Intronic TNR-retained ISOPROPYLMALATE ISOMERASE LARGE SUBUNIT1 transcripts impair leaf development in Arabidopsis

Intronic trinucleotide repeat (TNR) is widely distributed in plant genomes. In Arabidopsis accession Bur-0, abnormally expanded TTC repeat in intron-3 of the ISOPROPYLMALATE ISOMERASE LARGE SUBUNIT1 (IIL1) gene causes growth defects called the irregularly impaired leaves (iil) phenotype, triggered by DNA methylation-mediated IIL1 gene silencing at elevated temperature. However, little is known about how the reduced expression of IIL1 causes the iil phenotype. We demonstrated that the iil phenotype was resulted from the relative increase of intron-3-retained IIL1 transcripts through the experiments where the iil phenotype was reproduced by introducing the IIL1 gene harboring 100 copies of TTC repeat into Col-0. The iil phenotype appeared when the total amount of the IIL1 transcripts was decreased by co-suppression and the percentage of intron-3-retained IIL1 transcripts was increased. The IIL1 gene encodes an isopropylmalate isomerase large subunit, forming heterodimers with small subunits (AtLeuD1, AtLeuD2, or AtLeuD3). In the myb28 myb29 mutant lacking AtLeuD1 and AtLeuD2, the iil phenotype was almost completely suppressed regardless of higher percentage of intron-3-retained IIL1 transcripts. The results indicated that the iil phenotype was associated with interaction with AtLeuDs, suggesting that intronic TNR-containing transcripts were translated into abnormal proteins and perturbed the metabolic pathway supporting the leaf development.