Plant Molecular Biology最新文献

Macrophytes are critical primary producers in freshwater ecosystems and offer potential as crop resources to support the growing human population. They are also widely used to mitigate eutrophication. Aquatic plants adapt themselves to the more complicated, changeable, and unstable conditions compared to terrestrial plants, especially the fluctuating nutrient environments. Nitrogen (N) and phosphorus (P) are the key nutrient elements for plants, and their biogeochemical cycles have been significantly disrupted by anthropogenic activities in diverse ecosystems. However, there is still a lack of comprehensive understanding about the adaptive mechanisms of N and P stress in aquatic plants. In this study, the response mechanisms in the macrophyte Spirodela polyrhiza under various nutrient conditions were analyzed. S. polyrhiza showed universal changes under nutrient deficiencies at the physiological level, including enhanced root growth, lower Chl content, higher Root-Frond ratio, and starch content. Genes involved in nutrient acquisition and remobilization, carbon metabolism, transcriptional regulation, hormones, and antioxidant systems were identified. Physiological and transcriptional changes revealed that the macrophyte S. polyrhiza adopts a nutrient acquisition-prioritization strategy under nutrient deficiency conditions, employing strategies similar to those observed in terrestrial plants. Post-transcriptional regulatory networks also highlighted the critical role of non-coding RNAs nutrient stress responses. Overall, S. polyrhiza employs integrated physiological and molecular strategies to cope with nutrient deficiency in aquatic environments. This study provides comprehensive insights into its adaptive responses and offers a valuable genetic resource for further novel gene discovery and functional analysis.

Proper development of floral organs is essential for reproductive success and grain yield in wheat. However, the molecular mechanisms regulating wheat floral organ development remain largely unknown. In this study, we characterized the role of the wheat TaEPFL1 gene in floral organ development and its association with ethylene signaling. TaEPFL1 was highly expressed in immature spikes of the pistillody mutant HTS-1, particularly during the pistil and stamen specification stages. Its expression was responsive to both exogenous ethylene and the ethylene inhibitor 1-Methylcyclopropene (1-MCP). Overexpression of TaEPFL1 in transgenic wheat led to shortened stamens, defective pistils, male sterility, and complete reproductive failure. Histological analysis revealed delayed tapetum degradation, indicating disrupted programmed cell death (PCD). Gas chromatography (GC) showed significantly reduced ethylene production and release in TaEPFL1-overexpressing lines. Similar floral defects were observed in wild-type plants treated with 1-MCP. Transcriptome and qRT-PCR analyses further confirmed downregulation of multiple ethylene biosynthesis-related genes, including three homologs of TaACO. These results suggest that TaEPFL1 negatively regulates ethylene biosynthesis by repressing TaACO expression, thereby impairing floral organ differentiation. We propose a feedback model in which ethylene induces TaEPFL1, which in turn suppresses ethylene production to maintain hormonal homeostasis. This study reveals a novel regulatory mechanism linking TaEPFL1 to ethylene-mediated floral development and provides new insights for improving wheat fertility through molecular breeding.

Legumes are essential for agriculture and food security. Biotic and abiotic stresses pose significant challenges to legume production, lowering productivity levels. Most legumes must be genetically improved by introducing alleles that give pest and disease resistance, abiotic stress adaptability, and high yield potential. The quickest way to develop high-yielding elite legume varieties with long-lasting resistance is to tap into potential resistance alleles present in landraces and wild relatives and exploit them in legume resistance breeding programs using next-generation molecular breeding methods. Most of the reviews focus on the advancements made by genome editing technologies in generating climate-tolerant legumes for breeding. This review discusses the challenges of genome-based editing tools and how the integration of other popular breeding methodologies, such as QTLs and GWAS, as well as computational techniques, can aid in the development of climate-tolerant legume crops. This review highlights genomics-based methodologies and recent advances that make it easier to assess genetic diversity and uncover adaptive genes in legumes. Computational approaches, such as machine learning, are important in mining the breeding-related genes identified by CRISPR and other genomic tools, as well as detecting the key elements and factors that regulate the expression of these genes, which addresses the challenge of developing climate-resilient legume crops.

Plant growth and development are highly regulated processes and are majorly controlled by various environmental factors, whose extreme exposures lead to chronic stress conditions promoting reactive oxygen species (ROS) and carbonyl species (RCS) production. ROS and RCS extensively damage cellular biomolecules and organelles, affecting a plant's development. Emerging reports highlight that the multi-stress responding DJ-1 superfamily proteins are critical in attenuating cytotoxic effects associated with abiotic stress. The current report, validated in yeast and plant models, shows that AtDJ-1C and AtDJ-1E are robust antioxidants that scavenge ROS and improve survival under oxidative stress. Although they lack conventional glyoxalases and do not attenuate the glycation of proteins, AtDJ-1C and AtDJ-1E preserve the GSH pool and regulate redox homeostasis. Moreover, gene expression profiling indicates that levels of AtDJ-1C and AtDJ-1E are rapidly established to counter heat and oxidative stress conditions. Notably, the knockdown of AtDJ-1 C and AtDJ-1E promotes detrimental alterations such as reduced chlorophyll retention, impaired root morphogenesis, and induced sensitivity to heat stress due to ROS elevation. Contrastingly, overexpression of AtDJ-1C and AtDJ-1E improved plant height and rosette formation under physiological conditions. In conclusion, our study unravels the pivotal functions of Arabidopsis thaliana DJ-1C and DJ-1E in governing plant health and survival under heat and oxidative stress conditions.

