Search Results (63)

Argonaute (AGO) proteins are central components of RNA silencing. While OsAGO18 is a known defense factor in antiviral immunity, its involvement in basal development and its transcriptomic behavior during fungal stress remains to be fully elucidated. In this study, based on its specific dual-localization in chloroplasts and processing bodies (P-bodies), we investigated the pleiotropic effects of OsAGO18 through transcriptomic network analysis of rice responding to the blast fungus Magnaporthe oryzae B.C. Couch. Our analysis revealed that the OsAGO18-mediated co-expression network is highly correlated with ribosome biogenesis and cell wall organization. Notably, the analyzed datasets reveal that this growth-related network is significantly suppressed upon M. oryzae challenge, highlighting a transcriptomic shift in OsAGO18 during the growth-to-defense transition. Phenotypic evaluations demonstrated that OsAGO18 overexpression accelerates early seedling growth and primary root elongation by promoting endogenous indole-3-acetic acid (IAA) accumulation, whereas ago18 mutants maintain basal growth rates without significant IAA fluctuations, reflecting robust genetic compensation within the highly redundant AGO family. Mechanistically, our integrated analysis suggests that OsAGO18 acts as a putative molecular decoy to sequester miR396d, thereby relieving the repression of the Growth-Regulating Factor OsGRF6 and triggering downstream auxin-dependent cascades. Collectively, our findings highlight OsAGO18 as a pivotal regulator of early seedling development and characterize its transcriptomic responsiveness to biotic stress, providing a plausible molecular link between post-transcriptional RNA regulation and rice growth coordination. Full article

ZmSIG2A is a nuclear-encoded plastid sigma factor 2A in maize (Zea mays L.) that is essential for plastid gene transcription and chloroplast biogenesis. As a key regulator of chloroplast development and function, ZmSIG2A may also contribute to the coordination of plant growth and environmental adaptation; however, its roles in root development and stress responses remain largely unclear. We compared two ZmSIG2A mutants, eal1-1 (hypomorphic) and ems110 (nonsense). eal1-1 had increased root number and longer roots, while ems110 had normal root number but shorter roots and failed to mature. The zmsig2a^Val480del transcript was upregulated in eal1-1, and the root-promoting effect of OsSIG2A in rice suggests a conserved role in monocot root growth. DAP-seq indicated that zmsig2a^Val480del targets are involved in metabolism, transport, signaling, and antioxidants, with Chr4 peak clustering near multiple LRR-RLKs, suggesting a ZmSIG2A–LRR-RLK module in root development and stress integration. Physiologically, eal1-1 showed increased antioxidant enzyme activities and reduced MDA, indicating enhanced ROS scavenging, while ems110 exhibited decreased enzyme activities and elevated MDA, indicating compromised ROS detoxification. Upstream, Y1H and dual-luciferase assays demonstrated that the Mediator subunit ZmMed31 positively regulates transcription from the ZmSIG2A promoter. Given Mediator’s role in bridging transcription factors and the core transcriptional machinery, ZmMed31 likely links hormone-responsive transcription factors to the ZmSIG2A regulatory network. Collectively, we propose a stress-responsive ZmMed31–ZmSIG2A–LRR-RLK module that underpins maize root development and drought adaptation, offering mechanistic insight and potential targets for stress-resilient breeding. Full article

Mitochondrial biogenesis requires coordinated expression from both nuclear and mitochondrial genomes. To understand the consequences of mitochondrial genome loss, we generated a mitochondrial DNA-depleted line (crm⁻) in Chlamydomonas reinhardtii via long-term ethidium bromide treatment. We then examined how mtDNA disruption affects mitochondrial ultrastructure, chloroplast function, and the mitochondrial transcription termination factor (mTERF) gene family. Our results reveal that mitochondrial dysfunction is associated with severe organelle remodeling, including mitochondrial elongation, matrix condensation, and cristae collapse. Consequently, mitochondria reduce the electron sink capacity which appears to over-reduce the chloroplast electron transport chain, correlating with causing damage to photosystem II (PSII), as indicated by higher plastoquinone PQ redox state and PSII excitation pressure and lower non-photochemical quantum yield [Y(NPQ)]. Furthermore, we identified and characterized eight nuclear-encoded mTERF genes in C. reinhardtii (CrmTERFs). Phylogenetic analysis grouped them into three clades with potential functional conservation. Collinearity analysis suggested potential evolutionary relationships between mTERF genes in Chlamydomonas and Marchantia polymorpha. Gene ontology annotation linked CrmTERFs to transcription termination and RNA biosynthesis regulation. Additionally, in silico prediction identified twelve putative miRNAs targeting seven of the eight CrmTERFs, with CrmTERF3 as the only exception, providing candidates for future experimental validation. This study provides the first comprehensive analysis of the nuclear encoded mTERF gene family in Chlamydomonas and demonstrates that mtDNA loss is correlated with mTERF genes expression, as well as mitochondrial structure and chloroplast photoprotective impairments. These findings suggest a potential role for CrmTERFs in mitochondrial retrograde signaling and organellar crosstalk, though functional validation is required to establish causality. Full article

