Translation of eukaryotic genes is regulated by multiple features in mRNAs. Among them, uAUGs and associated uORFs are widely present in the 5′ leader sequences (around 64% in humans and around 54% in Arabidopsis)3. Most eukaryotic mRNAs are translated in a cap-dependent manner, with the 43S preinitiation complex scanning from the 5′ cap and initiating translation at a start codon by recruiting the 60S ribosomal subunit5,6,7. The presence of uAUGs provides potential alternative sites for the preinitiation complex to start translation before it reaches the main AUG (mAUG); and if translation initiates from uAUGs, it typically inhibits translation from downstream mAUGs2,8,9,10. This inhibitory role of uAUGs is crucial for controlling the production of specific proteins in normal conditions, particularly those involved in the stress response or in cell death11,12,13. For example, constitutive translation of the key plant immune transcription factor TL1-binding factor (TBF1; AT4G36990.1) without the two uAUGs and uORFs in its 5′ leader sequence causes lethality14. Notably, most uORFs do not have conserved primary sequences despite undergoing positive Darwinian selection3, which suggests that they inhibit the translation of main ORFs (mORFs) mostly through competition for ribosomes rather than through their translational products1.

uORF-mediated inhibition can be alleviated in a variety of conditions4,8,15,16, permitting the translation of downstream mORFs. This translational switch from uORF to mORF has been well studied in a few transcription factors, including yeast Gcn4 and mammalian ATF4, through stress-induced phosphorylation and inactivation of eukaryotic translation initiation factor 2α (eIF2α)11,13. However, inactivation of eIF2α leads to a global shutdown of translation, which, although essential for some stress responses (for example, nutrient deprivation11), is deleterious and absent during most eukaryotic developmental stages or in abiotic and biotic stress conditions17,18,19,20 (for example, immune responses in plants, such as pattern-triggered immunity; PTI20). This raises the fundamental question of what mRNA features, in conjunction with the translational machinery, dynamically dictate from which AUG to initiate translation and consequently control protein production under different conditions.

Translational switch after immune induction

To identify mechanisms involved in the uAUG-mediated regulation of translation, we first performed global ribosome sequencing (Ribo-seq; sequencing of ribosome-protected RNA fragments) in Arabidopsis seedlings in response to the induction of PTI by elf18 (N-terminal epitope of the bacterial elongation factor Tu)21. The optimized Ribo-seq pipeline had a sufficiently high resolution to examine the translational activities in 5′ leader sequences (Methods and Extended Data Fig. 1). Comparing elf18-treated samples to mock-treated controls, we identified, among the 13,051 expressed transcripts, 1,157 with increased translational efficiency (TE-up), 1,150 with decreased translational efficiency (TE-down), and the rest with no significant changes in translational efficiency (TE-nc) (Fig. 1a and Extended Data Fig. 2a,b). We selected 20 TE-up transcripts and used their 5′ leader sequences to drive the translation of the constitutively transcribed firefly luciferase (FLUC) reporter. Using the constitutively expressed Renilla luciferase (RLUC) as a control, this ‘dual luciferase’ assay22 confirmed the elf18-induced translation (Extended Data Fig. 2c) observed in the Ribo-seq results. Gene Ontology (GO) analysis23,24,25 of the TE-up genes revealed an enrichment of biological processes in response to a variety of environmental stresses, such as biotic stimuli, abiotic stimuli and chemicals, whereas GO terms for the TE-down genes were mostly growth-related metabolic processes (Extended Data Fig. 2d,e). Because the TE-up category includes key immune transcription factors, such as TBF1, a moderate increase in their translation could have a substantial effect on the downstream defence response.

Fig. 1: Translational dynamics of uORF-containing transcripts.
figure 1

a, Volcano plot of global changes in translational efficiency during PTI. TE-up, transcripts with upregulated translational efficiency (P < 0.05, log2-transformed fold change > 0.16); TE-nc, transcripts with no changes in translational efficiency (P > 0.05); TE-down, transcripts with downregulated translational efficiency (P < 0.05, log2-transformed fold change < –0.16). b, Number and percentage of transcripts with translating uAUGs in the TE-up, TE-nc and TE-down groups. Two-tailed Fisher’s exact test was used to determine the P value of the difference between groups. c, Box plot of ribosome occupancy (normalized read counts) on translating uAUGs in the TE-up (n = 347), TE-nc (n = 2,312), and TE-down (n = 192) transcripts in the mock condition. P values were calculated by two-tailed Mann–Whitney tests. Boxes, interquartile range (IQR); centre lines, median; whiskers, values within 1.5 × IQR of the top and bottom quartiles. d, Histograms with density curves of log2-transformed fold change of ribosome occupancy on translating uAUGs in the TE-up, TE-nc and TE-down transcripts in response to elf18 treatment. μ, average log2 transformed fold change value. P values were calculated by two-tailed paired t-tests. e, Ribosome occupancy on the uORF(s) in four TE-up transcripts, namely TBF1, ZIK10, CAF1J and ZF-MYND (AT1G70160.1), in response to mock and elf18 treatment. P values were calculated by two-tailed Student’s t-tests. NS, not significant. Values are mean ± s.d. (n = 3 independent biological replicates).

To systematically identify uAUGs that can be recognized by the preinitiation complex and initiate translation (‘translating uAUGs’), we focused on those uAUGs with ribosomal associations above the background levels (Methods and Extended Data Fig. 2a,b). We identified 5,626 translating uAUGs across the 13,051 expressed transcripts, with some transcripts having multiple translating uAUGs. Notably, we discovered that translating uAUGs were significantly enriched in the TE-up transcripts (30.0%), compared to the TE-nc (21.5%) and TE-down mRNAs (16.7%) (Fig. 1b). This finding suggests that translation initiation from uAUGs has a general role in regulating immune-associated translation.

Next, we examined the global translational dynamics of the translating uAUGs. In the mock condition, translating uAUGs in the TE-up transcripts had significantly higher ribosomal associations than did those in the TE-nc and TE-down transcripts (Fig. 1c), suggesting higher rates of translation initiation from these uAUGs in the TE-up transcripts without immune induction (mock). After treatment with elf18, there was a significant decrease in ribosomal association with these translating uAUGs in the TE-up transcripts, whereas this reduction was not observed in the TE-nc and TE-down transcripts (Fig. 1d). Closer examination of the Ribo-seq data for a few TE-up transcripts, including TBF1 (refs 14,19), showed that there was a significant reduction in ribosome occupancy on the inhibitory uORFs (uORF2 for TBF1 and ZIK10) in response to elf18 treatment (Fig. 1e). Because translation initiation from uAUGs typically inhibits the downstream mORF translation2,8,9,10, this elf18-triggered reduction in uAUG translation suggests an immune-induced release of the uAUG-mediated inhibition of downstream mORF translation. Collectively, our global characterization (Fig. 1c,d) and direct analysis on marker genes (Fig. 1e) revealed the common regulatory dynamics of translating uAUGs in the TE-up transcripts: they are preferentially recognized and translated under the mock condition, but are bypassed to permit translation initiation from mAUGs in response to immune induction.

