Plant Molecular Biology最新文献

Fruit color is a key feature of fruit quality, primarily influenced by anthocyanin or carotenoid accumulation or chlorophyll degradation. Adapting the pigment content is crucial to improve the fruit's nutritional and commercial value. Genetic factors along with other environmental components (i.e., light, temperature, nutrition, etc.) regulate fruit coloration. The fruit coloration process is influenced by plant hormones, which also play a vital role in various physiological and biochemical metabolic processes. Additionally, phytohormones play a role in the regulation of a highly conserved transcription factor complex, called MBW (MYB-bHLH-WD40). The MBW complex, which consists of myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WD40 repeat (WDR) proteins, coordinates the expression of downstream structural genes associated with anthocyanin formation. In fruit production, the application of plant hormones may be important for promoting coloration. However, concerns such as improper concentration or application time must be addressed. This article explores the molecular processes underlying pigment formation and how they are influenced by various plant hormones. The ABA, jasmonate, and brassinosteroid increase anthocyanin and carotenoid formation, but ethylene, auxin, cytokinin, and gibberellin have positive as well as negative effects on anthocyanin formation. This article establishes the necessary groundwork for future studies into the molecular mechanisms of plant hormones regulating fruit color, ultimately aiding in their effective and scientific application towards fruit coloration.

Photosynthetic proteins play a crucial role in agricultural productivity by harnessing light energy for plant growth. Understanding these proteins, especially within C₃ and C₄ pathways, holds promise for improving crops in challenging environments. Despite existing models, a comprehensive computational framework specifically targeting plant photosynthetic proteins is lacking. The underutilization of plant datasets in computational algorithms accentuates the gap this study aims to fill by introducing a novel sequence-based computational method for identifying these proteins. The scope of this study encompassed diverse plant species, ensuring comprehensive representation across C₃ and C₄ pathways. Utilizing six deep learning models and seven shallow learning algorithms, paired with six sequence-derived feature sets followed by feature selection strategy, this study developed a comprehensive model for prediction of plant-specific photosynthetic proteins. Following 5-fold cross-validation analysis, LightGBM with 65 and 90 LGBM-VIM selected features respectively emerged as the best models for C₃ (auROC: 91.78%, auPRC: 92.55%) and C₄ (auROC: 99.05%, auPRC: 99.18%) plants. Validation using an independent dataset confirmed the robustness of the proposed model for both C₃ (auROC: 87.23%, auPRC: 88.40%) and C₄ (auROC: 92.83%, auPRC: 92.29%) categories. Comparison with existing methods demonstrated the superiority of the proposed model in predicting plant-specific photosynthetic proteins. This study further established a free online prediction server PredPSP ( https://iasri-sg.icar.gov.in/predpsp/ ) to facilitate ongoing efforts for identifying photosynthetic proteins in C₃ and C₄ plants. Being first of its kind, this study offers valuable insights into predicting plant-specific photosynthetic proteins which holds significant implications for plant biology.

Histone deacetylation, one of most important types of post-translational modification, plays multiple indispensable roles in plant growth and development and abiotic stress responses. However, little information about the roles of histone deacetylase in regulating inflorescence architecture, fruit yield, and stress responses is available in tomato. Functional characterization revealed that SlHDT1 participated in the control of inflorescence architecture and fruit yield by regulating auxin signalling, and influenced tolerance to drought and salt stresses by governing abscisic acid (ABA) signalling. More inflorescence branches and higher fruit yield, which were influenced by auxin signalling, were observed in SlHDT1-RNAi transgenic plants. Moreover, tolerance to drought and salt stresses was decreased in SlHDT1-RNAi transgenic lines compared with the wild type (WT). Changes in parameters related to the stress response, including decreases in survival rate, chlorophyll content, relative water content (RWC), proline content, catalase (CAT) activity and ABA content and an increase in malonaldehyde (MDA) content, were observed in SlHDT1-RNAi transgenic lines. In addition, the RNA-seq analysis revealed varying degrees of downregulation for genes such as the stress-related genes SlABCC10 and SlGAME6 and the pathogenesis-related protein P450 gene SlCYP71A1, and upregulation of the pathogenesis-related protein P450 genes SlCYP94B1, SlCYP734A7 and SlCYP94A2 in SlHDT1-RNAi transgenic plants, indicating that SlHDT1 plays an important role in the response to biotic and abiotic stresses by mediating stress-related gene expression. In summary, the data suggest that SlHDT1 plays essential roles in the regulation of inflorescence architecture and fruit yield and in the response to drought and salt stresses.

