Plant and Cell Physiology最新文献

Branched broomrape (Phelipanche ramosa) is an obligate root parasitic weed that threatens tomato production in many regions. Progress in understanding host resistance mechanisms has been hindered by the parasite's subterranean life cycle and the technical limitations of traditional soil-based assays. Here, we introduce an integrated experimental framework that enables molecular, genetic, and cellular analysis of broomrape parasitism in tomato under controlled conditions. We implemented a transparent, soil-less co-cultivation system for non-destructive, real-time monitoring of broomrape development on tomato roots, and a dual-compartment in vitro co-culture system supporting parasite infection of transgenic hairy roots. This methodology enabled rapid functional testing of candidate host resistance genes, exemplified by CRISPR-edited mutants of the tomato transcription factor SCHIZORIZA (SlSCZ), which displayed localized lignin accumulation at the parasite entry site in the root. The observed lignification suggests a role for this gene in regulating inducible cell wall lignification against broomrape. Together, these tomato-focused integrated methods enable reproducible imaging, genetic perturbation, and high-resolution analysis of host-parasite interfaces. These provide a scalable platform for dissecting broomrape resistance and accelerating resistance gene discovery in tomato and a critical tool for combating the devastating consequences of this parasite on agriculture.

DNA methylation is an important epigenetic modification that regulates gene expression and supports genome stability. DNA methylation editing technology differs from conventional genome editing technology, which introduces mutations into genes, in that it enables changing gene expression without altering the base sequence. In this study, we attempted simple and locus-restricted DNA methylation editing in Arabidopsis thaliana using fusion proteins directly linking a nickase-type SpCas9 protein with DNA methylation-related enzymes. First, fusion of the human TET1 catalytic domain (TET1cd) to nSpCas9 led to removing 5-methylcytosine in the FWA promoter region of the wild-type plant, resulting in increased expression of the FWA gene and consequently, a late-flowering phenotype. Conversely, fusion of a mutant form of the bacterial DNA methyltransferase MQ1 (MQ1v) to nSpCas9 induced de novo DNA methylation in the fwa101-D mutant, in which the FWA promoter region is hypomethylated, and suppressed FWA gene expression, resulting in an early-flowering phenotype compared with the fwa101-D mutant. Of particular importance, our nSpCas9 system achieves targeted DNA methylation editing within a genomic window of approximately 10-20 kb. The nSpCas9 system features a compact and simplified vector structure due to the DNA methylation-related enzyme directly fusing to nSpCas9. Furthermore, sgRNA can be easily replaced, making it highly flexible. We propose a new method for targeted epigenome editing technology in plants, paving the way for innovative strategies in both basic research on epigenetics and crop development through epigenome editing.

Peanut is a vital oilseed legume with considerable nutritional and economic value worldwide. Considering the global agricultural importance of this legume, researchers have sequenced the whole genomes of both wild and cultivated peanut varieties. Furthermore, databases such as PeanutBase have been established to advance peanut research and breeding. These databases compile extensive genomic resources, including reference genomes, gene annotations, and molecular markers. However, very few genes in cultivated peanut have been functionally characterized. To address this research gap, we developed an enhanced version of the Peanut Genome Resource (PGR) platform (https://pgr.itps.ncku.edu.tw), specifically focusing on providing comprehensive genomic, annotation, and phenotypic data for Arachis hypogaea, especially the Chinese peanut var. Shitouqi. This updated platform integrates an extensive range of genomic annotations-such as information on gene functions, protein domains, transcription factor families, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes pathways. Furthermore, PGR offers gene expression profiles across tissues and conditions as well as tools for differential gene expression and coexpression analyses. To the best of our knowledge, PGR is the first peanut-related platform to incorporate advanced bioinformatics tools for cis-regulatory element analyses, such as those aimed at predicting transcription factor-binding sites; identifying CpNpG islands, tandem repeats, and single sequence repeats; and performing in silico polymerase chain reaction assays for genetic markers. With its user-friendly interface and comprehensive analytical capabilities, PGR serves as a powerful platform for advancing research on peanut genetics, breeding, and functional genomics.