Downstream hairpins dictate AUG selection

To address the question of how start codons are dynamically selected to initiate translation in different conditions, we first assessed the Kozak sequence context flanking the AUGs (–3 to +4, with A in AUG being +1) which is known to affect the recognition of start codons by the translation preinitiation complex26. A previous analysis suggested that in plants, a higher adenine and guanine (AG) content is associated with higher translational activity27. Using this criterion, we assessed the Kozak contexts for the uAUGs and mAUGs in all the expressed transcripts. We found that mAUGs have markedly higher AG contents than do translating uAUGs (Fig. 2a), in agreement with previous studies in animals, which found that mAUGs generally have more preferable Kozak sequence contexts than do uAUGs28,29. However, the Kozak contexts for translating uAUGs among the TE-up, TE-nc and TE-down transcripts are similar (Fig. 2a), suggesting that although the Kozak sequence context is important for start-codon recognition in static conditions, it is unlikely to be responsible for the elf18-mediated switch from uAUG to mAUG translation in the TE-up transcripts.

Fig. 2: Global SHAPE-MaP and deep learning analyses reveal hairpin structures downstream of mAUGs and uAUGs that have a role in dictating translation initiation.
figure 2

a, Kozak sequence contexts (AG content) flanking mAUGs and translating uAUGs. P values were calculated by two-sided chi-squared test. b, Average SHAPE reactivities across all expressed transcripts aligned by start codons of CDS in the mock condition. Red line, average reactivity for every three nucleotides. Ave., average SHAPE reactivity across all of the nucleotides. Blue shading, 100 nt downstream of mAUG. c, Violin plots showing comparisons of SHAPE reactivities 50 nt upstream and 50 nt downstream of mAUGs or uAUGs in the mock condition. d, Box plots showing differences in SHAPE reactivities 50 nt upstream and 50 nt downstream of translating uAUGs in four TE-up transcripts. Only the major inhibitory uAUGs (that is, uAUG2s in TBF1 and ZIK10) are shown. e, Box plots showing the differences in folding energy of RNA secondary structures downstream of predicted initiating and non-initiating AUGs. m/iAUGs, mAUGs and internal AUGs. f, Distributions of base-pair numbers and folding energies of RNA secondary structures downstream of predicted initiating AUGs. g, Heat maps showing the frequencies of nucleotides in the loop and the stem of hairpin structures downstream of predicted initiating AUGs that are significantly distinct from the background (P = 1.4 × 10–109 for the loop and P = 1.5 × 10–79 for the stem, calculated by chi-squared test). Numbers 1 to 25 show the position of each base pair, which were counted starting from the end of the loop. h, Models of RNA secondary structures downstream of uAUG2 (uAUG2-ds) of TBF1 and mAUG (mAUG-ds) of ERECTA. i, Box plot showing the difference in ribosome occupancy on predicted initiating and non-initiating uAUGs. For ce,i, boxes, IQR; centre lines, median; whiskers, values within 1.5 × IQR of the top and bottom quartiles. P values were calculated by two-tailed Mann–Whitney tests.

Beyond primary sequences, we next considered a possible involvement of RNA secondary structures in this dynamic selection of translation start codons. To probe in vivo RNA secondary structural dynamics, we adapted selective 2′-hydroxyl acylation analysed by primer extension and mutational profiling (SHAPE-MaP) to detect global in planta changes in RNA secondary structure at nucleotide resolution with and without immune induction. This strategy relies on SHAPE reagents (here, 2-methylnicotinic acid imidazolide, NAI)—a group of hydroxyl-selective electrophiles that react with the 2′-hydroxyl position of unpaired residues of RNA30. The resulting 2′-O-adducts cause mutations in the cDNA during reverse transcription, which are detected through sequencing to create SHAPE reactivity profiles, yielding quantitative measurements of RNA structures inside the cell (Extended Data Fig. 3a). Regions with higher SHAPE reactivities are likely to be more single-stranded. To validate our protocol, we performed a targeted in planta SHAPE-MaP analysis of the Arabidopsis 18S rRNA. The signal obtained was consistent and significantly improved from that reported previously31 (Extended Data Fig. 3b).

We then performed the global in planta SHAPE-MaP analysis of mRNAs in Arabidopsis seedlings in response to mock treatment or treatment with elf18, which resulted in high-quality data (Extended Data Fig. 3c,d). To ensure accurate structure modelling, only data that passed the stringent cut-offs for read depth and completeness were used for subsequent analyses30 (Methods). We observed that, although the overall SHAPE reactivities of the 5′ leader sequences and coding sequences (CDSs) were comparable (Extended Data Fig. 4a), the nucleotides immediately downstream of the mAUGs in all expressed transcripts exhibited noticeably lower SHAPE reactivities, with the lowest values observed around +100 nucleotides (nt) (Fig. 2b), suggesting higher levels of double-stranded structures, protein binding or both in this region. We wondered whether this feature was related to start-codon recognition and translation initiation from mAUGs, and whether a similar feature exists for uAUGs. To answer these questions, we first examined the SHAPE reactivity for each of the 50 nt upstream and downstream of AUGs to determine whether there was a statistically significant difference. We found that nucleotides downstream of mAUGs and translating uAUGs exhibited significantly lower SHAPE reactivities compared to those upstream, but this was not observed for non-translating uAUGs (Fig. 2c). We further investigated whether the observed feature might contribute to the dynamic regulation of uAUG-mediated translation in the TE-up, TE-nc and TE-down transcripts (Fig. 1c,d). We found that, in the mock condition, translating uAUGs in the TE-up transcripts had significantly lower SHAPE reactivities in their downstream regions compared to those in the TE-nc and TE-down transcripts (Fig. 2c), with four TE-up transcripts shown in Fig. 2d.

To assess the possibility that the low SHAPE reactivity that was found downstream of mAUGs and translating uAUGs was a result of association with ribosomes or RNA-binding proteins, we performed global in vitro SHAPE-MaP experiments on the same samples in the mock condition. The overall SHAPE reactivities in vitro were lower than those observed in vivo, suggesting a lower degree of single-strandedness in vitro (Extended Data Fig. 4b), in line with previous findings31,32,33,34,35. Of note, we found that in the absence of proteins, the overall SHAPE reactivities in regions immediately downstream of mAUGs and translating uAUGs in the TE-up transcripts were not significantly changed from those obtained from the in vivo SHAPE-MaP (Extended Data Fig. 4b,c), indicating that the low SHAPE reactivities observed in this region are unlikely to be due to protein binding, but are more likely to be attributed to double-stranded RNA (dsRNA) secondary structures. Hence, we named these structures downstream of mAUGs and uAUGs ‘mAUG-ds’ and ‘uAUG-ds’, respectively. Targeted in vitro SHAPE-MaP analysis of the TE-up marker transcript TBF1 also showed that the removal of proteins had no significant effect on the SHAPE reactivity patterns in its uAUG2-ds region (Extended Data Fig. 4d,e).