Plastid-encoded RNA polymerase (PEP) is a bacterial-type multisubunit RNA polymerase responsible for the majority of transcription in chloroplasts. PEP consists of four core subunits, which are orthologs of their cyanobacterial counterparts. In Arabidopsis thaliana, PEP is expected to interact with 14 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function are still poorly understood. We used ptChIP-seq to show that PAP1 (also known as pTAC3), a peripheral subunit of PEP, binds to the same genomic loci as RpoB, a core subunit of PEP. The pap1 mutant shows a complete loss of RpoB binding to DNA throughout the genome, indicating that PAP1 is necessary for RpoB binding to DNA. A similar loss of RpoB binding to DNA is observed in a mutant defective in PAP7 (also known as pTAC14), another peripheral PEP subunit. We propose that PAPs are required for the recruitment of core PEP subunits to DNA.

Leaf senescence and abscission in autumn are critical phenological events in deciduous woody perennials. After leaf fall, dormant buds remain on deciduous woody perennials, which then enter a winter dormancy phase. Thus, leaf fall is widely believed to be linked to the onset of dormancy. In Rosaceae fruit trees, DORMANCY-ASSOCIATED MADS-box (DAM) transcription factors control bud dormancy. However, apart from their regulatory effects on bud dormancy, the biological functions of DAMs have not been thoroughly characterized. In this study, we revealed a novel DAM function influencing leaf senescence and abscission in autumn. In Prunus mume, PmDAM6 expression was gradually up-regulated in leaves during autumn toward leaf fall. Our comparative transcriptome analysis using two RNA-seq datasets for the leaves of transgenic plants overexpressing PmDAM6 and peach (Prunus persica) DAM6 (PpeDAM6) indicated Prunus DAM6 may up-regulate the expression of genes involved in ethylene biosynthesis and signaling as well as leaf abscission. Significant increases in 1-aminocyclopropane-1-carboxylate accumulation and ethylene emission in DEX-treated 35S:PmDAM6-GR leaves reflect the inductive effect of PmDAM6 on ethylene biosynthesis. Additionally, ethephon treatments promoted autumn leaf senescence and abscission in apple and P. mume, mirroring the changes due to PmDAM6 overexpression. Collectively, these findings suggest that PmDAM6 may induce ethylene emission from leaves, thereby promoting leaf senescence and abscission. This study clarified the effects of Prunus DAM6 on autumn leaf fall, which is associated with bud dormancy onset. Accordingly, in Rosaceae, DAMs may play multiple important roles affecting whole plant growth during the tree dormancy induction phase.

l-Lactate is a commodity chemical used in various fields. Microorganisms have produced l-lactate via lactic fermentation using saccharides derived from crops as carbon sources. Recently, l-lactate production using microalgae, whose carbon source is carbon dioxide, has been spotlighted because the prices of the crops have increased. A red alga Cyanidioschyzon merolae produce l-lactate via lactic fermentation under dark anaerobic conditions. The l-lactate titer of C. merolae is higher than those of other microalgae but lower than those of heterotrophic bacteria. Therefore, an increase in the l-lactate titer is required in C. merolae. l-Lactate dehydrogenase (l-LDH) catalyzes the reduction of pyruvate to l-lactate during lactic fermentation. C. merolae possesses five isozymes of l-LDH. The results of previous transcriptome analysis suggested that l-LDHs are the key enzymes in the lactic fermentation of C. merolae. However, their biochemical characteristics, such as catalytic efficiency and tolerance for metabolites, have not been revealed. We compared the amino acid sequences of C. merolae l-LDHs (CmLDHs) and characterized one of the isozymes, CmLDH1. BLAST analysis revealed that the sequence similarities of CmLDH1 and the other isozymes were above 99%. The catalytic efficiency of CmLDH1 under its optimum conditions was higher than those of l-LDHs of other organisms. ATP decreased the affinity and turnover number of CmLDH1 for NADH. These findings contribute to understanding the characteristics of l-LDHs of microalgae and the regulatory mechanisms of lactic fermentation in C. merolae.

