Transcriptomic profiles of nodule senescence in Lotus japonicus and Mesorhizobium loti symbiosis

Nodule senescence is a complex developmental process during which essential nutrients are recycled. In order to understand the regulatory mechanism, transcript-profiling analysis during nodule senescence was performed in the Lotus japonicus-Mesorhizobium loti symbiosis. Microarray data showed significantly up-regulated expressions in 641 genes out of a total of 20,165 genes during nodule senescence, and down-regulated expressions were observed in 416 genes. These up-regulated genes during senescence were related to cell wall/membrane/envelope biogenesis and extracellular structures. Down-regulated genes were mainly responsible for defense mechanisms. We classified senescence up-regulated genes in two clusters. Genes in cluster 1 were induced at senescence specific stage and those in cluster 2 were induced from nitrogen fixation stage and expressed until nodule senescence. The genes in cluster 1 included typical marker for senescence like gene for heat shock protein. Four hundred sixteen down-regulated genes during nodule senescence were also classified in two clusters, cluster 3 and cluster 4. These genes corresponded to metabolisms for amino acid and plant hormones which are necessary for growth and cell division during nodule development and nitrogen fixation. These results provide the comprehensive data source for investigation of molecular mechanisms underlying nodule senescence in Lotus japonicus-Mesorhizobium loti symbiosis.