In all eukaryotic cells, protein prenylation and cytoplasmic isoprenoid biosynthesis pathways leading to sterols, dolichols and other isoprenoid compounds share a common precursor pool of isopentenyl diphosphate (IPP) and the isomeric dimethylallyl diphosphate (DMAPP). Despite this, little is known about the interplay between these processes. Here we ask whether perturbation of protein prenylation in plants influences isoprenoid biosynthesis in the endoplasmic reticulum (ER), and in particular if it affects sterol and dolichol biosynthesis. We use an Arabidopsis thaliana mutant with defects in the Rab geranylgeranyl transferase (RGT) as a viable model of protein hypoprenylation, and we show that sterol and dolichol content is significantly elevated in the mutant plants. Also sterol composition is changed: cholesterol content is increased and some atypical sterol pathway intermediates are accumulating. Our results show that plant sterol biosynthesis involves high levels of crosstalk between pathway branches than previously reported and receives regulatory input from protein prenylation pathways.

Cyanobacteria are widely distributed in various environmental conditions with dynamic changes in photosynthetic activity and chlorophyll content. However, it remains elusive how their chlorophyll biosynthesis is regulated by the redox state of photosynthetic electron transport chain (PETC). In this study, the effects of light-dark transition and inhibition of different sites within PETC on the transcriptional expression of chlorophyll biosynthesis related genes were investigated in Synechocystis PCC 6803. It was demonstrated that the transcript levels of chlorophyll biosynthesis related genes were generally stimulated upon light exposure and suppressed in darkness. The introduction of electron transport inhibitors changed the pattern of light-induced expression of these genes, suggesting the redox state of PETC governs the chlorophyll biosynthesis. Meanwhile, the transcription regulation pattern of chlorophyll biosynthesis related genes can be categorized into three groups based on their different transcriptional responses to the inhibition of PETC. The low-oxygen inducible gene chlAII, which encodes magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase, could be activated by over-reduced PQ pool. Several redox-sensitive transcription factors were identified to play some roles in regulating chlorophyll biosynthesis by constructing and screening a yeast one-hybrid library. The transcription factor cyAbrB1 was shown to bind to the promoters of most chlorophyll biosynthesis related genes, implying its global transcriptional regulatory role in chlorophyll biosynthesis. Our research provides a systematic understanding of the transcription regulation mechanism of chlorophyll biosynthesis triggered by the redox state of PETC in cyanobacteria.

Land plants have co-evolved with microorganisms since its transition to a terrestrial habitat around 500 million years ago. In angiosperms, salicylic acid (SA) activates plant immunity against hemibiotrophic pathogens through TGA transcription factors, which bind to the promoter of SA-responsive loci, such as pathogenesis-related (PR) genes, to enforce plant immunity. While those mechanisms are well-known in flowering plants, our understanding in bryophytes remains limited, as genetic evidences for the role of SA during plant immunity are still missing. Here, we explore the interaction between Marchantia polymorpha and the bacterium Pseudomonas syringae to gain insights into the evolutionary immune function of SA during bryophyte-pathogen interactions. We combined transcriptomic profiling of P. syringae-infected Marchantia with the generation of SA-deficient plants in this liverwort by overexpressing the bacterial NahG gene, a SA-degrading enzyme. Our results indicate that the P. syringae induced transcriptional footprint is enriched in SA-responsive genes and that SA-deficient Marchantia NahG plants are compromised in immune responses against P. syringae. We show that the unique MpTGA is essential for controlling resistance against Pseudomonas. Further transcriptional analyses into the coregulatory network controlled by SA and MpTGA indicate that an SA/MpTGA module activates plant defence responses through a variety of MpPRs, enriched in the regulation of class III of secretory peroxidases belonging to the MpPR9 subfamily during the early defensive response against P. syringae. Altogether, our data demonstrate the functional conservation of SA as an immune hormone and underpin the existence of a SA/MpTGA-regulated transcriptional cluster driving resistance against Pseudomonas in Marchantia.