Deep learning characterization of AUG-ds

To independently demonstrate that the observed structural patterns contribute to translation initiation from AUGs, we developed translation initiation site prediction using deep neural network (TISnet), based on the primary sequence, the structural data or both, to predict translation initiation sites. To train the TISnet model, data from mAUGs with high translational activities and internal AUGs were used as positive and negative samples, respectively (Methods). AUGs with a high probability (0.9 or higher) were classified as predicted initiating AUGs (Extended Data Fig. 5a,b). We found that the model achieved its best prediction performance—as shown by the high area under the receiver operating characteristic curve (AUC) score of 0.89 (Extended Data Fig. 5c)—only when both the sequence and the structural information were considered. There were clear differences in the predicted probabilities between mAUGs and internal AUGs (training data) and between translating uAUGs and non-translating uAUGs (testing data) (Extended Data Fig. 5d).

Our model further supports the hypothesis that mAUG-ds and uAUG-ds are responsible for the start-codon selection, because downstream regions of predicted initiating AUGs had significantly more negative folding energy than did predicted non-initiating AUGs (Fig 2e and Extended Data Fig. 5e,f). Most of the mAUG-ds and uAUG-ds exhibited a folding energy ranging from –19.9 kcal mol–1 to –34.1 kcal mol–1 and had 12 to 20 base pairs in the stem (Fig. 2f), with the nucleotide GC pair significantly enriched in the stem and UCU and UUC in the loop compared to the background (Fig. 2g). Hierarchical clustering on these elements according to the sequence similarities within loops and stems showed that the largest class (class 1) contains mAUG-ds and uAUG-ds in 341 out of 1,746 transcripts (19.5%), including TBF1, ERECTA, LRR1 and ZF-MYND (Fig. 2h and Extended Data Fig. 6a–c). Moreover, most of the double-stranded structures begin within 25 nt downstream of uAUGs (Extended Data Fig. 6d). We next examined ribosomal occupancy on the predicted initiating uAUGs and non-initiating uAUGs and found a significant higher ribosome occupancy on the former than on the latter (Fig. 2i), suggesting that TISnet can also be used to accurately identify potential initiating uAUGs that have translational activities.

The pervasive presence of uAUG-ds in the TE-up transcripts is likely to contribute to the translation inhibitory roles of uAUGs under normal conditions, because downstream structures could slow the scanning of the translation preinitiation complex to enhance the chance of whole ribosome assembly36,37 and initiate translation from uAUGs instead of mAUGs. It is worth emphasizing that, in contrast to dsRNA structures upstream of AUGs, which normally inhibit translation38, the dsRNA structures downstream of AUGs identified in our study promote translation initiation.

uAUG-ds dynamics in plants and human cells

Because our Ribo-seq data revealed an elf18-triggered shift in translation from uORFs to mORFs in the TE-up transcripts (Fig. 1c,d), we hypothesized that this global translational reprogramming is regulated by structural changes of uAUG-ds. Indeed, we observed an overall elf18-induced increase in SHAPE reactivities in the uAUG downstream regions (Fig. 3a), suggesting a general enhancement in the unwinding of these regions in response to immune induction. More importantly, the extent of the change is much bigger in the TE-up transcripts than in the TE-nc and TE-down transcripts (Fig. 3a), highlighting the greater effect of immune induction on the structural changes of uAUG-ds in the TE-up transcripts. Closer examination of the four TE-up transcripts confirmed our global observation (Fig. 3b). We propose that the immune-induced reduction in uAUG-ds structural complexity allows the preinitiation complex to scan beyond the uAUGs to initiate translation from downstream mAUGs.

Fig. 3: RNA secondary structures downstream of uAUGs dynamically regulate translation.
figure 3

a, elf18-induced average changes in SHAPE reactivity downstream of translating uAUGs in TE-up (red) or TE-nc and TE-down (grey) transcripts. b, elf18-induced changes in SHAPE reactivity across nucleotides downstream of major inhibitory translating uAUGs of four TE-up transcripts. Red bars, nucleotides with median-to-high SHAPE reactivities. Blue asterisks, elf18-induced increases in SHAPE reactivities. c, In vivo SHAPE-MaP probing of TBF1 and TBF1-uAUG2-Δds (left) and dual-luciferase assay on their activities in controlling FLUC translation (right). 5′ LSTBF1, TBF1 5′ leader sequence. TBF1-F and TBF1-uAUG2-Δds-F, FLUC fused in-frame with the first 66 nt of uORF2 (uORF2*). d, Addition of uAUG and/or dsRNA structures affects synthetic reporter translation. All reporters have the same 5′ leader sequence length but different folding energies in the downstream region (100 nt) of uAUG: TUB7, TUB7-m1 and TUB7-m2 (−9.8 kcal mol−1); TUB7-m5 (−14.3 kcal mol−1); TUB7-m4 (−16.9 kcal mol−1); TUB7-m3, TUB7-m6 and TUB7-m7 (−23.6 kcal mol−1). e, Addition of an artificial hairpin downstream of uAUG2 further inhibits mammalian ATF4 translation. mORF*-FLUC, FLUC fused in-frame with the first 84 nt of ATF4 mORF. ATF4-m2, uAUG2 mutated to AAG. ATF4-uAUG2-ds, the downstream region of uAUG2 substituted with a hairpin without changing its length. ATF4-m2-ds, ATF4-uAUG2-ds with uAUG2 mutated to AAG. ATF4-F and ATF4-uAUG2-ds-F, FLUC fused in-frame with uORF2. f,g, Translation of mammalian BRCA1 is regulated by uAUGs (f) and their downstream dsRNA structures detected by in vivo SHAPE-MaP (g). Boxes, IQR; centre lines, median; whiskers, values within 1.5 × IQR of the top and bottom quartiles. P values for cf, two-tailed Student’s t-test; for g, two-tailed Mann–Whitney tests. Values are mean ± s.d. (n = 5 biological replicates in c,d; n = 4 biological replicates in e,f). For d,f, different letters indicate statistically significant differences (P < 0.05).

To validate the role of uAUG-ds in dynamically dictating start-codon selection and thus regulating downstream protein production, we first examined the uAUG2-ds in the 5′ leader sequence of the TBF1 transcript (TBF1-uAUG2-ds), using dual-luciferase reporters that were transiently expressed in Nicotiana benthamiana22. When we disrupted the base pairs in the hairpin structure by introducing point mutations in uAUG2-ds (TBF1-uAUG2-Δds) to mimic its structural opening in response to elf18 (Fig. 3c, left and Extended Data Fig. 7a,b), we observed a significant increase in the FLUC/RLUC activity (Fig. 3c, right). The role of uAUG2-ds in enhancing translation initiation from uAUG2 was further substantiated using another reporter in which FLUC is fused in-frame with uAUG2 instead of mAUG (Fig. 3c, right). Altogether, these results show that a double-stranded structure downstream of uAUGs (uAUG2 for the TBF1 transcript), instead of specific protein binding, is conducive to the uORF-mediated inhibition of downstream mORF translation by facilitating translation initiation from the uAUGs. This inhibition may be alleviated during stress, when the RNA double-stranded structure is unwound to allow the translation preinitiation complex to scan beyond uAUGs to initiate mORF translation.

