Search Results (794)

Background/Objectives: Sweet potato is a tropical and subtropical crop and its growth and yield are susceptible to low-temperature stress. However, the molecular mechanisms underlying the low temperature stress of sweetpotato are unknown. Methods: In this work, combined transcriptome and metabolism analysis was employed to investigate the low-temperature responses of two sweet potato cultivars, namely, the low-temperature-resistant cultivar “X33” and the low-temperature-sensitive cultivar “W7”. Results: The differentially expressed metabolites (DEMs) of X33 at different time stages clustered in five profiles, while they clustered in four profiles of W7 with significant differences. Differentially expressed genes (DEGs) in X33 and W7 at different time points clustered in five profiles. More DEGs exhibited continuous or persistent positive responses to low-temperature stress in X33 than in W7. There were 1918 continuously upregulated genes and 6410 persistent upregulated genes in X33, whereas 1781 and 5804 were found in W7, respectively. Core genes involved in Ca²⁺ signaling, MAPK cascades, the reactive oxygen species (ROS) signaling pathway, and transcription factor families (including bHLH, NAC, and WRKY) may play significant roles in response to low temperature in sweet potato. Thirty-one common differentially expressed metabolites (DEMs) were identified in the two cultivars in response to low temperature. The KEGG analysis of these common DEMs mainly belonged to isoquinoline alkaloid biosynthesis, phosphonate and phosphinate metabolism, flavonoid biosynthesis, cysteine and methionine metabolism, glycine, serine, and threonine metabolism, ABC transporters, and glycerophospholipid metabolism. Five DEMs with identified Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were selected for correlation analysis. KEGG enrichment analysis showed that the carbohydrate metabolism, phenylpropanoid metabolism, and glutathione metabolism pathways were significantly enriched and played vital roles in low-temperature resistance in sweet potato. Conclusions: These findings contribute to a deeper understanding of the molecular mechanisms underlying plant cold tolerance and offer targets for molecular breeding efforts to enhance low-temperature resistance. Full article

Burkholderia gladioli is a multifaceted bacterium with both pathogenic and beneficial strains, and nonpathogenic Burkholderia species have shown potential as plant growth-promoting rhizobacteria (PGPRs) and biocontrol agents. However, the molecular mechanisms underlying their beneficial functions remain poorly characterized. This study systematically investigated the antimicrobial mechanisms and plant growth-promoting properties of B. gladioli strain ZBSF BH07, isolated from the grape rhizosphere, by combining genomic and functional analyses, including whole-genome sequencing, gene annotation, phylogenetic and comparative genomics, in vitro antifungal assays, and plant growth promotion evaluations. The results showed that ZBSF BH07 exhibited broad-spectrum antifungal activity, inhibiting 14 grape pathogens with an average inhibition rate of 56.58% and showing dual preventive/curative effects against grape white rot, while also significantly promoting grape seedling growth with increases of 54.9% in plant height, 172.9% in root fresh weight, and 231.34% in root dry weight. Genomic analysis revealed an 8.56-Mb genome (two chromosomes and one plasmid) encoding 7431 genes and 26 secondary metabolite biosynthesis clusters (predominantly nonribosomal peptide synthetases), supporting its capacity for antifungal metabolite secretion, and functional analysis confirmed genes for indole-3-acetic acid (IAA) synthesis, phosphate solubilization, and siderophore production. These results demonstrate that ZBSF BH07 suppresses pathogens via antifungal metabolites and enhances grape growth through phytohormone regulation and nutrient acquisition, providing novel insights into the dual mechanisms of B. gladioli as a biocontrol and growth-promoting agent and laying a scientific foundation for developing sustainable grapevine disease management strategies. Full article

Gibberellins (GAs) are essential phytohormones that regulate seed dormancy release and germination. Lomatogonium rotatum (L.) Fries ex Nym is a traditional medicinal plant whose seed germination is often hindered by physiological dormancy. In this study, we systematically investigated the effects of exogenous GA₃ on the seed germination of L. rotatum and elucidated the underlying molecular regulatory mechanisms via transcriptomic analysis. GA₃ treatment (500 mg/L for 24 h) significantly improved the germination rate, vigor index, and other germination traits. RNA-seq analysis identified time-dependent transcriptional changes in GA₃-treated seeds across three developmental stages (24 h, 72 h, and 96 h). KEGG enrichment and K-means clustering revealed dynamic actiSvation of hormonal signaling, secondary metabolism, and DNA replication pathways. WGCNA uncovered two hormone-responsive co-expression modules (Red and Lightcyan) corresponding to early and late stages of germination, respectively. Key genes related to ABA and GA biosynthesis and signal transduction showed phase-specific expression, highlighting the coordinated hormonal regulation during seed germination. Our findings provide new insights into the molecular basis of GA₃-regulated seed germination and offer theoretical support for the cultivation and utilization of L. rotatum. Full article