Chloroplast development plays a crucial role in plant de-etiolation, a process in which plants switch from growth in darkness to light-driven development, known as photomorphogenesis. This study provides evidence that CIA2 (Chloroplast Import Apparatus 2) and CIL (CIA2-Like) contribute to chloroplast biogenesis, likely by affecting and regulating PSII activity and related gene expression. Although their precise molecular roles remain unclear, our findings support their possible involvement in chloroplast development. This is indicated by downregulation of foliar chlorophyll content, chlorophyll a fluorescence parameters, chloroplast size, and gene expression of PSII molecular markers in the cia2cil double mutant during de-etiolation. Chlorophyll a fluorescence and quantitative gene expression analysis during de-etiolation revealed a significant reduction in PSII maximal efficiency and non-photochemical quenching, as well as deregulated expression of genes such as LHCB2.1 and psbA. According to the immunoblotting and microscopy imaging results, there is an impaired function of PSII and a compromised ultrastructure of the chloroplast membranes in cia2cil plants. However, in CIA2p::CIA2_cia2cil and 35Sp::CIA2_cia2cil complementation lines, reversion of this phenotype was observed. These results suggest a supporting role for CIA2 and CIL in the plant de-etiolation process, expanding our understanding of chloroplast biogenesis regulation. Full article

Chloroplasts are key organelles in plants that carry out photosynthesis, convert light energy into chemical energy, and synthesize organic compounds. In this study, a stably heritable chlorophyll-deficient mutant was screened from the ethyl methanesulfonate-induced mutation library of Wuyunjing 21 (WYJ21). This mutant was designated as chlorophyll deficient 6 (cde6). The cde6 mutant exhibits a low chlorophyll content, photosynthetic defects, an impaired chloroplast structure, a significant reduction in the number of stacked thylakoid layers, and a yellow-green leaf phenotype in the early tillering stage. Through MutMap analysis, it was found that the cde6 mutant harbors a single-base mutation (T→A) in the LOC_Os07g38300 gene. This mutation results in an amino acid substitution from valine (Val) to aspartic acid (Asp) in the encoded protein, thereby affecting the protein’s structure and function. The mutation of CDE6 leads to decreased expression of genes related to chloroplast development and chlorophyll biosynthesis. Further studies revealed that the CDE6, a potential chloroplast ribosome recycle factor, leads to high temperature sensitivity in rice when mutated. As high-temperature stress is a primary constraint to global rice productivity, the identification of CDE6 provides a genetic target for improving thermotolerance. In conclusion, these findings demonstrate that CDE6 plays a crucial role in chloroplast biogenesis and provide new insights into its regulatory function in high-temperature tolerance. Full article

Leaf color mutants are commonly characterized by altered chlorophyll content and aberrant chloroplast development, making them valuable models for investigating photosynthetic mechanisms and chloroplast biogenesis. In this study, an albino mutant was isolated from a population of transgenic maize breeding lines. Genetic analysis indicated that the mutant phenotype is inherited in a Mendelian manner and is controlled by a single nuclear locus. This was supported by a χ² test performed on the T₂ generation, which confirmed a segregation ratio consistent with 3:1 (176:68, χ² = 1.07 < χ²_0.05 = 3.84, p > 0.05). Microscopic examination revealed the absence of normally developed chloroplasts in mutant cells. Further expression analysis of chloroplast genes via Northern blotting and quantitative real-time PCR (qRT-PCR) suggested that the mutation impairs the regulation of plastid-encoded polymerase (PEP)-dependent chloroplast gene expression. Notably, PCR-based co-segregation analysis indicated that the mutant phenotype is associated with the entire inserted vector sequence, rather than a point mutation or a small genomic deletion. In conclusion, this paper reports the isolation and phenotypic characterization of an etiolated mutant from a transgenic maize breeding population, including comparative ultrastructural analysis of chloroplasts, co-segregation validation, and chloroplast gene expression profiling. These results enhance our understanding of the physiological and molecular mechanisms underlying chlorophyll-deficient mutations in plants. Full article