To show that the dynamic function of uAUG-ds in regulating translation initiation is generalizable, we engineered a reporter using the naive 5′ leader sequence of the Arabidopsis TUB7 (tubulin beta-7) gene to drive the translation of FLUC in the dual-luciferase reporter system. We then mutagenized the 5′ leader sequence, without changing its length (Extended Data Fig. 7b), to introduce a uAUG in a strong or a weak Kozak context with or without artificial dsRNA structures (Fig. 3d). The resulting reporter activities showed that in addition to the Kozak sequence context, the uAUG-ds structures within the optimal range (that is, 12–20 base pairs; –19.9 to –34.1 kcal mol–1 in Fig. 2f) enhanced the recognition of uAUG for translation initiation and consequently dampened downstream reporter translation (Fig. 3d). However, in the absence of the uAUG, the structure alone did not inhibit downstream reporter translation (Fig. 3d, TUB7-m7), as long as it was within the optimal range of folding energy (Extended Data Fig. 7c), further supporting the role of uAUG-ds in engaging the ribosome to initiate translation from uAUGs.

To test whether the uAUG-ds-mediated translation initiation occurs in animals, we expressed the in-vitro-transcribed synthetic TUB7 reporter mRNAs and the Arabidopsis TBF1 reporter mRNAs in human HEK293FT cells (Extended Data Fig. 7d), and found that uORF-mediated reporter translation was most inhibited when uAUG-ds was present (Extended Data Fig. 7e,f). This result indicates that dsRNA enhances uAUG translation initiation in both plants and a human cell line. This conclusion was further supported when we introduced a dsRNA structure downstream of the uAUG2 in in-vitro-transcribed ATF4, a well-known mammalian stress-responsive gene13. This further inhibited the translation of ATF4 through enhanced translation initiation from the uAUG2 (Fig. 3e and Extended Data Fig. 7d).

We then showed that uAUG-ds structures are present in mammalian transcripts, by performing in vivo SHAPE-MaP analysis on a mutant version of the tumour suppressor BRCA1 mRNA that is found in breast cancer tissue. The translation of this mutant BRCA1 mRNA is known to be inhibited by uAUG2 and uAUG3, with uAUG2 having a stronger inhibitory effect than uAUG339 (Fig. 3f). Significantly lower SHAPE reactivities were detected downstream of uAUG2 and uAUG3, as compared with their upstream regions (Fig. 3g, left), further supporting our claim that uAUG-ds (Fig. 3g, right), instead of a primary protein-binding sequence, could be a universal mechanism for dynamic start-codon selection for translation initiation.

Immune-induced helicases unwind uAUG-ds

We next sought to answer the question of how uAUG-ds is unwound to facilitate immune-induced translation in plants. Previous studies have suggested that some DEAD-box RNA helicases can serve as alternatives to the canonical eukaryotic translation initiation factor 4A (eIF4A) in the preinitiation complex to unwind RNA for translation40,41,42. To identify potential candidates for the elf18-induced unwinding of uAUG-ds, we examined the changes in translational efficiency of the 54 known RNA helicases in Arabidopsis, and found 4 candidates that showed significant translational induction in response to elf18 (Fig. 4a). Among them, only RH37 was predicted to be localized in the cytoplasm. A genome-wide homology analysis across angiosperms revealed another two close RH37 homologues, RH11 and RH52 (Extended Data Fig. 8a), consistent with another study43. The translational inducibility by treatment with elf18 was confirmed for RH37 and RH11 using the dual-luciferase assay, in which the 5′ leader sequences of these helicase transcripts were used to drive the FLUC translation (Fig. 4b). Moreover, through comparisons of protein amino acid sequences, functional domains and structures predicted by AlphaFold44, we found that RH11, RH37, and RH52 are orthologous to the yeast Ded1p and human DDX3X (Extended Data Fig. 8b–d). The sequence and structural homology to the yeast Ded1p also aligns well with the anticipated function for RH11, RH37 and RH52, because the yeast Ded1p, which functions with other translation initiation factors in the preinitiation complex, is required to unwind highly structured regions in 5′ leader sequences during translation initiation42,45. Consistently, a previous study revealed that the Arabidopsis RH11 interacts with translation initiation factors22. In addition, mutating the yeast Ded1p helicase causes enhanced translation initiation from near-cognate start codons upstream of structured regions46. We hypothesized that, opposite to the helicase mutant, immune-induced increases in the levels of RH11, RH37 and RH52 might promote the unwinding of uAUG-ds, thus alleviating the uAUG-mediated inhibition of mORF translation.

Fig. 4: RNA helicases unwind RNA secondary structures downstream of uAUGs to alleviate repression of mAUG translation.
figure 4

a, Volcano plot of changes in translational efficiency for 54 known Arabidopsis RNA helicases after treatment with elf18. b, Translational responses of the 5′ leader sequences of RH37 (5′ LSRH37) and RH11 (5′ LSRH11) to elf18. P values were calculated by two-tailed Student’s t-test. Values are mean ± s.d. (n = 5 independent biological replicates). c, Effect of dex-induced expression of YFP-tagged RNA helicases (RH37 and RH11) (bottom) on translation of the 35S:TBF1 5LS-FLUC/35S:RLUC dual-luciferase reporter (top). HA-tagged RLUC levels were detected as internal controls. d, Effect of dex-induced expression of YFP-tagged RH37 on translation of the TUB7 synthetic reporters (top). For c,d, P values were calculated by two-tailed Student’s t-test. Values are mean ± s.e.m. (n = 5 independent biological replicates). e, Box plots of in planta changes in SHAPE reactivity in the endogenous uAUG-ds regions of four TE-up and two TE-nc transcripts in wild-type (WT) and the helicase-mutant (rh37rh52) plants. For transcripts with two translating uAUGs (TBF1, ZIK10, ZIK6 and bZIP1), changes in the downstream region of the major inhibitory uAUGs (that is, uAUG2-ds) are shown. Data were analysed by two-tailed Wilcoxon signed-rank tests. *P < 0.05, **P < 0.01, ****P < 0.0001. Boxes, IQR; centre lines, median; whiskers, values within 1.5 × IQR of the top and bottom quartiles. f, Elf18-induced protection against Psm ES4326 in wild-type plants and helicase mutants (n = 12 plants). Bacterial growth (in colony-forming units; CFU) was measured two days after inoculation and is shown as mean ± s.e.m. P values were calculated by two-way ANOVA. The experiment was repeated twice with similar results. g, A model of RNA-secondary-structure-mediated translational regulation of uORF-containing transcripts during PTI.

To test our hypothesis, we built the constructs Dex:RH37-YFP and Dex:RH11-YFP to put the transcription of RH37-YFP and RH11-YFP under the control of a dexamethasone (dex)-inducible system47 and transiently coexpressed each with the dual-luciferase reporter driven by the 5′ leader sequence of TBF1 in N. benthamiana. Notably, we observed a significant increase in the FLUC activities four hours after treatment with dex (Fig. 4c). This suggests that a transient increase in the expression of these RNA helicases could lead to enhanced translation of TBF1.

