Auxin methylation by IAMT1, duplicated in the legume lineage, promotes root nodule development in Lotus japonicus

Takashi Goto, Takashi Soyano, Meng Liu, Tomoko Mori, and Masayoshi Kawaguchi

PNAS, March 2, 2022 | 119 (10) e2116549119

Significance

IAA carboxyl methyltransferase 1 (IAMT1) converts auxin (IAA) into its methyl ester (MeIAA). IAMT1 is reportedly critical for shoot development of the nonsymbiotic plant Arabidopsis. On the other hand, the function of IAMT1 in roots is unknown. Here, we found that IAMT1 is duplicated in the legume lineage, which evolved root nodule symbiosis. In the model legume Lotus japonicus, one of two paralogs (named IAMT1a) was mainly expressed in root epidermis, but its function is required in the adjacent cell layer, root cortex, where it promotes nodule development. Application of MeIAA, but not IAA, significantly induced NIN, a master regulator of nodule development, without rhizobia. These findings illuminate our understanding of intertissue communication acquired during evolution of root nodule symbiosis.

Abstract

Legumes attract symbiotic bacteria and create de novo root organs called nodules. Nodule development consists of bacterial infection of root epidermis and subsequent primordium formation in root cortex, steps that need to be spatiotemporally coordinated. The Lotus japonicus mutant “daphne” has uncoupled symbiotic events in epidermis and cortex, in that it promotes excessive bacterial infection in epidermis but does not produce nodule primordia in cortex. Therefore, daphne should be useful for exploring unknown signals that coordinate these events across tissues. Here, we conducted time-course RNA sequencing using daphne after rhizobial infection. We noticed that IAA carboxyl methyltransferase 1 (IAMT1), which encodes the enzyme that converts auxin (IAA) into its methyl ester (MeIAA), is transiently induced in wild-type roots at early stages of infection but shows different expression dynamics in daphne. IAMT1 serves an important function in shoot development of Arabidopsis, a nonsymbiotic plant, but the function of IAMT1 in roots has not been reported. Phylogenetic tree analysis suggests a gene duplication of IAMT1 in the legume lineage, and we found that one of the two IAMT1s (named IAMT1a) was induced in roots by epidermal infection. IAMT1a knockdown inhibited nodule development in cortex; however, it had no effect on epidermal infection. The amount of root MeIAA increased with rhizobial infection. Application of MeIAA, but not IAA, significantly induced expression of the symbiotic gene NIN in the absence of rhizobial infection. Our results provide evidence for the role of auxin methylation in an early stage of root nodule development.

See: https://www.pnas.org/doi/10.1073/pnas.2116549119

Figure 1: Time-course RNA-seq in WT and daphne. (A) Classification of DEGs with fold change >2 (1,181 genes) into four subgroups (I to IV) by hierarchical clustering. (B) Expression modules of genes with significant differences between WT (black lines) and daphne (orange lines) during early infection. Each dot in each cluster represents an average value.