Gene expression shows how a plant and its mutualists are better together

Medicago truncatula, in its model-organism habitat. (Flickr: Jeremy Yoder)

Medicago truncatula in its model-organism habitat. (Flickr: Jeremy Yoder)

No living thing is an island, and many of the encounters between living things that happen every day are not antagonistic or even indifferent, but mutually beneficial. Two such mutualisms that could be among the most important on the planet are the relationships plants have with nitrogen-fixing bacteria and mycorrhizal fungi. Rhizobial bacteria convert nitrogen from the biologically inaccessible form that makes up a large fraction of the atmosphere to a chemical compound plants can use to build amino acids; mycorrhizal fungi collect rare soil nutrients and water from sources a plant can’t access, like leaf litter. Many plants allow either rhizobia or mycorrhizae — or both — to colonize their roots, and feed them sugar in exchange for the nutrients they provide.
The possiblity of hosting both these relatively simple mutualists opens up interesting options — do they help each other, or compete for their hosts’ favor? How does a plant juggle both bacteria and fungus? One such plant is Medicago truncatula or barrel medick, a small, weedy relative of alfalfa that grows really well in greenhouses, and has become a “model species” for studying mutualism. A recent paper in Molecular Ecology examines how the “tripartite” relationship affects the activity of genes in the host plant.
If you’re not familiar with gene expression studies, the basic idea is this: Genes code for proteins, which collectively create the traits and responses of each living thing. To actually make a protein, the corresponding gene’s sequence of DNA is transcribed into RNA, which can be translated into a protein by ribosomes. The RNA copies of a gene’s sequence are, therefore, a kind of index for whether the gene is “turned on”, or expressed. Collecting the sequences of all the RNA in a tissue sample gives you a master list of all the genes that are expressed in the cells that compose the tissue, and comparing the relative frequency of a given gene’s RNA sequence in two tissue samples tells you something about whether that gene’s product is more active, and therefore more important, in one tissue or the other.
In this particular study, the authors compared gene expression in root tissue harvested from medick plants grown without rhizobia or mycorrhizae, with one mutualist or the other, or with both. The experimental plants were all self-fertized offspring from a highly inbred parent, and the symbionts were all propagated by cloning — so the players were effectively all genetically identical. They identified genes by comparing the RNA sequences they obtained to the Medicago truncatula reference genome, counted the copies of each gene observed in the sequencing from each treatment, and then binned the genes according to whether they showed statistically significant changes in expression, relative to the no-mutualist treatment, in plants with only rhizobia, plants with only mycorrhizae, or plants with both — and genes for which the change in expression with both mutualists was greater than the change attributable to the two mutualists individually.
Having both mutualists had, as you might expect, positive effects on how big the plants grew. Thousands of genes showed expression changes in response to each individual mutualist; hundreds of genes shifted expression in response to both. Just a few dozen showed the last class of effects, non-additive change in response to both mycorrhizae and rhizobia. So most of the changes in plant gene expression were due to effects of the individual mutualists, and the genes involved were fairly distinct sets. That makes sense, given the different nutrients provided by rhizobia and mycorrhizae, and the different ways the plants host them. Rhizobia stimulate the growth of nodules of specialized root tissue, where they reproduce and form specialized cells to fix nitrogen; mycorrhizae infiltrate root tissue and trade nutrients without special structures. Maybe because of that difference, a larger portion of all expressed genes showed changes in expression with mycorrhizae, and, in the genes affected by both mutualists, the expression response to both mutualists together was more similar to the response to mycorrhizae alone than the response to rhizobia alone.
Many of the genes with mutualist-related expression changes are involved in metabolic functions, as you might expect. One curious pattern, though, is in genes with roles in signaling between medick and the two mutualists that occurs before either mutualism actually starts — a specific set of genes are known to play roles in establishing mutualism with both rhizobia and mycorrhizae, but these genes only showed expression responses to mycorrhizae. The only genes in this set that were uniquely responsive to rhizobia had roles in development of rhizobia-hosting root nodules.
So, systematically looking at medick’s response to rhizobia and mycorrhizal fungi simultaneously reveals how the two mutualists are different, even in one of the ways we thought they were most similar.
Afkhami, M.E. and J.R. Stinchcombe. 2016. Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi. Molecular Ecology doi: 10.1111/mec.13809

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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