Background/Objectives: Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield. Methods: Here, using comparative leaf RNA-seq transcriptome analysis of plants grown at 6, 9, 12, and 15 °C, we explored key genes and metabolic pathways regulating Chinese cabbage cold response. Results: RNA-seq transcriptome analysis identified a total of 1832 differentially expressed genes (DEGs) in the three comparison groups, with 5452, 1861, and 752 DEGs specifically expressed in the A6_vs_A15, A9_vs_A15, and A12_vs_A15 groups, respectively. KEGG enrichment analysis of DEGs showed that sulfur metabolism, secondary metabolites biosynthesis and photosynthesis pathways were mostly affected by cold stress. K-means clustering revealed distinct expression profiles among the DEGs enriched in cold stress response-associated clusters. Subsequently, DEGs were divided into 18 modules by WGCNA, whereupon co-expression genes that clustered into similar modules exhibited diverse expression and were annotated to various GO terms at different temperatures. Module-trait association analysis revealed M1, M2, M3, and M6 modules as key clusters potentially linked to vernalization-related processes. These modules harbored candidate hub genes encoding transcription factors (including MYB, bZIP, and WRKY), protein kinases, and cold-stress-responsive genes. Additionally, phenotypic analysis showed that 12 °C to 15 °C supported optimal growth, whereas <9 °C temperature inhibited growth. Physiological measurements showed increased antioxidant enzyme activity and proline accumulation at 6 °C. Conclusions: Overall, our study provides a set of candidate cold-stress-responsive genes and co-expression modules that may support cold stress tolerance breeding in Chinese cabbage. Full article

Anaerobes, the oldest evolutionary life forms, have been unexplored for their potential to produce secondary metabolites due to the difficulties observed in their cultivation. Antimicrobials derived from anaerobic bacteria are an emerging and valuable source of novel therapeutic agents. The urgent need for new antimicrobial agents due to rising antibiotic resistance has prompted an investigation into anaerobic bacteria. The conventional method of antimicrobial discovery is based on cultivation and extraction methods. Antibacterial and antifungal substances are produced by anaerobic bacteria, but reports are limited due to oxygen-deficient growth requirements. The genome mining approach revealed the presence of biosynthetic gene clusters involved in various antimicrobial compound synthesis. Thus, the current review is focused on antimicrobials derived from anaerobes to unravel the potential of anaerobic bacteria as an emerging valuable source of therapeutic agents. These substances frequently consist of peptides, lipopeptides, and other secondary metabolites. Many of these antimicrobials have distinct modes of action that may be able to go around established resistance pathways. To this effect, we discuss diverse antimicrobial compounds produced by anaerobic bacteria, their biosynthesis, heterologous production, and activity. The findings suggest that anaerobic bacteria harbor significant biosynthetic potential, warranting further exploration through recombinant production for developing new antibiotics. Full article

Flavonoids are key bioactive compounds in plants that play important defense roles against abiotic stress and are involved in plant growth and development. Methyl jasmonate (MeJA) is a significant growth regulator that promotes the accumulation of flavonoids in a variety of plants, but the effect of MeJA in Hedera helix remains poorly understood. In the present study, the flavonoid content was significantly increased after MeJA treatment and peaked at 6 h post-treatment. A total of 31,931 genes were identified using transcriptome, and 6484 DEGs were identified at 6 h post-treatment. Through GO and KEGG enrichment analysis, it was shown that DEGs were primarily enriched in phenylpropanoid biosynthesis pathways. Based on the putative transcription factors derived from DEGs, growth-regulating factor (GRF), a transcription factor potentially linking MeJA signaling to flavonoid accumulation and participating in plant growth and stress responses, was further identified. A total of 20 Hh-GRFd genes were identified on the whole genome level and clustered into five phylogenetic groups with conserved subfamily characteristics. Abundant MeJA-responsive cis-elements were presented in the promoter regions of HhGRF1-HhGRF20. They exhibited a tissue-specific expression variation, and HhGRF10 was dominantly expressed in leaves of H. helix. Notably, HhGRF10 exhibited MeJA-induced expression that correlated temporally with flavonoid accumulation, suggesting that HhGRF10 might play a potential role in promoting flavonoid biosynthesis, and overexpression and knockout assay substantiated this conclusion. The finding provides the first transcriptome-wide resource for flavonoid biosynthesis in H. helix and identifies the candidate GRF-mediated regulator for flavonoid accumulation. Full article