Plant membrane steroid binding proteins (MSBPs) belong to the membrane-associated progesterone receptors (MAPRs) present in all eukaryotic kingdoms. Plant MSBP proteins have been shown to regulate the function of cytochrome P450 enzymes, bind different steroidal compounds and confer salt tolerance. However, the exact molecular function of plant MSBPs remains elusive. Here we perform phylogenetic analysis of the six MAPR genes encoded in the Sorghum bicolor genome. Of these, four group into a distinct MSBP clade characterized by being N-terminally membrane anchored followed by a cytochrome b5 domain and an extended disordered C-terminal. Biophysical of SbMSBP1 demonstrates that this protein can bind heme, which leads to dimerization potentially through a heme-heme stacking mechanism. We further show using untargeted proteomics that MSBPs are upregulated in both root and shoot tissue upon exposure to salt stress. Based on weighted gene co-expression network analysis (WGCNA) we find that SbMSBP1 abundance clusters with ER remodeling and vesicle transport proteins. We further show that overexpression of SbMSBP1 in Sorghum bicolor protoplasts and tobacco results in formation of structures consistent with organized smooth endoplasmic reticulum (OSER). Our data indicates that SbMSBP1 functions to remodel ER membranes, which may be directly linked to a functional role in stress resilience towards both biotic and abiotic stresses and furthermore could serve as a useful tool for metabolic engineering of ER-scaffolded biosynthetic pathways.

The liverwort Marchantia polymorpha is a key model organism for understanding land plant evolution, development, and gene regulation. To support the growing demand for high-quality genomic resources, we present MarpolBase, a comprehensive and integrated genome database that hosts newly assembled, high-accuracy reference genomes for both the male Tak-1 and female Tak-2 accessions, designated as ver. 7.1 reference genomes. These new assemblies, generated using PacBio HiFi long-read sequencing, represent nearly telomere-to-telomere chromosome-level genomes, with improvements in assembly continuity, annotation accuracy, and structural resolution-especially for repeat-rich regions and sex chromosomes. MarpolBase offers not only access to genome sequences and gene annotations but also provides a unified platform for data exploration, comparative analysis, and community-driven gene nomenclature for Marchantia polymorpha. It includes keyword-searchable gene pages with structural and functional annotations, expression data integration, genome browser visualization, and online analytical and utility tools. By unifying genome assembly, annotation, nomenclature, and analysis tools in a single platform, MarpolBase serves as a central resource for functional genomics and evolutionary studies in M. polymorpha, and a model for future plant genome databases. The genomic resources of MarpolBase are freely available at https://marchantia.info.

Photosystem II (PSII) is a multi-subunit complex embedded in the thylakoid membranes of all oxygenic photosynthetic organisms, ranging from cyanobacteria to algae and plants. PSII converts solar energy to chemical energy and produces oxygen by oxidizing water, thereby sustaining life on Earth. The basic structures of the PSII core and the fundamental mechanisms of light-driven water oxidation are well-conserved among the diverse oxyphototrophs. Meanwhile, the compositions of the extrinsic subunits, which have critical roles in supporting water oxidation, have largely changed during evolution. The light-harvesting antenna systems of PSII are even more diverse. In this review, we comprehensively summarize the commonality of PSII, while highlighting the diversity of PSII among various oxyphototrophs. This includes summaries on the overall PSII core structure, PSII assembly and repair, charge separation and electron transfer in PSII, water oxidation by PSII, peripheral light-harvesting antennas of PSII, and PSII-antenna supercomplex structures, as well as a summary on the extrinsic subunits. Special emphasis is given to the extrinsic subunits, updating our understanding of their roles, and discussing the structural and functional complementation of the different sets of extrinsic subunits in cyanobacterial, red-lineage, and green plant PSII.

Over 30 years ago, when we first reported the selective photoinhibition of photosystem I (PSI) in chilling-sensitive plants at chilling temperatures, the inhibition tended to be regarded as a specific phenomenon observed only under unusual conditions. We have since learned that PSI can be photoinhibited under many different conditions. The inhibition was observed in isolated thylakoid membranes under low light, or with some mutant plants under fluctuating light, or with plants illuminated by a series of saturating light pulses. Apparently, the sensitivity of PSI to photoinhibition is an intrinsic property of this photosystem. To understand the mechanism of PSI photoinhibition, which is now known to occur universally in nature, a comparison of different types of PSI photoinhibition should certainly be useful. In this review, similarities and differences in the mechanisms of photoinhibition between different types of PSI photoinhibition, as well as the protection mechanisms from the inhibition, are discussed.