Leaves are the primary photosynthetic organs, and alterations in leaf color can affect photosynthesis and plant biomass. In an EMS-mutagenized SN9816 population, we identified two white-striped mutants, ws21-1 and ws21-2. Both mutants showed severely reduced pigment content, defective chloroplasts, and elevated reactive oxygen species. The ws21-2 allele caused a near-complete albino phenotype, while ws21-1 resulted in milder striping. Genetic mapping and cloning identified causal mutations in OsRNRS1, encoding the small subunit of ribonucleotide reductase. The G583R (ws21-1) and Y365F (ws21-2) mutations likely impair enzyme activity, disrupting the dNTP pool for plastid genome replication and causing aberrant chloroplast development. Correspondingly, the expression of genes for chlorophyll synthesis, photosynthesis, and ROS metabolism was altered. Our findings directly link nuclear-encoded nucleotide metabolism to chloroplast biogenesis and demonstrate that dNTP homeostasis is critical for maintaining photosynthetic capacity and redox balance in plants. Full article

Leaf color mutants are valuable resources for studying photosynthesis, pigment metabolism, and gene regulatory networks in plants. In this study, a naturally occurring sweetpotato albino mutant exhibiting a stable white-leaf phenotype across developmental stages was identified and compared with its green-leaf wild type to elucidate the molecular mechanisms underlying albinism. The mutant showed a dramatic 98.8% reduction in total chlorophyll content and a markedly decreased Fv/Fm value (0.59), indicating severe impairment of PSII efficiency. Integrated transcriptomic analysis identified 3520 differentially expressed genes (DEGs), while metabolomic profiling revealed 270 differentially accumulated metabolites (DAMs). Genes involved in chlorophyll and carotenoid biosynthesis, chloroplast development, and photosynthetic electron transport were strongly repressed, including key regulators such as GLK1, PORA, and PORB. Metabolomic alterations were mainly enriched in flavonoids, phenylpropanoids, and amino acid-derived pathways, reflecting broad reprogramming of both primary and secondary metabolism. These changes were accompanied by severely disrupted chloroplast ultrastructure, suggesting a primary defect in plastid development. Collectively, the integrated multi-omics evidence provides a comprehensive understanding of the coordinated transcriptional and metabolic alterations driving the albino phenotype in sweetpotato and establishes this mutant as a potential model for studying the interplay between chloroplast biogenesis, photosynthesis, and secondary metabolism. Full article

MicroRNAs (miRNAs) play a critical role in gene regulation in plants. Several members of the pentatricopeptide repeat (PPR) family have been identified as predicted targets of Ahyp-miR0005, a miRNA specific to amaranth. PPR proteins are essential for mitochondrial and chloroplast biogenesis, as well as plastid-to-nucleus communication, processes fundamental for retrograde signaling between the plastid and nucleus (RSBPN). In this study, we identified the target of Ahyp-miR0005 and its association with the PPR protein family across Amaranthus hypochondriacus, Arabidopsis thaliana, Nicotiana tabacum, and Solanum lycopersicum. Cleavage inhibition by Ahyp-miR0005 was predicted, and the distribution of miRNA binding sites per target gene was analyzed, including their localization within coding PPR domains. Among the main Ahyp-miR0005 target genes, we identified GUN-1, ABO5, and MORF1. Interaction network analysis revealed that different target genes are co-expressed in response to the same stimulus. Gene expression profiling with the Arabidopsis eFP Browser revealed substantial transcriptional changes in predicted targets under six abiotic stress conditions. We further show that abiotic stresses alter the expression of Ahyp-miR0005 amaranth target genes. We anticipate that the expression of Ahyp-miR0005 in non-amaranth plants could replicate the reorganization and coordination of gene expression through RSBPN, thereby improving plant tolerance to various abiotic stresses. Full article

