RNA-Seq Links the Transcription Factors AINTEGUMENTA and AINTEGUMENTA-LIKE6 to Cell Wall Remodeling and Plant Defense Pathways

Plant Physiol. 2016 Jul;171(3):2069-84. doi: 10.1104/pp.15.01625. Epub 2016 May 20.


AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6) are two related transcription factors in Arabidopsis (Arabidopsis thaliana) that have partially overlapping roles in several aspects of flower development, including floral organ initiation, identity specification, growth, and patterning. To better understand the biological processes regulated by these two transcription factors, we performed RNA sequencing (RNA-Seq) on ant ail6 double mutants. We identified thousands of genes that are differentially expressed in the double mutant compared with the wild type. Analyses of these genes suggest that ANT and AIL6 regulate floral organ initiation and growth through modifications to the cell wall polysaccharide pectin. We found reduced levels of demethylesterified homogalacturonan and altered patterns of auxin accumulation in early stages of ant ail6 flower development. The RNA-Seq experiment also revealed cross-regulation of AIL gene expression at the transcriptional level. The presence of a number of overrepresented Gene Ontology terms related to plant defense in the set of genes differentially expressed in ant ail6 suggest that ANT and AIL6 also regulate plant defense pathways. Furthermore, we found that ant ail6 plants have elevated levels of two defense hormones: salicylic acid and jasmonic acid, and show increased resistance to the bacterial pathogen Pseudomonas syringae These results suggest that ANT and AIL6 regulate biological pathways that are critical for both development and defense.

MeSH terms

  • Arabidopsis / cytology
  • Arabidopsis / microbiology
  • Arabidopsis / physiology*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Cell Wall / genetics
  • Cell Wall / metabolism*
  • Cyclopentanes / metabolism
  • Flowers / genetics
  • Flowers / growth & development
  • Gene Expression Regulation, Plant
  • Indoleacetic Acids / metabolism
  • Inflorescence / genetics
  • Inflorescence / growth & development
  • Meristem / genetics
  • Meristem / metabolism
  • Mutation
  • Oxylipins / metabolism
  • Pectins / genetics
  • Pectins / metabolism
  • Plant Diseases / microbiology
  • Pseudomonas syringae / pathogenicity
  • Salicylic Acid / metabolism
  • Sequence Analysis, RNA
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • AINTEGUMENTA protein, Arabidopsis
  • Arabidopsis Proteins
  • Cyclopentanes
  • Indoleacetic Acids
  • Oxylipins
  • PLT3 protein, Arabidopsis
  • Transcription Factors
  • jasmonic acid
  • Pectins
  • Salicylic Acid
  • polygalacturonic acid