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Background  Post-translational modification of receptor proteins is involved in activation and de-activation of signalling systems in plants. Both ubiquitination and deubiquitination have been implicated in plant interactions with pathogens and symbionts.    Results  Here we present  LjPUB13,  a PUB-ARMADILLO repeat E3 ligase that specifically ubiquitinates the kinase domain of the Nod Factor receptor NFR5 and has a direct role in nodule organogenesis events in  Lotus japonicus . Phenotypic analyses of three LORE1 retroelement insertion plant lines revealed that  pub13  plants display delayed and reduced nodulation capacity and retarded growth.  LjPUB13  expression is spatially regulated during symbiosis with  Mesorhizobium loti , with increased levels in young developing nodules.    Conclusion   Lj PUB13 is an E3 ligase with a positive regulatory role during the initial stages of nodulation in  L. japonicus .    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1425-z) contains supplementary material, which is available to authorized users.

A Lotus japonicus E3 ligase interacts with the Nod Factor Receptor 5 and positively regulates nodulation