Conservation and variation in the 5′ UTR of mRNAs that harbor uAUG containing PREs and/or uORFs. Each subpanel shows the uORF pattern (colored rectangles) and, where present, the PRE (tall blue box) of one orthologous group; some orthologous groups were supplemented manually with members from additional species. The Gene Identifiers come from TAIR (At#g#####), PlantGDB (PUT…), or GenBank (all others). The start of the major ORF is symbolized by a white box. The 5′ upstream region is indicated by a thick line. Vertical lines inside the uORF stand for internal in-frame AUG codons. Unless indicated, identical color or number does not imply sequence similarity. uORFs centered on the UTR are in the same frame as the major ORF, while those above the line and below the line are in the −1 and +1 frames, respectively. Selected exon-exon junctions are indicated by black arrowheads. Species abbreviations are as follows: (At) Arabidopsis thaliana, (Cs) Citrus sinensis, (Gh) Gossypium hirsutum, (Gm) Glycine max, (Nt) Nicotiana tabacum, (Vv) Vitis vinifera. (A) Calcineurin CBL3 and CBL2. This 5′ UTR contains a highly conserved PRE with two AUGs in a conserved frame arrangement. The downstream uAUG leads into a uORF that overlaps the main ORF (orange). A third uORF is present in some species (yellow). Its uAUG overlaps the stop of uORF1. (B) ASSYMMETRIC1/PHANTASTICA. This 5′ UTR lacks a recognizable PRE, yet its uORF pattern is highly conserved. Invariable features include one overlap uORF (blue) and one upstream uORF (yellow). An additional uORF ends at the start codon of the main ORF (green); it is present in all species except soybean. The consistent pattern notwithstanding, the uORF nucleotide and peptide sequences are not highly conserved. (A. majus) Antirrhinum majus, (A. lyrata) Arabidopsis lyrata. (C) PSEUDO-RESPONSE REGULATOR2/TOC2. This 5′ UTR harbors a conserved PRE with a conserved uAUG that leads into a long overlap-uORF (green). An additional uORF is usually present upstream, except in Arabidopsis. (D) RING protein At1g71980. Its PRE invariably harbors the start codon of a short uORF (green). A second uAUG is usually present in the PRE (orange), except in Arabidopsis. Additional short uORFs are common. (E) smRNP protein At3g14080. A PRE with a conserved uAUG leads into a uORF of variable length (green), which may overlap the major ORF. Upstream uORFs may be present. In Arabidopsis, the uAUG and uORF have been lost from the PRE. (F) Spermidine synthase. The PRE contains a putative non-AUG start codon. The non-AUG uORF downstream (orange, stippled) is highly conserved in length and amino acid sequence (data not shown). Related to Supplemental Figure S2.
