Plant Molecular Biology最新文献

Cucumber (Cucumis sativus L.) is a major vegetable crop grown globally, with a cultivation history of more than 3000 years. The limited genetic diversity, low rate of intraspecific variation, and extended periods of traditional breeding have resulted in slow progress in their genetic research and the development of new varieties. Gamma (γ)-ray irradiation potentially accelerates the breeding progress; however, the biological and molecular effects of γ-ray irradiation on cucumbers are unknown. Exposing cucumber seeds to 0, 50, 100, 150, 200, and 250 Gy doses of ⁶⁰Co-γ-ray irradiation, this study aimed to investigate the resulting phenotype and physiological characteristics of seedling treatment to determine the optimal irradiation dose. The results showed that low irradiation doses (50-100 Gy) enhanced root growth, hypocotyl elongation, and lateral root numbers, promoting seedling growth. However, high irradiation doses (150-250 Gy) significantly inhibited seed germination and growth, decreasing the survival rate of seedlings. More than 100 Gy irradiation significantly decreased the total chlorophyll content while increasing the malondialdehyde (MDA) and H₂O₂ content in cucumber. Transcriptome sequencing analysis at 0, 50, 100, 150, 200, and 250 Gy doses showed that gene expression significantly differed between low and high irradiation doses. Gene Ontology enrichment and functional pathway enrichment analyses revealed that the auxin response pathway played a crucial role in seedling growth under low irradiation doses. Further, gene function analysis revealed that small auxin up-regulated gene CsSAUR37 was a key gene that was overexpressed in response to low irradiation doses, promoting primary root elongation and enhancing lateral root numbers by regulating the expression of protein phosphatase 2Cs (PP2Cs) and auxin synthesis genes.

MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression at the post-transcriptional level. In plants, miRNAs participate in diverse developmental processes and adaptive responses to biotic and abiotic stress. MiR827 has long been recognized to be involved in plant responses to phosphate starvation. In rice, the miR827 regulates the expression of OsSPX-MFS1 and OsSPX-MFS2, these genes encoding vacuolar phosphate transporters. In this study, we demonstrated that miR827 plays a role in resistance to infection by the fungus Magnaporthe oryzae in rice. We show that MIR827 overexpression enhances susceptibility to infection by M. oryzae which is associated to a weaker induction of defense gene expression during pathogen infection. Conversely, CRISPR/Cas9-induced mutations in the MIR827 gene completely abolish miR827 production and confer resistance to M. oryzae infection. This resistance is accompanied by a reduction of leaf Pi content compared to wild-type plants, whereas Pi levels increase in leaves of the blast-susceptible miR827 overexpressor plants. In wild-type plants, miR827 accumulation in leaves decreases during the biotrophic phase of the infection process. Taken together, our data indicates that silencing MIR827 confers resistance to M. oryzae infection in rice while further supporting interconnections between Pi signaling and immune signaling in plants. Unravelling the role of miR827 during M. oryzae infection provides knowledge to improve blast resistance in rice by CRISPR/Cas9-editing of MIR827.

Australian wild limes occur in highly diverse range of environments and are a unique genetic resource within the genus Citrus. Here we compare the haplotype-resolved genome assemblies of six Australian native limes, including four new assemblies generated using PacBio HiFi and Hi-C sequencing data. The size of the genomes was between 315 and 391 Mb with contig N50s from 29.5 to 35 Mb. Gene completeness of the assemblies was estimated to be from 98.4 to 99.3% and the annotations from 97.7 to 98.9% based upon BUSCO, confirming the high contiguity and completeness of the assembled genomes. High collinearity was observed among the genomes and the two haplotype assemblies for each species. Gene duplication and evolutionary analysis demonstrated that the Australian citrus have undergone only one ancient whole-genome triplication event during evolution. The highest number of species-specific and expanded gene families were found in C. glauca and they were primarily enriched in purine, thiamine metabolism, amino acids and aromatic amino acids metabolism which might help C. glauca to mitigate drought, salinity, and pathogen attacks in the drier environments in which this species is found. Unique genes related to terpene biosynthesis, glutathione metabolism, and toll-like receptors in C. australasica, and starch and sucrose metabolism genes in both C. australis and C. australasica might be important candidate genes for HLB tolerance in these species. Expanded gene families were not lineage specific, however, a greater number of genes related to plant-pathogen interactions, predominantly disease resistant protein, was found in C. australasica and C. australis.

Members of the glycosyltransferase 8 (GT8) family play an important role in regulating gene expression in response to many kinds of biotic and abiotic stress. In this study, 56 members of the apple GT8 family were identified, and their gene structure, phylogenetic relationships, chromosomal localization, and promoter cis-acting elements were comprehensively analyzed. Subsequently, 20 genes were randomly selected from the evolutionary tree for qRT-PCR detection, and it was found that MhGolS2 was significantly overexpressed under stress conditions. MhGolS2 was isolated from M.halliana and transgenic Arabidopsis thaliana, tobacco and apple callus tissues were successfully obtained. The transgenic plants grew better under stress conditions with higher polysaccharide, chlorophyll and proline content, lower conductivity and MDA content, significant increase in antioxidant enzyme activities (SOD, POD, CAT) and maintenance of low Na⁺/K⁺ as compared to the wild type. Meanwhile, the expression levels of reactive oxygen species-related genes (AtSOD, AtPOD, and AtCAT), Na⁺ transporter genes (AtCAX5, AtSOS1, and AtHKT1), H⁺-ATPase genes (AtAHA2 and AtAHA8), and raffinose synthesis-related genes (AtSTS, AtRFS1, and AtMIPS) were significantly up-regulated, while the expression levels of K⁺ transporter genes (AtSKOR, AtHAK5) were reduced. Finally, the Y2H experiment confirmed the interaction between MhGolS2 and MhbZIP23, MhMYB1R1, MhbHLH60, and MhNAC1 proteins. The above results indicate that MhGolS2 can improve plant saline-alkali tolerance by promoting polysaccharide synthesis, scavenging reactive oxygen species, and increasing the activity of antioxidant enzymes. This provides excellent stress resistance genes for the stress response regulatory network in apple.

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.