Katharina Markmann

Projects

Small RNAs inovlved in Lotus japonicus root symbiosis

Most genes in both plants and animals encode proteins. If such a gene is active, the cell first produces a corresponding RNA transcript, which then is translated into a protein – and it is in this form that the gene exerts its biological role. But an increasing number of RNAs are being discovered that never get translated. Certain groups of such noncoding transcripts are processed into small RNAs only 19-24 nt in length. These can regulate the activity of protein coding genes in diverse developmental and physiological processes. We are investigating the roles of regulatory small RNAs, in particular micro RNAs, in Lotus japonicus interactions with symbiotic bacteria and fungi. The project involves high throughput detection of small RNA populations using next generation sequencing, bioinformatic data analysis, as well as plant experiments to validate small RNA functions.

The Lotus japonicus small RNA machinery

To understand the role of regulatory small RNAs in root symbiosis, we have identified loss-of-function mutants in a number of genes that are potentially necessary for small RNA production and activity in the cell. We are examining these mutants and evaluate their ability to interact with nitrogen fixing rhizobial bacteria as well as mycorrhizal fungi. Defects or differences in symbiosis development in these mutants compared to genetically healthy wild type plants where small RNA regulation is intact help us identify the roles the respective genes, and their associated small RNAs, play in these processes.

Cell type specific transcript and small RNA responses in Lotus japonicus roots

Although we begin to understand more about the plant genes as well as small RNAs that respond to an encounter with root symbiotic microorganisms, we know little about where in the plant root these genes are active. Most previous studies rely on pooling different cell types of the root organ such that we can no longer pinoint precisely where changes in gene activity occur during symbiosis initiation. Based on promoters expressed in particular cell types only, we have therefore developed a system that allows the analysis of both coding and small noncoding RNA transcripts in defined root cell types. We are using this system for cell type specific detection as well as manipulation of transcript abundances in a quest to gain further insights into plant responses during root symbiosis.