Teratosphaeria leaf blight disease caused by Teratosphaeria destructans poses a serious threat to Eucalyptus plantations worldwide. The pathogen infects leaves via stomatal penetration from 24 to 72 h after inoculation. Symptoms are visible after two weeks and pathogen sporulation commonly occurs four weeks after inoculation of a susceptible host. We studied the responses of a susceptible Eucalyptus clone during the entire disease cycle to identify susceptibility factors. RNA from healthy and infected leaves was isolated at 3, 14 and 28 days post inoculation. Differential expression and gene enrichment analysis showed that members of the transcription factor family TGA and MYB, involved in the salicylic acid and abscisic acid pathways, and genes involved in these hormone signaling pathways, were up-regulated. Overall, plant defense response pathways were enriched only at the late stage of infection (28 dpi). In contrast, both gene expression and chemical analysis revealed that the synthesis of the major flavonoids in Eucalyptus leaves was enhanced during pathogen infection, while the synthesis of terpenoids and flavan-3-ols declined. The flavonols, rutin and quercetin enhanced spore germination in-vitro while, the terpenoid eucalyptol and the flavan-3-ol catechin inhibited germination. This study provides insights into the molecular and chemical responses at different stages of infection of a susceptible host by T. destructans, thereby improving the current understanding of the pathosystem.

The recognition of translational initiation sites (TISs) offers complementary insights into identifying genes encoding novel proteins or small peptides. Conventional computational methods primarily identify Ribo-seq-supported TISs and lack the capacity of systematic and global identification of TIS, especially for non-AUG sites in plants. Additionally, these methods are often unsuitable for evaluating the importance of mRNA sequence features for TIS determination. In this study, we present TISCalling, a robust framework that combines machine learning (ML) models and statistical analysis to identify and rank novel TISs across eukaryotes. TISCalling generalized and ranks important features common to multiple plant and mammalian species while identifying kingdom-specific features such as mRNA secondary structures and "G"-nucleotide contents. Furthermore, TISCalling achieved high predictive power for identifying novel viral TISs. Importantly, TISCalling provides prediction scores for putative TIS along plant transcripts, enabling prioritization of those of interest for further validation. We offer TISCalling as a command-line-based package [ https://github.com/yenmr/TISCalling ], capable of generating prediction models and identifying key sequence features. Additionally, we provide web tools [ https://predict.southerngenomics.org/TISCalling/ ] for visualizing pre-computed potential TISs, making it accessible to users without programming experience. The TISCalling framework offers a sequence-aware and interpretable approach for decoding genome sequences and exploring functional proteins in plants and viruses.

A storage polysaccharide in the red alga Cyanidioschyzon merolae is semi-amylopectin, a glucan with properties intermediate between noncrystalline glycogen and semicrystalline amylopectin. The debranching enzyme isoamylase plays a crucial role in determining the semicrystalline nature of glucans. In amylopectin-storing organisms, isoamylases consist of the isozymes ISA1, ISA2, and ISA3, with the former two primarily responsible for semicrystallinity. While the semicrystallinity of C. merolae semi-amylopectin is weaker than that of amylopectin, it retains a semicrystalline structure. Based on a previous analysis of isoamylase-deficient strains of C. merolae, the isoform CMI294C is the main contributor to glucan synthesis. Although the biochemical properties of isoamylases involved in amylopectin synthesis have been characterized, those of isoamylases involved in semi-amylopectin synthesis remain largely unknown. Here, we performed a detailed biochemical analysis of CMI294C to gain insights of isoamylases in semi-amylopectin synthesis. Similar to isoamylases in amylopectin-synthesizing organisms, CMI294C hydrolyzes amylopectin more efficiently than glycogen. However, unlike typical isoamylases, CMI294C is uniquely more active against pullulan than against glycogen; and it is strongly inhibited by Zn²⁺. Our results indicate that CMI294C can be potentially used for industrial maltose production due to its enzymatic properties. Overall, our findings provide molecular insights into the isoamylase in glucan structure modulation and enhance our understanding of glucan metabolism in C. merolae.

Paclitaxel is an important natural anticancer drug. Its biosynthesis is very complex and 18 enzymes likely involved have been characterized. However, the regulatory mechanism of these enzyme genes still remains to be elucidated. Here we identified a novel transcription factor in the MYC family of Taxus chinensis TcJAMYC5 function in paclitaxel biosynthesis. TcJAMYC5 was highly expressed in the roots and regulated by MeJA. Transient overexpression of TcJAMYC5 in T. chinensis cambial meristematic cells resulted in a significant increase in paclitaxel and bacctin III content and upregulated expression of nearly all of paclitaxel biosynthesis related genes except T13αOH. Suppression of TcJAMYC5 expression in cambial meristematic cells resulted in a significant decrease in paclitaxel content. TcJAMYC5 could bind to promoters of paclitaxel biosynthesis pathway enzyme genes TASY, DBTNBT and T5αH for directly activating their expression. Taken together, we conclude that TcJAMYC5 is an activator that improves the accumulation of paclitaxel in T. chinensis through a MeJA-medicated signaling pathway.