Guvermectin, a Streptomyces-derived purine nucleoside compound, exhibits dual bioactivities as a plant growth regulator and an antibacterial agent. While its biosynthetic gene cluster (BGC) is regulated by the cluster-situated activator GvmR and the adjacent repressor GvmR2, the role of distal transcriptional regulators (TRs) in guvermectin biosynthesis remains unexplored. Here, we identified ScnR1, a highly conserved LacI-family TR located far from the guvermectin BGC, which is directly activated by GvmR. Overexpression of scnR1 significantly suppressed guvermectin biosynthesis. Further investigations revealed that ScnR1 competitively binds to the gvmR, gvmA, and O1 promoters (overlapping with the GvmR-binding sites), thereby inhibiting the guvermectin BGC transcription. Moreover, ScnR1 formed a reciprocal feedback loop with the adjacent repressor GvmR2, where each repressor inhibits the other’s expression. These findings reveal a multi-layered regulatory mechanism wherein LacI-family TRs fine-tune guvermectin biosynthesis through competitive DNA binding and reciprocal feedback control. This study offers new perspectives on the hierarchical control of secondary metabolism in Streptomyces and provides valuable theoretical guidance for the engineering of strains with enhanced natural product production. Full article

Monascus produces various bioactive compounds, including monacolin K (MK), γ-aminobutyric acid (GABA), and Monascus pigments (MPs). Studies have shown that overexpressing genes within the MK biosynthetic cluster significantly enhances MK production. Additionally, MK synthesis in Monascus is regulated by other genes. Based on previous transcriptomic analyses conducted in our laboratory, a significant positive correlation was identified between the expression level of the GAD gene and MK production in M. pilosus. In this study, the GAD gene from M. pilosus was selected for overexpression, and a series of engineered M. pilosus strains were constructed. Among the 20 PCR-positive transformants obtained, 13 strains exhibited MK production increases of 12.84–52.50% compared to the parental strain, while 17 strains showed GABA production increases of 17.47–134.14%. To elucidate the molecular mechanisms underlying the enhanced production of MK and GABA, multi-omics analyses were performed. The results indicated that GAD overexpression likely promotes MK and GABA synthesis in M. pilosus by regulating key genes (e.g., HPD, HGD, and FAH) and metabolites (e.g., α-D-ribose-1-phosphate, β-alanine) involved in pathways such as tyrosine metabolism, phenylalanine metabolism, the pentose phosphate pathway, propanoate metabolism, and β-alanine metabolism. These findings provide theoretical insights into the regulatory mechanisms of MK and GABA biosynthesis in Monascus and suggest potential strategies for enhancing their production. Full article

This study evaluated the acaricidal effects of biosurfactants produced by Serratia ureilytica against the two-spotted spider mite Tetranychus urticae and their compatibility with the predatory mite Ambliseus swirski. The biosurfactants were obtained via liquid cultures of the bacterial strains. In the laboratory, T. urticae was exposed via acaricide-immersed leaves and A. swirskii via acaricide-coated glass vials. In the greenhouse, mite-infested plants were sprayed with the biosurfactants. In the laboratory, biosurfactants produced by S. ureilytica NOD-3 and UTS exhibited strong acaricidal activity, causing 95% mortality in adults and reducing egg viability by more than 60%. In the greenhouse trial, all biosurfactants significantly suppressed T. urticae populations at all evaluated periods (7, 14, and 21 days post-application). Gas chromatography–mass spectrometry (GC-MS) analysis of the biosurfactants identified several fatty acids, including hexadecanoic acid, pentanoic acid, octadecanoic acid, decanoic acid, and tetradecanoic acid, as well as the amino acids L-proline, L-lysine, L-valine, and glutamic acid. These fatty acids and amino acids are known structural components of lipopeptides. Furthermore, the bioinformatic analysis of the genomes of the three S. ureilytica strains revealed nonribosomal peptide synthetase (NRPS) gene clusters homologous to those involved in the biosynthesis of lipopeptides. These findings demonstrate that S. ureilytica biosurfactants are promising eco-friendly acaricides, reducing T. urticae populations by >95% while partially sparing A. swirskii. Full article