Salinity is one of the major environmental factor that can greatly impact the growth, development, and productivity of barley. Our study aims to detect the natural phenotypic variation of morphological and physiological traits under both salinity and potassium nanoparticles (n-K) treatment. In addition to understanding the genetic basis of salt tolerance in barley is a critical aspect of plant breeding for stress resilience. Therefore, a foliar application of n-K was applied at the vegetative stage for 138 barley accessions to enhance salt stress resilience. Interestingly, barley accessions showed high significant increment under n-K treatment compared to saline soil. Based on genome-wide association studies (GWAS) analysis, causative alleles /reliable genomic regions were discovered underlying improved salt resilience through the application of potassium nanoparticles. On chromosome 2H, a highly significant QTN marker (A:C) was located at position 36,665,559 bp which is associated with APX, AsA, GSH, GS, WGS, and TKW under n-K treatment. Inside this region, our candidate gene is HORVU.MOREX.r3.2HG0111480 that annotated as NAC domain protein. Allelic variation detected that the accessions carrying C allele showed higher antioxidants (APX, AsA, and GSH) and barley yield traits (GS, WGS, and TKW) than the accessions carrying A allele, suggesting a positive selection of the accessions carrying C allele that could be used to develop barley varieties with improved salt stress resilience.

The regulation mechanism of bamboo height growth has always been one of the hotspots in developmental biology. In the preliminary work of this project, the function of LBD transcription factor regulating height growth was firstly studied. Here, a gene PheLBD12 regulating height growth was screened. PheLBD12-overexpressing transgenic rice had shorter internodes, less bioactive gibberellic acid (GA3), and were more sensitive to GA3 than wild-type (WT) plants, which implied that PheLBD12 involve in gibberellin (GA) pathway. The transcript levels of OsGA2ox3, that encoding GAs deactivated enzyme, was significantly enhanced in PheLBD12-overexpressing transgenic rice. The transcript levels of OsAP2-39, that directly regulating the expression of EUI1 to reduce GA levels, was also significantly enhanced in PheLBD12-overexpressing transgenic rice. Expectedly, yeast one-hybrid assays, Dual-luciferase reporter assay and EMSAs suggested that PheLBD12 directly interacted with the promoter of OsGA2ox3 and OsAP2-39. Together, our results reveal that PheLBD12 regulates plant height growth by modulating GA catabolism. Through the research of this topic, it enriches the research content of LBD transcription factors and it will theoretically enrich the research content of height growth regulation.

Maize is a valuable raw material for feed and food production. Healthy seed germination is important for improving the yield and quality of maize. Seed aging occurs relatively fast in crops and it is a process that delays germination as well as reduces its rate and even causes total loss of seed viability. However, the physiological and transcriptional mechanisms that regulate maize seeds, especially aging seed germination remain unclear. Coronatine (COR) which is a phytotoxin produced by Pseudomonas syringae and a new type of plant growth regulator can effectively regulate plant growth and development, and regulate seed germination. In this study, the physiological and transcriptomic mechanisms of COR-induced maize seed germination under different aging degrees were analyzed. The results showed that 0.001-0.01 μmol/L COR could promote the germination of aging maize seed and the growth of primary roots and shoots. COR treatment increased the content of gibberellins (GA₃) and decreased the content of abscisic acid (ABA) in B73 seeds before germination. The result of RNA-seq analysis showed 497 differentially expressed genes in COR treatment compared with the control. Three genes associated with GA biosynthesis (ZmCPPS2, ZmD3, and ZmGA2ox2), and two genes associated with GA signaling transduction (ZmGID1 and ZmBHLH158) were up-regulated. Three genes negatively regulating GA signaling transduction (ZmGRAS48, ZmGRAS54, and Zm00001d033369) and two genes involved in ABA biosynthesis (ZmVP14 and ZmPCO14472) were down-regulated. The physiological test results also showed that the effects of GA and ABA on seed germination were similar to those of high and low-concentration COR, respectively, which indicated that the effect of COR on seed germination may be carried out through GA and ABA pathways. In addition, GO and KEGG analysis suggested that COR is also highly involved in antioxidant enzyme systems and secondary metabolite synthesis to regulate maize seed germination processes. These findings provide a valuable reference for further research on the mechanisms of maize seed germination.