Soybean Root Hairs: A Single-Cell Model For Systems Biology

Our laboratory continues to use the soybean root hair cell as a model to investigate the rhizobial infection process and as a platform for systems biology (see soyroothair.org).  We have now characterized the early stages of the rhizobial infection process at the level of the transcriptome, proteome, metabolome, phosphoproteome, as well as profiling small RNA expression and the chemistry of the root hair cell wall. Our data reminds us of the extensive remodeling that occurs in the plant cell as a consequence of rhizobial infection. The data generated from our project is deposited in our soyKB.org database, which provides tools to integrate the various data and to carry out a variety of analyses. This database is evolving into a platform not only for storage and analysis but to generate new hypotheses that can be experimentally tested. Complex regulation is a feature of the rhizobial infection process and new algorithms for the analysis of co-expression data are providing avenues to investigate this complexity. Recent highlights in the laboratory relate to the role of miRNA in regulating key nodulation processes. We identified over 90 miRNAs whose expression levels responded to rhizobial inoculation. We identified the mRNA targets for these miRNAs. In the few cases examined, we see that ectopic expression of specific miRNA can either significantly increase or decrease nodule numbers, supporting a key role for these regulators in nodulation. These and other results will be described, as well as how we intend to extend this model system to explore abiotic stress.