Translational landscape during seed germination revealed by ribosome profiling

TL;DR

This study uses ribosome profiling to uncover how translation is regulated during seed germination in Arabidopsis, revealing new insights into the molecular mechanisms that support early plant development.

Contribution

The study provides the first ribosome profiling analysis across seed germination stages, identifying translational control mechanisms and seed-specific regulatory elements.

Findings

Dry seeds show unique ribosome association patterns with higher ribosome density at the 5′ and 3′ UTRs.

Start codon-specific ribosome stalling in dry seeds is linked to adenine-enriched sequence motifs.

Seed-specific upstream open reading frames (uORFs) and long non-coding RNAs are involved in translational regulation during germination.

Abstract

Seed germination is crucial for agricultural reproduction. A deep understanding of this process can secure healthy growth at the early phases of plant development and therefore yield. Recent research indicates that germination is a complex process involving translational regulation. A large group of seed‐stored mRNAs together with newly synthesized transcripts are regulated by post‐transcriptional mechanisms and selectively translated at different stages to support the germination process. To investigate the mechanism of translational control, we performed ribosome profiling on mRNAs of distinct physiological stages during Arabidopsis thaliana seed germination. The presence of ribosome association on mRNAs with three‐nucleotide periodicity indicates their capacity for translation. Dry seeds, in which translation is on hold, are characterized by a unique ribosome association landscape with a higher ribosome association at the 5′ and 3′ UTR, compared with physiological stages that show active translation. Start codon‐specific stalling of ribosomes in dry seeds is associated with an adenine‐enriched sequence motif. Throughout germination, codons encoding glycine, aspartate, tyrosine, and proline are the most frequent ribosome pausing sites. Moreover, the non‐coding ribosome‐associated RNAs that we identified are indeed translated, as was revealed by investigating total seed proteome data. Seed‐specific upstream open reading frames (uORFs) have been identified that may play a role in translational regulation of early seed germination. Altogether, we present a first ribosome profiling analysis across seed germination that illuminates various regulatory mechanisms that potentially contribute to the seed's survival strategy.

We have performed polysome profiling to reveal mechanisms underlying the translational control of seed germination. In dry seeds, we identified ribosome stalling at both the 5′ and 3′ untranslated regions (UTR) and start codon‐specific stalling at adenine‐enriched sequence motifs. Moreover, we have identified a role for seeds specific upstream open reading frames (uORFs) and long non‐coding mRNAs in the regulation of translation during seed germination.

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