We next showed that the effect of these helicases is through remodelling of uAUG-ds, because it was only observed when RH37 was coexpressed with the synthetic TUB7 reporter that contains uAUG-ds (Fig. 4d). This result once again demonstrates that uAUG-ds can serve as a molecular switch to dynamically regulate translation initiation.

Finally, to confirm the roles of the RH11, RH37 and RH52 helicases in elf18-induced translation genetically, we generated rh37rh52, rh11rh52, and rh11rh37 double-mutant lines using a high-efficiency CRISPR method48 (Extended Data Fig. 9a–c). Because the rh11rh37 mutant exhibited a developmental defect, whereas the rh37rh52 and the rh11rh52 plants had almost wild-type morphology (Extended Data Fig. 9d), we chose to use rh37rh52 for targeted in planta SHAPE-MaP of the endogenous transcripts representing the TE-up and TE-nc groups. We found that in the TE-up transcripts, the elf18-induced structural opening in the downstream regions of uAUGs was observed in wild-type plants, but diminished in the helicase double mutant (Fig. 4e), supporting the involvement of RH11, RH37 and RH52 in elf18-induced unwinding of uAUG-ds. Moreover, we examined elf18-induced changes in the levels of four proteins with available antibodies in wild-type and helicase-mutant (rh37rh52) plants and showed that increases in protein levels from those two transcripts containing translating uAUGs were dependent on the helicase activities (Extended Data Fig. 9e).

To examine the global effect of the helicase mutations on elf18-induced resistance against pathogens, we performed bacterial infection using Pseudomonas syringue pv. maculicola ES4326 (Psm ES4326) in wild-type, rh37rh52 and rh11rh52 mutant plants after pre-treating plants with elf18. As a negative control, we included the elf18 receptor mutant, efr. We found that the helicase mutants had higher basal resistance to Psm ES4326 than did the wild-type plants (Fig. 4f), suggesting that they might affect transcripts other than those involved in PTI. Nevertheless, the helicase mutants had significantly diminished sensitivity to elf18-induced resistance, resulting in more overall bacterial growth (Fig. 4f); this clearly shows that these helicases have indispensable roles in the translational regulation of PTI. Altogether, our results show that the elf18-inducible RNA helicase RH37 and its homologues RH11 and RH52 are involved in unwinding uAUG-ds in the TE-up transcripts and in promoting the translation of downstream defence proteins against pathogen challenges.


In this study we have discovered that uAUG-ds is crucial for dynamic start-codon selection for translation initiation during plant PTI. Without stress, the translation of defence proteins is inhibited by uORFs, owing to the presence of uAUG-ds, which slows the scanning of the preinitiation complex to engage the ribosome to initiate translation from uAUGs instead mAUGs. In response to stress, the expression of RH37-like helicases, known to be associated with the translation preinitiation complex22,42,45,46, is increased to facilitate the unwinding of uAUG-ds, thus promoting the bypass of uAUGs and the translation of downstream defence proteins (Fig. 4g).

Although this study was initiated to study uAUG-modulated translation in a plant immune response, the pervasive presence of the dsRNA structures downstream of both mAUGs and translating uAUGs (Fig. 2b,c), the unbiased deep learning results (Fig. 2e–i and Extended Data Figs. 5 and 6), and the functional data obtained from studies in both plants and mammalian systems (Fig. 3 and Extended Data Fig. 7) strongly support the fundamental importance of mAUG-ds and uAUG-ds in regulating translation in general. In contrast to the Kozak sequence context, which is crucial for start-codon recognition in static conditions, the uAUG-ds discovered in this study can be dynamically remodelled in response to stimuli to reprogram translation. Notably, such dynamic regulation also occurs for transcripts that contain only mAUG-ds, which are enriched with transcripts in the TE-down category in response to elf18 treatment and found to encode growth-related proteins (Extended Data Fig. 10a,b). This finding indicates that immune-induced helicases can also unwind mAUG-ds and reduce translation from mAUG to inhibit the production of growth-related proteins (Extended Data Fig. 10c).

Our discovery of AUG-ds in this study was only possible through the integrated application of transcriptome-wide translational and structural analyses and deep learning algorithms, because such structural features are unlikely to be detected through sequence homology. The strategy used here can be readily expanded to identify and characterize AUG-ds structures in other organisms, as AUG-ds regulate translation in different organisms (Fig. 3 and Extended Data Fig. 7). Indeed, the observed global structural patterns of mRNA surrounding mAUGs in yeast49 and Caenorhabditis elegans50 are consistent with the presence of mAUG-ds. Together with the fact that Ded1p, DDX3X and RH37 helicases are highly conserved from plants to humans (Extended Data Fig. 8), we hypothesize that the uAUG-ds–RNA helicase regulatory module is broadly present in eukaryotes. Moreover, the general features of mAUG-ds and uAUG-ds revealed in this study (Fig. 2e–g) provide information for the rational design of protein synthesis for basic research as well as for applications in agriculture, in medicine and beyond. Using well-trained deep learning models in different organisms, potential uAUG-ds of functional genes can be identified to manipulate their translation. Our success in engineering an inducible translational reporter that functions in plants as well as in human cells (Figs. 3d and 4d and Extended Data Fig. 7f) gives us confidence in the applicability of uAUG-ds as a molecular switch for regulating gene expression.


Plant growth, treatment with elf18 and transformation

Arabidopsis seedlings were grown on 1/2 Murashige and Skoog (MS) plates containing 0.8% agar and 1% sucrose or in soil, both at 22 °C under 12–12-h light–dark cycles with 55% relative humidity. Unless specified, all Arabidopsis plants used in the experiments were in the Col-0 background. N. benthamiana plants were grown under the same conditions in soil as those for Arabidopsis for four to five weeks before experiments. For treatment with elf18, Arabidopsis seedlings were grown on plates for seven days, transferred to liquid 1/2 MS solution and grown for one more day before being treated with 10 μM elf18 or water for 1 h. Transgenic plants were generated using the agrobacterium-mediated transformation method involving floral dipping51.

Cell line

The HEK293FT cell line was purchased from the Duke Cell Culture Facility (Invitrogen, R700-07). All cells tested negative for mycoplasma contamination. Cell line identity was confirmed by STR authentication. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum and 100 U ml−1 penicillin-streptomycin at 37 °C and incubated with 5% CO2, 95% air.

Plasmid construction

The backbone (pTC090-32) for the dual-luciferase constructs used for expression in plants was generated in a previous study22. The 5′ leader sequences of the transcripts being tested were PCR-amplified from the Col-0 cDNA, and that of the TUB7 transcript was synthesized by IDT before being inserted into the backbone through ligation-based reactions (NEB) or using the ClonExpress II One Step Cloning Kit (Vazyme). The site mutations and hairpin structures were introduced by primer-based PCR.

For in vitro transcription and expression in the mammalian cell line, the 5′ leader sequence of the ATF4 transcript was PCR-amplified from the normal lung fibroblast cell line IMR90 cDNA. The 5′ leader sequence of the BRCA1 transcript was PCR-amplified from genomic DNA from the human breast cancer cell line MCF7. All of the 5′ leader sequences were cloned into the plasmid backbone with the FLUC reporter by Gibson Assembly (NEB). The site mutations and hairpin structures were introduced by primer-based PCR.