Screens for specific phenotypes have long been a cornerstone of biology. Here, we present an updated synthesis of our large-scale visual screens for Arabidopsis (Arabidopsis thaliana) mutants that exhibit leaf morphology defects. In our 2009 review, we used phenotypes to group the leaf mutants that we had isolated and characterized since 1992; here, by contrast, we functionally classified the mutations that we studied over the last 16 years based on the biological programs they disrupt. Since 2009, we have identified and analyzed 38 genes required for proper leaf development; these genes are involved in translation, chloroplast function, cell wall construction, auxin homeostasis, microRNA biogenesis, and epigenetic regulation. Many of the identified mutants have pleiotropic phenotypes, consistent with the central roles of the affected pathways in development. In this review, we systematically link morphological traits to specific molecular dysfunctions, highlighting the enduring utility of forward genetic approaches. We found that the Arabidopsis leaf is a model organ of a model organism, and we have used this model-in-a-model system to dissect whole-plant traits such as cell proliferation and expansion, and to improve our understanding of the genetic control of plant form and size. Full article

Background: Centella asiatica, a medicinally important species that is rich in bioactive compounds, lacks a characterized mitochondrial genome, despite nuclear and chloroplast assemblies. We sequenced and annotated its mitochondrial genome to elucidate its genetic foundations and evolutionary mechanisms. Methods: Assembly using Illumina short-reads and Nanopore long-reads was used to characterize the mitochondrial genome. Analyses included structural characterization, codon usage bias, repetitive sequences, horizontal gene transfer (HGT), collinearity, and phylogeny. The resulting tissue-specific (root, stem, and leaf) long non-coding RNA (lncRNA) profiles identified RNA editing sites. Results: The complete mitochondrial genome (249,777 bp, 45.5% GC) comprises three circular contigs encoding 51 genes (33 protein-coding, 15 tRNA, and 3 rRNA). Comparative genomics revealed synteny with the Apiaceae family of plants and evidence of HGT. Phylogenetic analysis resolved taxonomic relationships within Apiales. We predicted that 547 RNA editing sites would be identified in its protein-coding genes. Tissue profiling identified 725 (root), 711 (stem), and 668 (leaf) editing sites, with >71% concordance to predictions. RNA editing-generated cryptic promoters/terminators occur in mitochondrial core function genes (e.g., ATP synthase, cytochrome c reductase/oxidase, ribosome large subunit, and cytochrome c biogenesis), exhibiting a lower frequency in the leaves compared to the roots and stems. Conclusions: We provide the first complete mitochondrial genome assembly for C. asiatica, delineating its complex structure, tissue-modulated RNA editing, and evolutionary trajectory. This high-quality genomic resource establishes a foundation for molecular evolutionary studies and enhances the genomic toolkit for this pharmacologically significant species. Full article

Nowadays, with the accumulation of large amounts of stress-response transcriptomic data in plants, it is possible to clarify the key genes and transcription factors (TFs) involved in these processes. Here, we present the comprehensive transcriptomic meta-analysis of the high light (HL) response in photosynthetic tissues of Arabidopsis thaliana (L.) Heynh., offering new insights into adaptation mechanisms of plants to excessive light and involved gene regulatory networks. We analyzed 21 experiments covering 58 HL conditions in total, yielding 218,000 instances of differentially expressed genes (DEGs) corresponding to 19,000 unique genes. Based on these data, we developed the publicly accessible AraLightDEGs resource, which offers multiple search filters for experimental conditions and gene characteristics, and we conducted a detailed meta-analysis using our R pipeline, AraLightMeta. Our meta-analysis highlighted distinct transcriptional programs between short- and long-term HL responses in leaves, revealing novel regulatory interactions and refining the understanding of key DEGs. In particular, long-term HL adaptation involves key TFs such as CRF3 and PTF1 regulating antioxidant and jasmonate signaling; ATWHY2, WHY3, and emb2746 coordinating chloroplast and mitochondrial gene expression; AT2G28450 governing ribosome biogenesis; and AT4G12750 controlling methyltransferase activity. We integrated these findings into a conceptual scheme illustrating transcriptional regulation and signaling processes in leaf cells responding to long-term HL stress. Full article

