The Plant Journal最新文献

Bread wheat (Triticum aestivum L.) is an allohexaploid (AABBDD) whose three ancestral subgenomes generate complex patterns of gene regulation. Most genes exist as homoeologous triads, and the relative expression balance among copies, homoeolog expression bias, is central to polyploid evolution and adaptation. Recent high-quality assemblies, long-read transcriptomics, and pan-transcriptome resources have uncovered extensive cultivar-specific transcriptional diversity. Because transposable elements (TEs) compose over 80% of the wheat genome, they are prime candidates for shaping subgenome asymmetry. We synthesize recent pan-genomic and transcriptomic evidence, including genome-wide associations between TE insertions and genome-specific expression, and propose a unifying framework in which TEs modulate homoeolog expression by donating cis-regulatory sequences, altering chromatin states, producing small RNAs, and driving structural variation. We discuss experimental and computational challenges for establishing causality, and outline future functional and translational strategies to leverage TE-associated regulatory diversity in wheat breeding.

Transcription factor structural dynamics has emerged as a critical frontier in plant molecular biology, as many transcription factors (TFs) belong to plant-specific families with unique structural features that reveal mechanisms static structural approaches cannot capture. These advances, combining molecular dynamics simulations, NMR spectroscopy, and single-molecule techniques, have demonstrated that structural dynamics play crucial roles in driving DNA recognition, environmental responsiveness, and regulatory precision. Such computational and experimental breakthroughs have revealed rotation-coupled diffusion processes in WRKY proteins and allosteric regulation through ensemble redistribution in disordered domains. Despite these discoveries, fundamental questions remain about how plant TFs achieve specificity within complex regulatory networks and integrate multiple environmental signals. We outline current understanding of the static structures across transcription factor families before examining breakthrough discoveries in structural dynamics. These encompass the diverse architectures of DNA binding and regulatory domains, as well as the conformational flexibility and transition kinetics governing DNA binding, cofactor interactions, and environmental signal transduction. We subsequently explore how these insights are transforming biotechnological applications, from rational protein design to crop engineering strategies. Finally, we discuss remaining challenges and future directions for harnessing transcription factor dynamics in agricultural and synthetic biological applications.

The spine, which is usually composed of a base and stalk, is an important economic trait in cucumber fruits. Although previous studies have reported that genes regulate the size of the cucumber fruit spines, the regulatory mechanism is not clear, and the genes that regulate stalk formation have not been identified. Here, we obtained Csmyb36 mutant by inducing mutagenesis using ethylmethylsulfone. This mutant exhibited two phenotypes of spines. First, in the Csmyb36 mutant, the spine base became smaller. Second, a new type of ‘spine-like’ trichome appeared on the mutant fruit peel. Similar results were obtained after the knockout of CsMYB36, which had the mutant trichome phenotype. The complementation line restored the spine-like phenotype, but the spine base size phenotype was not restored. pCsMYB36-GUS analysis showed that CsMYB36 was highly expressed in the fruit spine, and the expression of CsMYB36 in large spine-based cucumber varieties was higher than that in small spine-based cucumber varieties. Biochemical analyses showed that CsMYB36 interacted with CsSBS1 to regulate fruit spine size through the ethylene pathway. Two ethylene-activated signalling pathway genes were identified as candidate genes involved in spine-like formation. In conclusion, our findings indicated that CsMYB36 regulated the development of cucumber fruit spines via the ethylene pathway. Our findings provide valuable genetic resources for cucumber breeders to cultivate cucumber varieties by developing different types of fruit spines.

Deficiency in the chloroplast metalloprotease FtsH2 causes the Arabidopsis leaf-variegated mutant yellow variegated2 (var2) to develop leaves with irregular green sectors and white sectors. This raises an intriguing question: why do genetically identical cells exhibit such dramatic phenotypic differences? The phenomenon highlights the probabilistic fates of chloroplasts in var2. Previous studies proposed that patchy expression of FtsH8—a functionally redundant gene of FtsH2—explains this variegation. Here, we employed single-cell RNA sequencing (scRNA-seq) to investigate leaf variegation for the first time. We demonstrated the patchy expression of FtsH8 at the single-cell level, which supports the threshold model. Our pseudotime analysis suggests that white sector formation in developing var2 leaves enables cells to reduce reactive oxygen species (ROS) via suppression of photosynthetic genes. Supporting this, treatment with a ROS scavenger markedly reduced the proportion of white sectors. Furthermore, we showed that suppression of photosynthetic genes in var2 is a trade-off that ensures proper progression of the cell cycle. Taken together, our study offers new insights into the mechanisms underlying leaf variegation.