To generate the plasmids with dex-inducible expression of RNA helicases, the CDSs of RH11 and RH37 were PCR-amplified from the Col-0 cDNA and cloned into pBSDONR p1-p4, separately. Each of these clones was then paired with the YFP tag, which was cloned in pBSDONR p4r-p2, to generate fusion constructs in the pBAV154 destination vector by multisite LR reaction (LR clonase II plus, Thermo Fisher Scientific). The CRISPR knock-out lines were built through a highly efficient multiplex editing method48. In brief, to construct the shuttle vectors, four guide RNA sequences, TAAACCGCCCGTGAACCACG, TAGACTCCCCGAACTCCACG, TAGACTGTTCGTGAACCACG and TGGTCTTGACATTCCCCACG, were loaded into the pDEG332, pDEG333, pDEG335 and pDEG337 modules, respectively. Then these guide RNA sequences were assembled into arrays in the recipient vector (pDGE666).

All of the primers and oligos used in this study are listed in Supplementary Table 1. All constructs were confirmed by Sanger sequencing before use.

Ribo-seq and RNA sequencing

Arabidopsis seedlings treated with elf18 or water as described above were collected, frozen in liquid nitrogen and ground using the Genogrinder (SPEX SamplePrep). Polysome profiling was performed as described previously20. In brief, the ground tissue was homogenized in the polysome extraction buffer and centrifuged to remove cell debris. The supernatant was then layered on top of a sucrose cushion and the ribosome pellet was collected after ultracentrifugation. The pellet was then washed with cold water and subjected to RNase I (Ambion) digestion. The reaction was quenched by adding SUPERaseIn (Invitrogen). Ribosome-bound RNA was purified and subjected to treatment with PNK (NEB) and size selection through gel (Invitrogen) extraction. The recovered RNA was then subjected to library preparation using the NEBNext Multiplex Small RNA Library Prep Kit with slight modifications. Specifically, after the reverse transcription, rRNA depletion was performed. In brief, the cDNA product was cleaned up with the Oligo Clean & Concentrator Kit (Zymo) and then eluted with water. The eluted product was mixed with 0.4-nmol probes used in previous studies20,52 in the saline-sodium citrate (SSC) solution, and the mixture was subjected to denaturation at 100 °C for 90 s, followed by a gradual decrease of temperature from 100 °C to 37 °C to allow annealing of the ribosomal DNA (rDNA) and the biotinylated oligos. The mixture was then incubated with 200 μg pre-washed Dynabeads MyOne Streptavidin C1 beads (Invitrogen) for 15 min at 37 °C with constant shaking. The tube was then placed on a magnetic rack for another 5 min and the flow-through was collected and cleaned up using the Oligo Clean & Concentrator Kit (Zymo). This rDNA-depleted product was used as the template for PCR amplification and library preparation. The Agilent 2100 Bioanalyzer was used for the sample quality control (Extended Data Fig. 1a). RNA from the same lysate was isolated and subjected to library preparation using the KAPA Stranded mRNA-Seq Kit (Roche). The six libraries for Ribo-seq (three mock and three elf18-induced) were pooled at equal amounts of DNA and subjected to next-generation sequencing using the Illumina NovaSeq (S2, full flow cell) with paired-end reads of 50 bp in length. The six libraries for RNA sequencing (RNA-seq) (three mock and three elf18-induced) were pooled at equal amounts of DNA and subjected to next-generation sequencing using the Illumina NovaSeq (S Prime, 1 lane) with paired-end reads of 50 bp in length.

Ribo-seq and RNA-seq data processing

Ribo-seq read processing was performed following the steps shown in Extended Data Fig. 2a. Specifically, raw reads were trimmed using Trim Galore v.0.6.6, a wrapper tool of Cutadapt53 and FastQC54. The trimmed reads with a length longer than or equal to 24 nt and shorter than or equal to 35 nt were kept and mapped to the rRNA and tRNA library from the Arabidopsis TAIR 10 genome using Bowtie 2 v.2.4.2 (ref. 55). The unmapped reads were then assigned to the Arabidopsis TAIR 10 genome using STAR v.2.7.8a (ref. 56) with –outFilterMismatchNmax 3 –outFilterMultimapNmax 20 –outSAMmultNmax 1 –outMultimapperOrder Random. FastQC v.0.11.9 (ref. 54) and MultiQC v.1.9 (ref. 57) were applied for quality control during each step. Similarly, RNA-seq reads were trimmed and mapped using the same programs under default parameters.

To assess the data quality, we first determined the read length distribution (Extended Data Fig. 1b) and the reads per kilobase of transcript per million mapped reads (RPKM) for all the transcripts in each replicate for the RNA-seq- and Ribo-seq-mapped reads using the featureCount program58 embedded in the Subread package v.2.0.3, and plotted the Pearson correlations between every two replicates (Extended Data Fig. 1c,d). Then we determined the P-site offset near start and stop codons for reads with a length ranging from 24 nt (24-mers) to 35 nt (35-mers) in Ribo-seq using Plastid v.0.6.1 (ref. 59; Extended Data Fig. 1e). Next, we determined the nucleotide periodicity 300 nt downstream of the start codons by calculating the power spectral density (Extended Data Fig. 1f). In addition, we calculated the distribution of RNA-seq and Ribo-seq reads in the 5′ leader sequence, CDS and 3′ UTR of each transcript from mock- and elf18-treated samples (Extended Data Fig. 1g). A metaplot of the normalized distribution of Ribo-seq reads on the normalized transcript was calculated using the computational genomics analysis toolkit (CGAT)60 (Extended Data Fig. 1h). Changes in translational efficiency were calculated using deltaTE61. GO enrichment was performed online using the Gene Ontology resource23,24,25 ( and the results were visualized using enrichplot62.

Identification of translating mAUGs and uAUGs

To identify transcripts with detectable translation initiation from mAUGs, we analysed 25,554 detected transcripts that had an RPKM of exon ≥ 1 in all of the six RNA-seq samples and a RPKM of CDS ≥ 1 in all of the six Ribo-seq samples (Extended Data Fig. 2a). We then calculated ribosome footprints spanning every mAUG for all the 25,554 detected transcripts and normalized each count by total read count and transcript abundance. To set the background read count, we took the top (Q3) quartile of the normalized read counts from regions 50 nt upstream of mAUGs of 5,482 transcripts that have 5′ leader sequences ≥ 100 nt without uAUGs (Extended Data Fig. 2b). Using the resulting background cut-off at 23.17, transcripts with normalized read counts at mAUG ≥ 23.17 and with raw read counts at mAUG ≥ 10 in all of the six Ribo-seq samples were retained, and this yielded 13,051 ‘expressed transcripts’ with detectable translation initiation from mAUGs (Extended Data Fig. 2a).