Lichens, symbiotic organisms with a high tolerance to harsh environments, possess a greater diversity of sterols than other organisms. Sterols are involved in maintaining membrane integrity, hormone biosynthesis, and signal transduction. (1) Background: A characteristic feature of lichen sterols is a high degree of unsaturation, which influences membrane properties. Desaturases play an important role in the synthesis of unsaturated sterols, in particular, sterol C-5 desaturase (ERG3), which controls the conversion of episterol to ergosterol. Earlier, we demonstrated that the treatment of the lichen Peltigera canina with low and elevated temperatures results in changes in the levels of episterol and ergosterol. (2) Methods: Here, for the first time, we identified ERG3 in P. canina and, using an in silico analysis, we showed that PcERG3 belongs to the superfamily of fatty acid hydrolyases. A phylogenetic analysis was conducted to determine the evolutionary relationships of PcERG3. (3) Results: A phylogenetic analysis showed that PcERG3 clusters with ERG3 from other Peltigeralian and non-Peltigeralian lichens and also with ERG3 from free-living fungi. This suggests that PcERG3 has an ancient evolutionary origin and is related to fungi with lichenized ancestors, e.g., Penicillium. The differential expression of PcERG3 in response to temperature stress, a dehydration/rehydration cycle, and heavy metal exposure suggests that it plays a crucial role in maintaining the balance between more and less saturated sterols and, more generally, in membrane functioning. The multifaceted response of P. canina to abiotic stresses was documented by simultaneously measuring changes in the expression of PcERG3, as well as the genes encoding the heat shock proteins, PcHSP20 and PcHSP98, and PcSOD1, which encodes the antioxidant enzyme superoxide dismutase. (4) Conclusions: These findings suggest that PcERG3 is similar to the sterol C-5 desaturases from related and free-living fungi and plays important roles in the molecular mechanisms underlying the tolerance of lichens to environmental stress. Full article

Advances in whole genome sequencing have transformed GenBank into a veritable goldmine of uncharacterized and predicted proteins, many of which still await functional characterization. Notably, natural product biosynthetic pathways are often organized in gene clusters, unlocking thrilling avenues for the discovery of novel metabolites and distinctive enzymatic reactions. In this review, we focus on the versatile ThiF-like adenylyltransferase superfamily (TLATs), a group of enzymes essential for the biosynthesis of a diverse array of ribosomally synthesized and post-translationally modified peptides (RiPPs). Recent researches have revealed that TLATs are widespread in numerous yet uncharacterized RiPP biosynthetic pathways, highlighting significant gaps in our understanding of their extensive catalytic potential. Here, we critically review the latest insights into RiPP gene clusters containing these enzymes, discussing the natural products they generate, their enzymatic functions, catalytic mechanisms, and promising directions for future research. Full article

Aspergillus flavus can produce aflatoxins, posing a threat of contamination to peanuts. To mitigate this issue, the use of biocontrol isolates, which do not produce aflatoxins (AF⁻), has been considered to reduce aflatoxin levels. In this study, we evaluated five different AF⁻ isolates belonging to different vegetative compatibility groups, all of which exhibited varying degrees of deletion in aflatoxin biosynthesis gene clusters. One isolate that exhibited poor competitive ability against toxigenic A. flavus was eliminated, and the remaining four isolates were formulated as biocontrol agents and applied to a peanut field in Tai’an, Shandong, as a combination. Three months after application, the soil aflatoxin content was reduced from 0.62 ± 0.01 to 0.19 ± 0.03 μg/kg (inhibition rate: 69.35%). Among filamentous fungi in the soil, the proportion of AF⁻ isolates increased from 0% to 4.33%. Using SSR-specific primers, the microbial agents were recovered. We discovered that among the four AF⁻ isolates, CA04 had a lower colonization rate compared to the other three (only 12.00% of the total AF⁻ population), suggesting that the absence of sclerotia may result in poor reversibility and weaker dispersal ability. We utilized Illumina sequencing to investigate the changes in soil fungal ecology. The results showed a reduction in the population density of harmful fungi, such as Fusarium spp. (66.18%) and Plectosphaerella spp. (79.90%), but an increase in the density of Nothopassalora personata. This is the first study on the dispersal distance and soil fungal community structure following the application of AF⁻ agents in peanut fields in China. Full article

