bims-plasge 2025-03-02 papers

Issue of 2025–03–02
two papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Planta. 2025 Feb 22. 261(4): 64

Dek570-1, a PPR-DYW protein, is required for maize seed and plant development via modulation of C-to-U RNA editing in mitochondria and chloroplasts.

Wenjie Li, Mengsha Zhao, Baiyu Liu, Yecan Liu, Jiaying Deng, Yu Gu, Min Liu, Wen Cheng, Zhaohua Ding, Kunpeng Li.

MAIN CONCLUSION: Maize Dek570-1 affects the expression and function of organellar genes by performing cytidines-to-uridines RNA editing at specific sites of mitochondrial and chloroplast transcripts, thereby regulating seed and plant development. Cytidines-to-uridines (C-to-U) RNA editing at specific sites of mitochondrial and plastid transcripts is crucial for the expression and function of organellar genes, which requires PPR proteins. Here, we report the map-based cloning and characterization of Defective Kernel 570-1 (Dek570-1), which encodes a PPR-DYW protein and is an allele of Emp17. However, compared to the empty pericarp and embryonic lethality of emp17 (W22 background), dek570-1 (Zheng58 background) can produce small but viable seeds despite reducing the size of embryo and endosperm. dek570-1 plants are short and yellowed, but they can reproduce offspring. In mitochondria, loss-of-function of Dek570-1 abolishes the C-to-U editing at nad2-677 and ccmFC-799 sites, and reduces the editing at ccmFC-906 site, consistent with Emp17 deficiency. But unlike the reduced editing of the ccmFC-966 site in emp17, the ccmFC-966 site in dek570-1 is fully edited, and several other editing sites such as ccmFC-87, ccmFC-301, and ccmFC-306 are also found. More noteworthy is that Dek570-1 is not only located in mitochondria like Emp17, but also in chloroplasts. Correspondingly, the editing at rpl20-308 site of dek570-1 chloroplasts was significantly reduced, affecting the expression of some rRNAs, plastid-encoded RNA polymerase (PEP)- and nuclear-encoded single-subunit RNA polymerase (NEP)-dependent genes, thereby reducing chlorophyll accumulation and photosynthetic rate. Together, these results indicate that Dek570-1 is essential for C-to-U editing at several sites in mitochondrial and chloroplast transcripts, as well as for seed and plant development, and that this locus (Zm00001d028422) may have generated some functional evolutionary divergence in maize with different genetic backgrounds.

Keywords: C-to-U RNA editing; Chloroplasts; Maize; Mitochondria; Pentatricopeptide repeat protein; Seed and plant development

DOI: https://doi.org/10.1007/s00425-025-04634-z

Curr Issues Mol Biol. 2025 Feb 01. pii: 94. [Epub ahead of print]47(2):

Metabolomics and Transcriptomics Jointly Explore the Mechanism of Pod Color Variation in Purple Pod Pea.

Xiaojuan Zhong, Mei Yang, Xiaoyan Zhang, Yuanfang Fan, Xianshu Wang, Chao Xiang.

Although the pod color was one of the seven characteristics Mendel studied in peas, the mechanism of color variation in peas with purple pods has not been reported. This study systemically analyzed the difference between two pea accessions with green pods (GPs) and purple pods (PPs) at two pod developmental stages from the metabolome and transcriptome levels, aiming to preliminarily explore the mechanism and of color variation in PPs and screen out the candidate genes. A total of 180 differentially accumulated metabolites (DAMs) belonged to seven flavonoid subgroups and 23 flavonoid-related differentially expressed genes (DEGs) were identified from the analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, respectively. Among the 180 flavonoid metabolites, ten anthocyanin compounds, which were the principal pigments in PPs and might be the major reason for the purple color formation, were significantly up-accumulated in both of the different pod development stages of PPs. A transcriptome analysis revealed that eight genes encoding enzymes (C4H, CHI, F3H, F3'H, F3'5'H, DFR, ANS, and FLS) involved in the flavonoid synthesis pathway were significantly upregulated in PPs and finally resulted in the significant accumulation of flavonoid and anthocyanin metabolites. The joint analysis of two omics and a weighted gene co-expression network analysis (WGCNA) also screened out that the WD-40 protein-encoding gene, one WRKY and three MYB transcription factor genes exhibited significant upregulation in PPs, and highly correlated with several structural genes in flavonoid synthesis pathways, indicating that these genes are involved in the regulation of pod color formation in PPs. Overall, the results of this study first explored the mechanism underlying the purple color variation between PPs and GPs, and then preliminarily screened out some candidate genes responsible for the pod color formation in PPs.

Keywords: Pisum sativum L.; anthocyanin; flavonoid metabolism; metabolome; pod color; transcriptome

DOI: https://doi.org/10.3390/cimb47020094