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Nitrogen-fixing bacteria talk to soybean roots via tiny RNAs, suggesting new avenue to improve yields

rhizobia nodules on soybean roots contain a heretofore under-appreciated mechanism that could open the door to better yields. Image credit: Bo Ren, Purdue University

Rhizobia bacteria make transfer RNA-derived small RNA fragments that influence plant gene expression, helping to create the  crucial nitrogen-fixing nodules on soybean roots. Image credit: Bo Ren, Purdue University

In order for soybean plants to get their necessary dose of nitrogen, they partner with bacteria called rhizobia, which can convert atmospheric nitrogen into organic forms the plant can use. But scientists don’t have the full picture of what facilitates this symbiosis.

A recent study suggests that tiny RNAs are a crucial player. According to the work, published  in Science, those rhizobia bacteria can directly silence genes in the host plant by secreting shreds of their own RNAs.

It’s the first study to find bacterial small RNAs tuning gene activity in a eukaryote, notes senior author Jianxin Ma, a soybean geneticist at Purdue University in West Lafayette, Indiana. “What we are more excited about,” he adds, “is the transferability of our findings to the soybean field for better yields.” With the world’s population expected to soar beyond 9 billion by mid-century, the more beans, the better.

Ma and colleagues focused on a small RNA called a transfer RNA-derived small RNA fragment, or tRF. These originate from transfer RNAs, molecules with the primary job of delivering amino acids for protein assembly. But tRFs also perform another task: they can pair with messenger RNAs if the nucleic acid sequences are complementary; this kicks off a process by which that mRNA is degraded, preventing production of that protein. Ma and colleagues wondered if tRFs might mediate communication from the rhizobia to the soybean root, which together form a globular, nitrogen-fixing structure called a nodule.

To find out, they first sequenced the tRFs made by the bacterium Bradyrhizobium japonicum, and looked for complementary messenger RNAs in the soybean (Glycine max). The team focused on three rhizobial tRFs that looked like partners for five soybean genes—genes that were known to be related to a set of Arabidopsis genes involved in plant development and the formation of root hairs (which curl around the bacteria to initiate nodule construction). The researchers then confirmed that the expression of these five genes was lower in soybean nodules than in rhizobia-free roots.

Then the team asked what effect these tRFs and genes have on root nodule formation in soybeans. They blocked the tRFs in soybean roots, and the expression of target genes went up, while the number of root nodules went down. When they inactivated the target genes, plants made more root nodules. Together, these experiments strongly suggest that rhizobia make tRFs that bind specific plant genes, turning them off and promoting formation of nodules.

Legumes and rhizobia are already known to communicate during nodule formation, with both secreting factors influencing the other. But tRFs are new players. “This is a really novel mechanism that’s kind of filling out this stable of different tricks that both the plant and bacteria have coevolved,” says Liana Burghardt, an evolutionary ecologist and postdoctoral researcher at the University of Minnesota Twin Cities in Saint Paul, who was not involved in the work.

Ma hopes to use this system to develop soybeans that more efficiently obtain nitrogen through rhizobia instead of from fertilizer. He even envisions making non-legume crops, such as corn or rice, that can interface with rhizobia to fix their own nitrogen.

One potential advantage of targeting tRFs is that “it is much easier to manipulate bacteria than to make transgenic plants,” says Flavio Blanco, a biologist at the National University of La Plata in Argentina. Blanco, who was not involved in the study, suggests scientists could manipulate tRFs to improve nitrogen fixation or improve the compatibility between rhizobia and plant partners.

Although Ma’s discovery enables scientists to “tinker” with the nodule system, more nodules shouldn’t necessarily be the ultimate goal, cautions Burghardt. Nodules cost the plant resources. Ideally researchers will zero in on an optimum number for optimum yield.

Transfer RNA fragments likely have roles beyond soybeans, too. Ma and colleagues found evidence of tRFs and potential mRNA targets among RNA sequence data from the common bean (Phaseolus vulgaris) and its rhizobial partner, Rhizobium etli. Indeed, Burghardt suggests farmers might be able to use tRFs to precisely tune other plant genes, moving beyond nodules and legumes, to improve yields.

Categories: Agriculture | Biochemistry | Genetics | Journal Club | Plant Biology and tagged | | | | | | | |
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One Response to Nitrogen-fixing bacteria talk to soybean roots via tiny RNAs, suggesting new avenue to improve yields

  1. garry says:

    Nitrogen-fixing bacteria are known to form symbiotic associations with some members of all major groups of plants, as well as with some mycorrhizal fungi. nitrogen-fixing bacteria capture the root hairs of host plants, where they grow and stimulate the formation of root nodules, increasing plant cells and bacteria in intimate association. Within the nodules, the bacteria convert free nitrogen to ammonia, which the host plant utilizes for its development. For more details go to

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