To identify the uAUGs that can engage ribosomes and facilitate translation initiation, we performed similar calculation and normalization steps for ribosome footprints spanning every uAUG located in the 5′ leader sequences of all the 13,051 expressed transcripts. uAUGs with normalized read counts ≥ 23.17 and with raw read counts ≥ 10 in all of the three replicates in the mock condition and/or in response to elf18 were selected and termed ‘translating uAUGs’ (Extended Data Fig. 2a). A total of 5,626 translating uAUGs were identified from the 13,051 expressed transcripts. The remaining 7,968 uAUGs in the 13,051 expressed transcripts are ‘non-translating uAUGs’.

In vivo SHAPE-MaP in plants and in mammalian cells

The SHAPE reagent, 2-methylnicotinic acid imidazolide (NAI), was synthesized as described previously63. For in vivo SHAPE-MaP in plants, Arabidopsis seedlings treated with elf18 or water or tobacco leaves transiently expressing the dual-luciferase reporters were collected and immediately immersed in the fresh NAI solution (100 mM NAI) or in dimethyl sulfoxide (DMSO) solution as previously described64. To enhance the permeability of NAI, samples immersed in the solution were vacuum-infiltrated and incubated at room temperature for 20 min. To quench the reaction, DTT (dithiothreitol; Roche) was added to the solution for a final concentration of 0.5 M, and incubated for 2 min. The tissue was then washed with water three times, frozen in liquid nitrogen, ground and subjected to total RNA isolation using the Direct-zol RNA Miniprep Plus Kit (Zymo).

For in vivo SHAPE-MaP in the human HEK293FT cell line, cells were collected, washed once with cold 1× PBS after the removal of culture medium and collected in a 1.5-ml tube. Cells were immediately resuspended in 500 μl fresh NAI solution (100 mM NAI) or in 500 μl DMSO solution, and incubated at room temperature with gentle rotation for 5 min. The reaction was stopped by centrifuging the samples at 100,00g at 4 °C for 1 min and removing the supernatant. The sample was immediately resuspended in Trizol (Invitrogen) for total RNA isolation using the Direct-zol RNA Miniprep Plus Kit (Zymo).

The purified total RNA from plants or HEK293FT cells was subjected to DNase treatment by adding 2 μl Turbo DNase (2 U μl−1) and incubated at 37 °C for 30 min, followed by the addition of another 2 μl Turbo DNase (2 U μl−1) and incubation for another 30 min. RNA was then purified by the RNA Clean & Concentrator Kit (Zymo). mRNA was enriched twice through poly(A) selection using Oligo d(T)25 Magnetic Beads (NEB), and subjected to reverse transcription (mRNA in 2.5 μl nuclease-free water, 1 μl 10 mM dNTP (NEB), 1 μl Random Primer 9 (NEB) and 2 μl 5× First-Strand Buffer (Invitrogen), 0.5 μl 0.2 M DTT (Invitrogen), 0.5 μl TGIRT-III (InGex), 0.5 μl SUPERaseIn (Invitrogen) and 2 μl 5 M betaine solution (Sigma-Aldrich)). The cDNA product was cleaned up using the Oligo Clean & Concentrator Kit (Zymo) and the library preparation was performed as described previously65, under the randomer library preparation workflow. Agilent 2100 Bioanalyzer was used for the sample quality control. For the global SHAPE-MaP, libraries were pooled and subjected to next-generation sequencing using the Illumina NovaSeq (S4, full flow cell) with paired-end reads of 150 bp in length. For the targeted SHAPE-MaP, gene-specific PCR primers (Supplementary Table 1) were used for the library preparation as described previously65, under the amplicon library preparation workflow.

In vitro SHAPE-MaP in plants

Arabidopsis seedlings treated in the mock condition were collected, frozen in liquid nitrogen, ground and subjected to total RNA isolation using the Direct-zol RNA Miniprep Plus Kit (Zymo). The purified RNA was subjected to DNase treatment, clean-up and poly(A) selection as mentioned above. To probe the in vitro RNA secondary structures, 500 ng purified mRNA was mixed with NAI (100 mM) or DMSO in a SHAPE reaction buffer (100 mM HEPES, 6 mM MgCl2 and 100 mM NaCl) and incubated at room temperature for 5 min. The reaction was then quenched by purifying RNA using the RNA Clean & Concentrator Kit (Zymo). The treated mRNA was then subjected to reverse transcription, library preparation and next-generation sequencing as described above.

SHAPE-MaP data processing

For global SHAPE-MaP data processing, raw reads were trimmed with Trim Galore v.0.6.6. The trimmed reads were mapped to the rRNA and tRNA library from the Arabidopsis TAIR 10 genome using Bowtie 2 v.2.4.2 (ref. 55), and the unmapped reads were aligned to the Arabidopsis TAIR 10 transcriptome using Bowtie 2 v.2.4.2 (ref. 55). Mapped reads from all four replicates in each group were combined for the following analyses66,67: (1) parse the mutations using shapemapper_mutation_parser; (2) count mutation events using shapemapper_mutation_counter; (3) summarize mutation events and calculate SHAPE reactivities using and Unless specified, only nucleotides with ≥1,000 read coverage and with 0 ≤ SHAPE reactivities ≤ 6 were used for subsequent analyses to ensure accurate structural prediction30. To examine the correlation between replicates, SHAPE reactivity for every transcript in each replicate was calculated individually, and the Pearson correlation coefficient for each transcript was determined in R v.4.1.0 using the Hmisc package ( For targeted SHAPE-MaP data processing, raw reads were processed using ShapeMapper 266. To ensure adequate read coverage and completeness, more than 100,000 reads per nucleotide were achieved for more than 90% of the targeted regions. Delta SHAPE reactivity was calculated by taking the log2-transformed fold change (elf18/mock) for the SHAPE reactivities of the nucleotide in each position. These values were then smoothed over 10-nt sliding windows68. It is worth noting that among the four nucleotides, the increases in mutation rates for adenines in NAI-modified samples were comparably modest (Extended Data Fig. 3d), suggesting that adenine might be less sensitive than the other three residues to NAI modification. However, this does not affect the conclusion of this study, which focuses on identifying the base-pairing status of a region rather than individual nucleotides.

Training and validation of TISnet

To analyse the structure patterns in downstream regions of initiating AUG, we trained a deep neural network to predict translation initiation sites by adapting the PrismNet model69. Downstream regions (101 nt) of mAUGs in transcripts with the top 40% translational efficiency (mAUGs, high likelihood of initiating translation) were used as positive samples and downstream regions of AUGs randomly selected from CDSs or 3′ UTRs (internal AUGs, unlikely to initiate translation) were used as negative samples. Both positive and negative samples must have high SHAPE reactivity coverage (>25%). For the downstream region (101 nt) of each AUG, we predicted RNA secondary structures using RNAfold70 with SHAPE reactivity data used as a soft constraint involving a pseudo-free energy calculation under default parameters (the slope ‘m’ is 1.8 and the intercept is –0.6)71. Then we trained TISnet to classify initiating and non-initiating AUGs by integrating sequence and secondary structure information.

