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The D1 subunit of photosystem II (PSII) is subject to light-induced damage. In plants, D1 photodamage activates translation of chloroplastpsbAmRNA encoding D1, providing D1 for PSII repair. Three D1 assembly factors have been implicated in the regulatory mechanism: HCF244 and RBD1 activatepsbAtranslation, whereas HCF136 repressespsbAtranslation in the dark. To clarify the regulatory circuit, we analyzedpsbAribosome occupancy in dark-adapted and illuminatedrbd1andrbd1;hcf136double mutants in Arabidopsis and in Zm-hcf244and Zm-hcf244;Zm-hcf136double mutants in maize. The results show that RBD1 is required for light-inducedpsbAtranslation but has only a small effect onpsbAribosome occupancy in the dark. RBD1 is not required forpsbAtranslation when HCF136 is absent, indicating that RBD1 activatespsbAtranslation in the light by inhibiting HCF136’s repressive effect. By contrast, HCF244 is required to recruit ribosomes topsbAmRNA in light, dark, and in the absence of HCF136. We demonstrate further that HCF244 is not required for the translational activator HCF173 to bind thepsbA5’UTR. These results show that RBD1 is central to the perception of the D1 photodamage that triggers D1 synthesis and that it activatespsbAtranslation by relieving repression by an HCF136-dependent assembly intermediate. HCF244 activates downstream of those events without impacting HCF173’s binding topsbAmRNA. The results implicate a feature of nascent D1 that is affected by both HCF136 and RBD1 as the signal that reports D1 photodamage to regulatepsbAtranslation rate as needed for PSII repair.
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This content will become publicly available on June 17, 2026
Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model
Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pretrained on large-scale biological sequences can capture evolutionary conservation and offer cross-species prediction better than supervised models through fine-tuning limited labeled data. We introduce PlantCaduceus, a plant DNA LM that learns evolutionary conservation patterns in 16 angiosperm genomes by modeling both DNA strands simultaneously. When fine-tuned on a small set of labeledArabidopsisdata for tasks such as predicting translation initiation/termination sites and splice donor/acceptor sites, PlantCaduceus demonstrated remarkable transferability to maize, which diverged 160 Mya. The model outperformed the best existing DNA language model by 1.45-fold in maize splice donor prediction and 7.23-fold in maize translation initiation site prediction. In variant effect prediction, PlantCaduceus showed performance comparative to state-of-the-art protein LMs. Mutations predicted to be deleterious by PlantCaduceus showed threefold lower average minor allele frequencies compared to those identified by multiple sequence alignment-based methods. Additionally, PlantCaduceus successfully identifies well-known causal variants in bothArabidopsisand maize. Overall, PlantCaduceus is a versatile DNA LM that can accelerate plant genomics and crop breeding applications.
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- Award ID(s):
- 2145577
- PAR ID:
- 10618170
- Publisher / Repository:
- PNAS
- Date Published:
- Journal Name:
- Proceedings of the National Academy of Sciences
- Volume:
- 122
- Issue:
- 24
- ISSN:
- 0027-8424
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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