Two microRNAs linked to nodule infection and nitrogen-fixing ability in the legume Lotus japonicus

Plant Physiol. 2012 Dec;160(4):2137-54. doi: 10.1104/pp.112.204883. Epub 2012 Oct 15.


Legumes overcome nitrogen shortage by developing root nodules in which symbiotic bacteria fix atmospheric nitrogen in exchange for host-derived carbohydrates and mineral nutrients. Nodule development involves the distinct processes of nodule organogenesis, bacterial infection, and the onset of nitrogen fixation. These entail profound, dynamic gene expression changes, notably contributed to by microRNAs (miRNAs). Here, we used deep-sequencing, candidate-based expression studies and a selection of Lotus japonicus mutants uncoupling different symbiosis stages to identify miRNAs involved in symbiotic nitrogen fixation. Induction of a noncanonical miR171 isoform, which targets the key nodulation transcription factor Nodulation Signaling Pathway2, correlates with bacterial infection in nodules. A second candidate, miR397, is systemically induced in the presence of active, nitrogen-fixing nodules but not in that of noninfected or inactive nodule organs. It is involved in nitrogen fixation-related copper homeostasis and targets a member of the laccase copper protein family. These findings thus identify two miRNAs specifically responding to symbiotic infection and nodule function in legumes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Bradyrhizobium / physiology
  • Copper / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gene Library
  • Genes, Plant / genetics
  • Homeostasis / genetics
  • Laccase / genetics
  • Lotus / genetics*
  • Lotus / microbiology*
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Nitrogen Fixation / genetics*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Reproducibility of Results
  • Root Nodules, Plant / genetics*
  • Root Nodules, Plant / microbiology*
  • Sequence Analysis, RNA
  • Species Specificity
  • Symbiosis / genetics
  • Transcription Factors / metabolism
  • Up-Regulation / genetics


  • MicroRNAs
  • Plant Proteins
  • Transcription Factors
  • Copper
  • Laccase