Post-translational modifications (PTMs) play crucial regulatory roles in plants, orchestrating protein functions to maintain metabolic homeostasis, enable adaptation to dynamic environments, and regulate diverse cellular processes. Thus, the identification of PTM sites is essential for elucidating the mechanisms underlying plant growth, development, and stress responses. However, reliable and cost-effective computational approaches for predicting PTM sites in plants remain lacking. Here, we present PlantPTM, an integrated deep learning framework for predicting nine PTM types in plants. By combining protein language models (PLMs) with evolutionary information, PlantPTM demonstrates robust generalizability across a wide range of PTM types and plant species. Our method achieves state-of-the-art performance, with a mean AUROC of 0.8640 and a peak AUROC of 0.9699 across the nine PTM types. Notably, PlantPTM maintains strong performance even under low-data scenarios and unseen species. Extensive comparative benchmarks demonstrate that PlantPTM outperforms existing PTM prediction tools by an average of 15.46%, with improvements ranging from 2.90% to 19.08% over the best-performing tools for each PTM type. Furthermore, independent in-house MS data confirmed the accuracy of PlantPTM for ubiquitination, acetylation, and N-glycosylation sites, with all AUROC values exceeding 0.8. To facilitate PTM studies in plants, we provide the PlantPTM online service and source code freely available at https://ai4bio.online/PlantPTM and https://github.com/wky0422/PlantPTM, respectively.
S-domain receptor-like kinases (S-RLKs) represent a typical RLK subfamily, which plays key roles in various biological processes in plants. However, the genome-wide evolutionary and functional differentiation of this family remains unclear in rice. In the present study, a comprehensive computational analysis was employed and identified 109 S-RLKs in 9311 genome and 103 S-RLKs in Nipponbare (Nip) genome. The S-RLKs were unevenly distributed across 12 chromosomes. Bioinformatics analysis indicate large-scale gene duplication and family expansion may be the main driving forces for the expansion of S-RLK family members. Although the S-RLKs are highly conserved between the two subspecies, it remains unknown whether these members have undergone functional differentiation during long-term evolution. Given the differences of roots and nitrogen (N) utilization in 9311 and Nip, we focused on the S-RLKs which exhibit different expressions in roots. OsNRS1 (Nitrogen-responsive Root S-domain kinase 1) was selected due to its expression in the roots of 9311 notably more than that in Nip. Phenotypic analysis showed that OsNRS1 CRISPR/Cas9 mutants in 9311 significantly inhibited the length of primary root and total root, and N accumulation, whereas OsNRS1 CRISPR/Cas9 mutants in Nip showed significant functional divergence. In-depth research revealed that these functional divergence of OsNRS1 may be caused by the sequence variation of an auxin response element AuxRR in its promoter. Collectively, this study not only provides novel insights into the evolution of the S-RLK gene family, but also identifies OsNRS1 as a potential key target for the genetic improvement of root and N utilization in rice.
Cong Chen, Jiajia Jin, Shujie Shi et al.· Plant physiology and biochem...· 0 citations
Homologous replacement of genomic sequences with large DNA fragments (> 100 bp) holds great potential for crop breeding, yet an efficient method to achieve such edits is lacking in plants. Here, in rice, we developed template-jumping prime editing (TJ-PE), a recently reported PE strategy for large targeted insertion, as an efficient tool for homologous replacement with DNA fragments ranging from dozens to hundreds of base pairs, and using TJ-PE, we replaced genomic fragments of up to 340 bp with homologous fragments of the same length. In addition, our TJ-PE tool also enabled precise deletion of 944- to 2024-bp fragments in rice, with efficiencies of up to 34.6% for c. 2000-bp precise deletions. Collectively, this study expands the editing scope of PE in rice and establishes TJ-PE as a generalist tool for precise deletion and replacement of large DNA fragments.
Huixia Liu, Yu Wang, Shuhui Guan et al.· New Phytologist· 0 citations