Chloroplast biogenesis and development are essential processes in plants, profoundly influencing their growth, survival, and productivity. However, the transcription factors controlling chloroplast development, especially in roots, are poorly characterized. Here, we demonstrate that the ectopic expression of the seed-specific transcription factor Plant Growth Regulator 37 (PGA37) promotes chloroplast development in roots, causing root-greening. Using a steroid-inducible gene expression system and RNA-Seq, we identified 97 potential PGA37 target genes. Notably, PGA37 directly activates the transcription factor GOLDEN2-LIKE (GLK2), which governs chloroplast biogenesis. An overexpression of GLK2 replicated the root-greening phenotype observed in PGA37-overexpressing plants, while GLK2 mutation significantly reduced chlorophyll content and suppressed root-greening in PGA37-overexpressing seedlings. Furthermore, PGA37 directly binds to the promoters of type-B response regulators ARR13 and ARR21, thereby activating the cytokinin signaling pathway. Mutations in these regulators partially diminished chlorophyll accumulation in PGA37-overexpressing seedlings, suggesting that PGA37-regulated chloroplast development is partially mediated by the cytokinin signaling through ARR13 and ARR21. Taken together, we propose that PGA37 orchestrates chloroplast development by coordinately regulating transcription factors from various families, including GLK2, ARR13, and ARR21, positioning it as a key regulator of chloroplast development. Full article

Chloroplast biogenesis is a crucial biological process in plants. Endoribonuclease E (RNase E) functions in the RNA metabolism of chloroplast and plays a vital role for chloroplast development in Arabidopsis. However, despite sharing 44.7% of its amino acid sequence identity with Arabidopsis RNase E, the biological function of rice OsRNE (Oryza sativa RNase E) remains unknown. Here, we identified a white leaf and lethal 1 (wll1) mutant that displayed white leaves and died at the seedling stage. The causal gene OsRNE was isolated by MutMap+ method. CRISPR/Cas9-mediated knockout of OsRNE resulted in white leaves and seedling lethality, confirming OsRNE as the causal gene for the wll1 phenotype. The albino phenotype of osrne mutant was associated with decreased chlorophyll content and abnormal thylakoid morphology in the chloroplast. The absence of OsRNE led to a significant reduction in the Rubisco large subunit (RbcL), and the 23S and 16S chloroplast rRNAs were nearly undetectable in the osrne mutant. OsRNE transcripts were highly expressed in green tissues, and the protein was localized to chloroplasts, indicating its essential role in photosynthetic organs. Furthermore, transcriptome analysis showed that most of the genes associated with photosynthesis and carbohydrate metabolism pathways in the osrne mutant were significantly down-regulated compared with those in WT. Chlorophyll- and other pigment-related genes were also differentially expressed in the osrne mutant. Our findings demonstrated that OsRNE plays an important role in chloroplast development and chlorophyll biosynthesis in rice. Full article

Background: The proper development of grana and stroma within chloroplasts is critical for plant vitality and crop yield in rice and other cereals. While the molecular mechanisms underpinning these processes are known, the genetic networks governing them require further exploration. Methods and Results: In this study, we characterize a novel rice mutant termed yellow leaf and dwarf 7 (yld7), which presents with yellow, lesion-like leaves and a dwarf growth habit. The yld7 mutant shows reduced photosynthetic activity, lower chlorophyll content, and abnormal chloroplast structure. Transmission electron microscopy (TEM) analysis revealed defective grana stacking in yld7 chloroplasts. Additionally, yld7 plants accumulate high levels of hydrogen peroxide (H₂O₂) and exhibit an up-regulation of senescence-associated genes, leading to accelerated cell death. Map-based cloning identified a C-to-T mutation in the LOC_Os07g33660 gene, encoding the YLD7 protein, which is a novel ankyrin domain-containing protein localized to the chloroplast. Immunoblot analysis of four LHCI proteins indicated that the YLD7 protein plays an important role in the normal biogenesis of chloroplast stroma and grana, directly affecting leaf senescence and overall plant stature. Conclusions: This study emphasizes the significance of YLD7 in the intricate molecular mechanisms that regulate the structural integrity of chloroplasts and the senescence of leaves, thus providing valuable implications for the enhancement of rice breeding strategies and cultivation. Full article