The RNA effector SERRATE is required for the Arabidopsis polycistronic ctr1-10 main open reading frame translation

The T-DNA insertion at the 5'-untranslated region (5'-UTR) of CONSTITUTIVE TRIPLE-RESPONSE1 (CTR1) results in an extended 5'-UTR of the ctr1-10 mRNA, and the main ORF (mORF) translation requires FRAGILE HISTIDINE TRIAD (FHIT) in the face of upstream open reading frame (uORF) inhibition. The RNA effector SERRATE (SE) was isolated from an enhancer screen for ctr1-10, and CTR1 levels were substantially reduced in se ctr1-10 plants. RNA profiling and genetic analyses revealed changes in CTR1 levels independent of pri-miRNA or ctr1-10 mRNA processing. Ribosome footprinting analyses revealed an impact on ctr1-10 mORF translation efficiency by se. Mutation of the SE-binding cap-binding complex component CAP BINDING PROTEIN20 (CBP20) had effects similar to those of se on CTR1 levels in ctr1-10 plants. Sucrose density gradient fractionation of membrane proteins was used to determine the associations of SE with polysome fractions. In situ editing that disrupted an upstream ATG codon proximal to the ctr1-10 mORF elevated CTR1 levels in an SE-independent manner. Our study revealed the involvement of SE/CBP20 in the translational regulation of polycistronic ctr1-10 mRNAs independent of miRNA biosynthesis and ctr1-10 mRNA processing, advancing the knowledge of the heterogeneity of the translation machinery, which plays roles in fine translation control.