells at the valve-replum boundaries. In the 2011 paper, AP2 was specifically found to prevent overgrowth of both the replum and the valve margin. Further, although the AP2 promoter was active in the valve, its protein was not and the loss of AP2 did not affect valve development — all of which suggested some level of post-transcriptional regulation of the gene in that tissue.

Because AP2 had been previously shown to be regulated by the miR-172 miRNA family, once the gene's role in fruit development was established, Yanofsky's lab started investigating whether the miRNA had a part to play, as well.

To test this, the investigators expressed a wild-type version of the AP2 complementary DNA and a version of the gene that is immune to miR-172 in Arabidopsis fruit valves.

While fruit valves expressing the wild-type AP2 cDNA appeared normal, fruit expressing the miR172-immune version of AP2 failed to undergo the typical valve elongation that occurs after fertilization, which corresponded to the failure of valve cell differentiation and expansion, they wrote in Nature Plants.

To further demonstrate miR-172's involvement in the control of fruit growth, the team wanted to test loss-of-function mutations in the miRNA. However, there are five miR-172 loci in Arabidopsis and mutants are not available for most of them.

To overcome this issue, they used target mimics to lower the abundance of active mature miR-172, and found that, as expected, the overall size of fruit in the plants was reduced.                   

Yanofsky's group also looked upstream of miR-172 to better understand its regulation and discovered a relationship between the miRNA and FUL.

They found that the FUL MADS-domain protein acts with ARF proteins to directly activate a valve-specific miR172-encoding gene in order to promote valve growth. Additionally, they showed that MADS and ARF proteins, including FUL and ARF8, interact in plants and that this interaction might contribute to the miRNA-encoding gene's expression.

Taken together, the data point to an miRNA-dependent regulatory module that integrates developmental and hormone signaling pathways in the control of plant growth, the scientists concluded in their paper.

Since this study was completed, Yanofsky and his team have identified other miRNAs that appear to be influencing fruit growth and development in Arabidopsis, he said. Work is underway to better understand the upstream regulation of miR-172 and these other miRNAs.

Ultimately, Yanofsky sees these findings as having many applications in agriculture, noting that "we're certainly intrigued about the possibility of controlling fruit growth." However, he cautioned that translating the discoveries around miR-172 and other miRNAs to the real world will likely require years of work.

Nevertheless, a number of players in the ag-bio field have been actively working to commercialize products involving miRNAs. For instance, both DuPont and Bayer CropScience have been working to identify miRNAs associated with crop characteristics such as drought tolerance, while Syngenta recently struck a collaboration with Nexgen to develop virus-resistant crop plants through microRNA targeting.

And in 2013, Monsanto bought Rosetta Green, the agricultural spin off of miRNA diagnostics firm Rosetta Genomics.