A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness

Plant Cell. 2013 Oct;25(10):4166-82. doi: 10.1105/tpc.113.116251. Epub 2013 Oct 4.


cis-natural antisense transcripts (cis-NATs) are widespread in plants and are often associated with downregulation of their associated sense genes. We found that a cis-NAT positively regulates the level of a protein critical for phosphate homeostasis in rice (Oryza sativa). PHOSPHATE1;2 (PHO1;2), a gene involved in phosphate loading into the xylem in rice, and its associated cis-NATPHO1;2 are both controlled by promoters active in the vascular cylinder of roots and leaves. While the PHO1;2 promoter is unresponsive to the plant phosphate status, the cis-NATPHO1;2 promoter is strongly upregulated under phosphate deficiency. Expression of both cis-NATPHO1;2 and the PHO1;2 protein increased in phosphate-deficient plants, while the PHO1;2 mRNA level remained stable. Downregulation of cis-NATPHO1;2 expression by RNA interference resulted in a decrease in PHO1;2 protein, impaired the transfer of phosphate from root to shoot, and decreased seed yield. Constitutive overexpression of NATPHO1;2 in trans led to a strong increase of PHO1;2, even under phosphate-sufficient conditions. Under all conditions, no changes occurred in the level of expression, sequence, or nuclear export of PHO1;2 mRNA. However, expression of cis-NATPHO1;2 was associated with a shift of both PHO1;2 and cis-NATPHO1;2 toward the polysomes. These findings reveal an unexpected role for cis-NATPHO1;2 in promoting PHO1;2 translation and affecting phosphate homeostasis and plant fitness.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Enhancer Elements, Genetic*
  • Gene Expression Regulation, Plant
  • Homeostasis
  • Molecular Sequence Data
  • Oryza / genetics*
  • Oryza / metabolism
  • Phosphates / metabolism*
  • Plants, Genetically Modified / genetics
  • Plants, Genetically Modified / metabolism
  • Promoter Regions, Genetic
  • Protein Biosynthesis
  • RNA, Antisense / genetics*
  • RNA, Messenger / genetics
  • RNA, Plant / genetics
  • Xylem / metabolism


  • Phosphates
  • RNA, Antisense
  • RNA, Messenger
  • RNA, Plant

Associated data

  • GENBANK/AK071338
  • GENBANK/AK100323
  • GENBANK/AK121590