Redox homeostasis and Fe–S protein maturation are critical for chloroplast function. Chloroplast-localized glutaredoxins (Grxs) are versatile enzymes that function either as oxidoreductases or Fe–S cluster transferases. However, their target proteins and underlying molecular mechanisms remain incompletely understood. Here, we demonstrate that the cysteine 34 within the active site motif of chloroplast-localized Arabidopsis GrxS12 is the key residue governing its oxidoreductase activity, while the C-terminal cysteine 92 plays a secondary role. These cysteines undergo glutathionylation or form an intramolecular disulfide bond, which can be reduced by Trx-m1. Although GrxS12 is unable to bind Fe–S clusters itself, it interacts with and reduces the Fe–S cluster assembly protein SufB, thereby regulating Fe–S protein maturation. Loss of GrxS12 induces redox alterations of multiple chloroplast proteins, increased oxidation of SufB, and decreased abundances of several Fe–S proteins. These changes likely underlie the observed structural damage to chloroplasts, reduced photosynthetic efficiency, and slower growth in grxs12 mutants. Our results reveal a novel mechanism by which GrxS12 regulates chloroplast Fe–S cluster biogenesis through its oxidoreductase activity.

Proteostatic control of chloroplast biogenesis and homeostasis is crucial for photosynthetic efficiency. However, previous studies of this process have primarily focused on the model plant Arabidopsis and C3 crops, and its role in C4 species remains unexplored. The Clp protease complex, which is located in the stroma, plays a crucial role in proteostatic degradation. Mutations in the genes encoding this complex can result in embryonic and seedling lethality, stunted plant growth and development, and chlorosis. Here, we report that disruption of ZmClpP6 in maize results in transversely green and yellow striped leaves, with alternating green and yellow sectors forming during the night and day, respectively, and with yellow sectors especially prominent under high light conditions. High light treatment of mutants and wild-type maize leaves caused different changes in reactive oxygen species distribution and photosystem II stability, coinciding with progressive thylakoid membrane reorganization during leaf development. Intriguingly, the light-dependent alternating of transverse yellow-green crossbands diminished as leaves matured, suggesting compensatory regulation during developmental progression and phase transition. The zmclpP6 mutant phenotype is associated with altered accumulation of the photoprotective protein ZmELIP2 under high light, which interacts with the Clp protease complex and may be a potential degradation substrate. Our findings highlight the Clp protease as a key mediator of chloroplast plasticity in response to light. Functional analysis of the Clp protease complex in maize provides insights into how C4 plants balance photoprotection with chloroplast differentiation, offering a framework for understanding the integration of proteostatic control with environmental adaptation in crops.

The increased abundance and functionality of fruit chloroplasts could promote the accumulation of nutrients and flavor in the fruit. Tomato fruit has fully developed fruit chloroplasts, whose abundance and functionality have much untapped potential in improving fruit quality by controlling fruit chloroplast development. Previous studies have identified many regulatory factors that specifically regulate fruit chloroplast development in tomatoes, but there are fewer reports on tomato phytochrome-interacting factors (SlPIFs). Arabidopsis AtPIFs have been implicated in chloroplast development and chlorophyll biosynthesis. In this study, we identified and characterized an SlPIF1b mutant in tomato, named GS, which exhibited a dark green fruit shoulder with enhanced chloroplast development. RNA-seq and genotyping analysis identified a − 21 bp (A → T) mutation in the promoter of SlPIF1b, resulting in the absence of the TATA-box core transcriptional element and inhibiting SlPIF1b transcription. The overexpression of SlPIF1b in GS inhibited chloroplast development of fruits, leading to a lighter green shoulder color, decreased chlorophyll content, reduced photosynthetic activity, diminished starch accumulation, and compromised fruit quality upon ripening. Conversely, the down expression of SlPIF1b significantly enhanced fruit chloroplast development and functionality in fruits, resulting in increased chlorophyll and carotenoid accumulation. Further analysis of expression profile and transcriptional activity indicated that SlPIF1b could bind to G/PBE-box elements present in SlGLK2, SlTKN4, SlCAO1a, SlPOR1, SlPOR3, SlCAB1 and SlCAB1b promoters, thereby inhibiting their expression. This study revealed the specific regulatory mechanism by which SlPIF1b modulates chloroplast development and chlorophyll synthesis in tomato fruit and provided valuable genetic resources and a theoretical basis for tomato quality improvement.