More specifically, we labelled the positive samples as 1, and negative samples as 0. We then encoded the sequence by one-hot encoding (A, C, G, U, 4-dimension), and encoded RNA secondary structures of each nucleotide to 0 or 1 (0 for nucleotides in double-stranded structures; 1 for nucleotides in single-stranded regions). The labels and encodings of samples were used as the input for the deep neural network. We then randomly split the positive and negative samples into a training set and a validation set by 4:1, and trained the network and validated the prediction performance of the network using the two sets, respectively.

Identification of structural elements

To find the sequence pattern of hairpin elements, we extracted the hairpin elements with long stems (more than 15 base pairs) from the downstream regions of predicted initiating AUGs. Then we calculated the k-mer (k = 3) frequency of the loop sequences and the frequency of base pairs in each position (for example, base pairs are counted starting from the loop) of the stem. We further identified conserved structure elements by clustering hairpin elements into classes, on the basis of the sequence similarity between each two hairpin elements. For two sequences, we aligned them by the Needleman–Wunsch algorithm and defined sequence identity as:

$${\rm{Sequence\; identity}}=\,\frac{{\rm{Number\; of\; aligned\; nucleotides}}}{{\rm{Number\; of\; aligned\; and\; unaligned\; nucleotides}}}$$

We divided each hairpin element into 5′ stem sequence (stem-1), loop sequence and 3′ stem sequence (stem-2) (Extended Data Fig. 6c), and calculated the average of sequence identities of these three parts to represent the sequence similarity between two hairpin elements. We calculated the sequence similarity between each two hairpin elements and clustered all hairpin elements in downstream regions of predicted initiating AUGs by the hierarchical clustering algorithm. For each class of hairpin elements, we performed multiple alignment of the stem sequences and the loop sequences and calculated the frequency of nucleotides in each position to construct the position weight matrix (PWM) of the sequence motif. The secondary structures of downstream regions of AUGs were visualized by VARNA72.

5′ rapid amplification of cDNA ends

For the 5′ rapid amplification of cDNA ends (RACE) experiment on the RNA products from all the constructs expressed in plants, a FLUC-specific reverse transcription primer (Supplementary Table 1) and the Template Switching RT Enzyme Mix (NEB) were used during cDNA synthesis; this was followed by template switching using the Template Switching Oligo. PCR amplification of the 5′ region of transcripts was performed using Q5 Hot Start High-Fidelity Master Mix (2×) (NEB).

In vitro transcription

For in vitro transcription, the PCR product containing a T7 RNA polymerase promoter (GCTAATACGACTCACTATAGGG) was used to generate mRNA by using the mMESSAGE mMACHINE T7 ULTRA Transcription Kit (Ambion, AM1344) according to the manufacturer’s instructions. The mRNA product was purified using the MEGAclear Transcription Clean-Up Kit (Ambion, AM1908). To validate the quality of the mRNA product, samples were run on 1% denaturing agarose gel and stained with SYBR Gold (Invitrogen).

Dual-luciferase assay

The dual-luciferase assay for plant samples was performed as described20. In brief, an overnight culture of the Agrobacterium strain GV3101 transformed with the dual-luciferase construct was collected, resuspended in the infiltration buffer (10 mM MgCl2, 10 mM MES and 200 μM acetosyringone), adjusted to an optical density at 600 nm (OD600 nm) of 0.2 and incubated at room temperature for an additional 2 h before infiltrating into N. benthamiana for transient expression. After 24 h of incubation, leaf discs were collected, ground in liquid nitrogen and lysed with 1× passive lysis buffer (Promega). The lysate was centrifuged at 12,000g for 3 min, and 10 μl supernatant was used for measuring FLUC and RLUC activities as previously described20. For the experiment with dex-induced expression, the Agrobacterium strain with the dual-luciferase construct and the strain with the dex-inducible RNA helicase construct were co-infiltrated into N. benthamiana leaves and incubated for 20 h. Then, the leaves were sprayed with 25 μM dex solution in water and incubated for another 4 h before sample collection.

The dual-luciferase assay in the human cell line was performed according to the manufacturer’s instructions (Promega). In brief, HEK293FT cells were seeded into 96-well plates and grown overnight to approximately 70% confluence at the time of transfection. Then, 100 ng of FLUC mRNAs and 100 ng of RLUC mRNAs were co-transfected into HEK293FT cells using 0.3 µl Lipofectamine MessengerMAX Transfection Reagent (Invitrogen) for each well. After a 5-h incubation, cells were collected and washed once with cold 1× PBS after the removal of the culture medium. Fifty microlitres of 1× passive lysis buffer (Promega) was used to extract the proteins according to standard procedures, and 10 µl lysate was used for measuring FLUC and RLUC activities as previously described20.

Western blotting assay

To detect the dex-induced YFP-tagged proteins, the blot was probed with anti-GFP (Clontech, 632381, 1:5,000) primary antibodies. To detect HA-tagged proteins, the blot was probed with anti-HA HRP-conjugated antibody (Cell Signaling Tech, 2999, 1:3,000). To detect endogenous proteins, the blot was probed with anti-ARF2 primary antibody (PhytoAB, PHY2435A, 1:2,000), anti-CH1 primary antibody (PhytoAB, PHY1909S, 1:2,000), anti-RBOHD primary antibody (Agrisera, AS15 2962, 1:2,000), anti-ICS1 primary antibody (Agrisera, AS16 4107, 1:2,000) or anti-β-tubulin primary antibody (Santa Cruz Biotech, sc-166729, 1:2,000). For secondary antibodies, anti-rabbit-HRP antibody (Cell Signaling Tech, 7074, 1:3,000) or anti-mouse-HRP antibody (Abcam, Ab97040, 1:10,000) were used.

Elf18-induced resistance to Psm ES4326

The elf18-induced resistance experiment was performed as previously described20. In brief, Arabidopsis plants were grown in soil for three to four weeks and infiltrated with 1 μM elf18 or mock treatment (water) one day before infection with Psm ES4326 (in 10 mM MgCl2 solution at OD600 nm = 0.001) in the same leaf. Bacterial growth was measured two days after infection.

Statistics and reproducibility

Unless specified, statistical tests were performed using GraphPad Prism v.8.0 or in R v.4.1.0. The statistical methods and number of experimental replicates are indicated in the figure legends. Unless specified in the figures or legends, no adjustments were made for multiple comparisons. In the graphs (except for Fig. 3b,c), asterisks and lower-case letters indicate statistical significance reflecting the P values (*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001; NS, not significant). The number of data points for the analyses shown in Figs. 2c,d and 3g and Extended Data Fig. 4d are as follows: upstream, n = 50; downstream, n = 50. For Fig. 2e, m/iAUG, predicted non-initiating AUG, n = 7,083; predicted initiating AUG, n = 2,917; uAUG, predicted non-initiating AUG, n = 895; predicted initiating AUG, n = 933. For Fig. 2i, only transcripts with high expression levels (RPKM > 19) were used for the analysis. Predicted non-initiating AUG, n = 450; predicted initiating AUG, n = 464. For Fig. 4e, WT, n = 50; rh37rh52, n = 50. For Extended Data Fig. 4c,e, in vivo, n = 50; in vitro, n = 50. Unless specified, experiments were repeated at least three times with similar results. Original gel images can be found in Supplementary Fig. 1.

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.