Annexins (ANNs) are a family of calcium (Ca²⁺)-dependent and phospholipid-binding proteins, which are implicated in the regulation of plant growth and development as well as protection from biotic and abiotic stresses. Corydalis saxicola Bunting, an endangered benzylisoquinoline alkaloid (BIA)-rich herbaceous plant, widely used in traditional Chinese medicine, is endemic to the calciphilic karst region of China. However, whether and how ANNs are involved in the biosynthesis pathway of BIAs and/or help C. saxicola plants cope with abiotic properties, such as calcareous soils, are largely unknown. Here, nine CsANN genes were identified from C. saxicola, and they were divided into three subfamilies, namely subfamilies I, II, and IV, based on the phylogenetic tree. The CsANNs clustered into the same clade, sharing similar gene structures and conserved motifs. The nine CsANN genes were located on five chromosomes, and their expansions were mainly attributed to tandem and whole-genome duplications. The CsANN transcripts displayed organ-specific and Ca²⁺-responsive expression patterns across various tissues. In addition, transient overexpression assays showed that CsANN1 could positively regulate the accumulation of BIA compounds in C. saxicola leaves, probably by directly interacting with key BIA-biosynthetic-pathway enzymes or by interacting with BIA-biosynthetic regulatory factors, such as MYBs. This study sheds light on the profiles and functions of the CsANN gene family and paves the way for unraveling the molecular mechanism of BIA accumulation, which is regulated by Ca²⁺ through CsANNs. Full article

Yam (Dioscorea spp.) provides various nutritional and medicinal benefits, including a high starch content, dietary fiber, essential micronutrients, and bioactive compounds. The molecular mechanisms underlying tuber expansion have not yet been clarified. Rapid alkalinization factor (RALF) genes, which mediate various processes in plants, are thought to contribute to the regulation of tuber growth; however, their role in yam development, especially in gibberellin (GA)-mediated processes, remains unclear. Here, we characterized seven DrRALF genes in the yam genome. Analysis of gene duplication demonstrated that the expansion of DrRALF genes was primarily driven by whole-genome duplication or segmental duplication. Phylogenetic analysis revealed that DrRALF genes were concentrated in specific clusters, indicating that their functions are relatively conserved. DrRALF5 was specifically expressed in the roots, and DrRALF2, DrRALF3, DrRALF4, and DrRALF6 were highly expressed in flowers. DrRALF1, DrRALF2, DrRALF3, DrRALF4, DrRALF5, and DrRALF6 were shown to play a role in tuber expansion. Subsequent qRT-PCR validation of four selected DrRALF genes confirmed the regulation of DrRALF2, DrRALF4, DrRALF5, and DrRALF6 by GA and PP333 (paclobutrazol, a GA biosynthesis inhibitor). Yeast one-hybrid assays further showed that the DrRALF6 promoter region interacted with the GA-signaling protein, DrDELLA1. Our findings provide novel insights into the regulatory network controlling yam tuber expansion, especially through the interaction between DrRALF6 and GA signaling pathways. Our results clarify the molecular mechanisms involved in tuber growth and propose a promising strategy for improving yam production through genetic manipulation of the GA-RALF signaling pathway. Full article

The genus Xanthomonas (family Xanthomonadaceae) comprises 39 validly published species and is associated with a broad host range, infecting hundreds of monocot and dicot plants worldwide. While many Xanthomonas species are notorious for causing leaf spot and blight diseases in major agricultural crops, less attention has been given to their impact on ornamental plants. In Hawaii and other key production regions, xanthomonads have posed persistent threats to popular ornamentals in the Araceae and Araliaceae families. This review synthesizes the evolving phylogenetic and taxonomic framework of Xanthomonas strains isolated from Araceae and Araliaceae, highlighting recent advances enabled by multilocus sequence analysis and whole genome sequencing. We discuss the reclassification of key pathovars, unresolved phylogenetic placements, and the challenges of pathovar delineation within these plant families. Additionally, we examine current knowledge of molecular determinants of pathogenicity, including gene clusters involved in exopolysaccharide and lipopolysaccharide biosynthesis, flagellar assembly, cell-wall-degrading enzymes, and secretion systems (types II, III, and VI). Comparative genomics and functional studies reveal that significant gaps remain in our understanding of the genetic basis of host adaptation and virulence in these xanthomonads. Addressing these knowledge gaps will be crucial for developing effective diagnostics and management strategies for bacterial diseases in ornamental crops. Full article