A molecular map of chloroplast development is established, elucidating how transcriptional, post-transcriptional, and post-translational layers may contribute to efficient plastid maturation.
Abstract
Abstract Photosynthetic efficiency, a pivotal determinant of crop yield, is governed by chloroplast development—a process that remains poorly understood in polyploid crops. Using tetraploid oilseed rape (Brassica napus) as a model, we phenotypically characterized chloroplast development under light induction and performed a high-resolution, multi-omics analysis of this process. Through the integration of time-series transcriptome, proteome, and post-translational modification (PTM) data—encompassing acetylation, phosphorylation, and ubiquitylation—we reveal a multi-layered regulatory network coordinating chloroplast maturation. A core, sequential transcription factor cascade orchestrates the temporal program, which is finely modulated by crosstalk between alternative splicing and PTMs. PTMs further fine-tune the activity of proteins within essential photosynthetic pathways. We also demonstrate differential subfunctionalization of homeologous gene pairs, a polyploid-specific strategy that enhances regulatory flexibility and robustness. Our findings establish a molecular map of chloroplast development, elucidating how transcriptional, post-transcriptional, and post-translational layers may contribute to efficient plastid maturation. This study also identifies upstream regulators, particularly within the photosystem and chlorophyll biosynthesis pathways, as potential candidates for functional validation to assess their roles in improving photosynthetic performance. Collectively, our findings provide a resource for future research in chloroplast biology, photosynthesis, polyploid biology, and comparative-omics studies.
Leaf-color mutants are crucial for elucidating chlorophyll metabolism mechanisms. Here, we identified yel, a stably inherited rice mutant with a dwarf and yellow-green leaf phenotype controlled by a single recessive nuclear gene. Using BSA-seq, we mapped the candidate causal gene to OsMPEC, encoding a magnesium protoporphyrin IX monomethyl ester cyclase with a G→T substitution. Multi-omics analysis revealed that the functional deficiency of OsMPEC protein—despite unchanged transcript levels—triggers global transcriptional repression of the chlorophyll metabolic network. This defect caused distinct metabolic consequences: impaired synthesis at the early stage (yel1) and toxic metabolite accumulation at the later stage (yel2). Furthermore, metabolic collapse induced systemic reprogramming of hormone signaling, shifting from pro-growth to stress and senescence modes. We propose that the yel phenotype is associated with a self-reinforcing inhibitory loop of “passive synthesis inhibition” and “active degradation acceleration.” This study clarifies OsMPEC’s role in chlorophyll homeostasis and demonstrates how a single genetic defect drives phenotype- through to network-level cascading effects.
Guang Li, Jiawei Liu, Xiao Yang et al.· Current Issues in Molecular...· 0 citations
This study provides a systems-level view of posttranscriptional regulation during salt stress in wheat and identifies potential targets for enhancing salt tolerance.
J. Zang, Qian Zhang, Yuyu Zhang et al.· Plant Physiology· 0 citations
This work represents the first systematic integration of transcriptomic and lipidomic data focusing on dynamic changes during the germination stage in B. napus, systematically illustrating the global molecular and lipid metabolic features of rapeseed seeds across sequential imbibition stages.
Bo Zhang, Junyan Wu, Li Ma et al.· BMC Genomics· 0 citations
ABSTRACT Anthocyanin accumulation in Rosaceae fruits is governed by a multi‐layered regulatory network integrating transcriptional control, epigenetic modulation, environmental signaling, and metabolic flux allocation. This review presents a critical synthesis of recent advances in this field, moving beyond descriptive gene lists to examine the mechanistic underpinnings of pigment regulation. We first outline the core biosynthetic pathway and post‐synthetic modifications that ensure pigment stability. The central focus is on the MYB–bHLH–WD40 transcriptional complex and its integration with epigenetic mechanisms (DNA methylation, histone modifications, non‐coding RNAs) and post‐transcriptional regulation. We further examine how environmental cues—light, temperature, and hormones—are transduced through these molecular networks, and analyze metabolic flux control at pathway branch points. A cross‐species comparative perspective across major Rosaceae crops (Malus, Pyrus, Fragaria, Prunus) reveals conserved regulatory nodes and genus‐specific innovations. Finally, we discuss how this integrated knowledge, combined with multi‐omics and gene editing tools, is driving targeted strategies in molecular breeding and postharvest quality management. This framework provides a foundation for rational manipulation of fruit coloration and nutritional quality.
Ubiquitination is a reversible post-translational modification that orchestrates a wide spectrum of fundamental processes throughout the plant life cycle. Executed by a hierarchical E1-E2-E3 cascades, this modification tags targets with ubiquitin to modulate their turnover, activity, or subcellular compartmentalization. Among the diverse E3 ligase families, plant U-box (PUB) proteins stand out as a prominent class that determines substrate selection and has emerged as a focal point of stress biology. In this review, we first delineate the structural features of PUB proteins, highlighting their conserved domains and associated regulatory motifs. We then systematically dissect their multifaceted functions in abiotic stress adaptation, encompassing drought, salinity, extreme temperatures, oxidative stress, heavy metal toxicity, with particular emphasis on their integration with ABA signaling networks. We further outline critical knowledge gaps and propose future strategies to decode the regulatory architecture of PUBs. Collectively, this review provides a theoretical foundation and new insights for facilitating the genetic improvement of crop resilience in the face of continuously intensifying environmental stresses through the manipulation of PUB-mediated ubiquitination networks.
Yu-Jie Fang, Han Wu, Yu-Han Wang et al.· Plant Science· 0 citations
This review synthesizes recent progress in how BBX activity is modulated through chromatin remodeling, alternative splicing and E3-ligase-mediated protein stability, among other mechanisms, and proposes that understanding BBX function requires a shift from identifying isolated target genes to decoding the combinatorial logic of their interactions.
J. Botto, G. Gómez-Ocampo, C. Barraza· Plant physiology and biochem...· 0 citations
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