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Lichens have developed numerous adaptations to optimize their survival in various environmental conditions, largely by producing secondary compounds by the fungal partner. They often have antibiotic properties and are involved in protection against intensive UV radiation, pathogens, and herbivores. To contribute to the knowledge of the arsenal of secondary compounds in a crustose lichen species, we sequenced and assembled the genome of Toniniopsis dissimilis , an indicator of old-growth forests, using Oxford Nanopore Technologies (ONT, Oxford, UK) long reads. Our analyses focused on biosynthetic gene clusters (BGCs) and specifically on Type I Polyketide (T1PKS) genes involved in the biosynthesis of polyketides. We used the comparative genomic approach to compare the genome of T. dissimilis with six other members of the family Ramalinaceae and twenty additional lichen genomes from the database. With only six T1PKS genes, a comparatively low number of biosynthetic genes are present in the T. dissimilis genome; from those, two-thirds are putatively involved in melanin biosynthesis. The comparative analyses showed at least three potential pathways of melanin biosynthesis in T. dissimilis , namely via the formation of 1,3,6,8-tetrahydroxynaphthalene, naphthopyrone, or YWA1 putative precursors, which highlights its importance in T. dissimilis . In addition, we report the occurrence of genes encoding ribosomally synthesized and posttranslationally modified peptides (RiPPs) in lichens, with their highest number in T. dissimilis compared to other Ramalinaceae genomes. So far, no function has been assigned to RiPP-like proteins in lichens, which leaves potential for future research on this topic.

Floral scent is an essential and genetically complex trait in herbaceous peonies (Paeonia lactiflora Pall.); however, specific genes related to metabolic and regulatory networks remain scantily studied. Our study integrated metabolite profiling and RNA-sequencing to screen floral scent biosynthetic genes. Hence, the major molecules identified by headspace collection combined with cultivar-specific GC-MS analysis were geraniol, β-caryophyllene, 2-phenylethanol (2-PE), citronellol, and 1,8-cineole. Genes related to terpenoids and 2-PE biosynthesis were identified after the assembly and annotation of the P. lactiflora transcriptomes. Eight angiosperm-specific terpene synthases (TPSs) from the TPS-a and TPS-b clades, as well as enzymes linked to 2-PE synthesis such as aromatic amino acid decarboxylase (AADC), phenylacetaldehyde reductase (PAR), and geranial reductase (GER) were identified. The biochemical analysis of the enzymes encoded by PlPAR1 and PlGER1 generated 2-PE from phenylacetaldehyde (PAld). The pairwise alignment of AADC1 reveals a splice variant lacking a 124 bp fragment, thus highlighting the possible role of alternative splicing in modulating floral scent composition. This study offers insights into the molecular-level biosynthesis of terpenoids and 2-PE in Peonia taxa, and provides the basis for the functional characterization, breeding, and bioengineering of prospective candidate genes for the production of floral volatiles in the Paeonia genus. [ABSTRACT FROM AUTHOR]

The decreased profitability of important apple cultivars, such as 'Honeycrisp', results from the poor red skin coloration and high fruit drop in the mid-Atlantic US. Apple red skin coloration is determined by the anthocyanin concentration. Reflective groundcovers promote red skin coloration, whereas aminoethoxyvinylglycine (AVG) decreases the ethylene production and fruit drop, thus reducing the coloration. Although our previous study showed that combinations of these practices impact the fruit quality and color, research is lacking regarding their effects at the gene and metabolite levels. In this work, for two years, we compared the differences in the internal ethylene concentration (IEC), red skin coloration, fruit drop, transcript accumulation of key ethylene and anthocyanin biosynthetic pathway-related genes, and total anthocyanin concentration of 'Honeycrisp' apples. The fruit was treated with combinations of reflective groundcover (Extenday) and AVG (130 mg L−1) and was assessed throughout ripening. Extenday-only-treated fruit displayed the highest upregulation of ethylene and anthocyanin biosynthetic-related genes and of total anthocyanins, exceeding 50% blush, while boosting the IEC. In contrast, AVG significantly decreased the expression of key ethylene and anthocyanin biosynthetic-related genes and total anthocyanins, thus preventing apples from reaching 50% blush, while also decreasing the IEC and fruit drop. The combination of Extenday x AVG fine-tuned the transcript accumulation of ethylene and anthocyanin biosynthetic-related genes as well as the total anthocyanins, allowing the 'Honeycrisp' fruit to exceed 50% blush, while increasing the IEC moderately and reducing the fruit drop (as compared to Extenday-only and control), thus enhancing the fruit economic value. [ABSTRACT FROM AUTHOR]

Carotenoids, biotechnologically significant pigments, play crucial biological roles in marine microorganisms. While various environments have been explored to understand the diversity of carotenoids and their biosynthesis, the Antarctic Ocean remains relatively under-investigated. This study conducted a metagenomic analysis of seawater from two depths (16 and 25 m) near the King Sejong Station in the Antarctic Ocean. The analysis revealed a rich genetic diversity underlying C40 (astaxanthin, myxol, okenone, spheroidene, and spirilloxanthin), C30 (diaponeurosporene, diapolycopene, and staphyloxanthin), and C50 (C.p. 450) carotenoid biosynthesis in marine microorganisms, with notable differential gene abundances between depth locations. Exploring carotenoid pathway genes offers the potential for discovering diverse carotenoid structures of biotechnological value and better understanding their roles in individual microorganisms and broader ecosystems. [ABSTRACT FROM AUTHOR]

Catharanthus roseus (C. roseus) can produce over 150 types of monoterpenoid indole alkaloids (MIAs), including vinblastine and vincristine, which are currently the primary sources of these alkaloids. Exploring the complex regulatory mechanisms of C. roseus is significant for resolving MIA biosynthesis. The Lateral Organ Boundaries Domain (LBD) is a plant-specific transcription factor family that plays crucial roles in the physiological processes of plant growth, stress tolerance, and specialized metabolism. However, the LBD gene family has not been extensively characterized in C. roseus, and whether its members are involved in MIA biosynthesis is still being determined. A total of 34 C. roseus LBD (CrLBD) genes were identified. RNA-Seq data were investigated to examine the expression patterns of CrLBD genes in various tissues and methyl jasmonate (MeJA) treatments. The results revealed that the Class Ia member CrLBD4 is positively correlated with iridoid biosynthetic genes (p < 0.05, r ≥ 0.8); the Class IIb member CrLBD11 is negatively correlated with iridoid biosynthetic genes (p < 0.05, r ≤ −0.8). Further validation in leaves at different growth stages of C. roseus showed that CrLBD4 and CrLBD11 exhibited different potential expression trends with iridoid biosynthetic genes and the accumulation of vindoline and catharanthine. Yeast one-hybrid (Y1H) and subcellular localization assays demonstrated that CrLBD4 and CrLBD11 could bind to the "aattatTCCGGccgc" cis-element and localize to the nucleus. These findings suggest that CrLBD4 and CrLBD11 may be potential candidates for regulating MIA biosynthesis in C. roseus. In this study, we systematically analyzed the CrLBD gene family and provided insights into the roles of certain CrLBDs in the MIA biosynthesis of C. roseus. [ABSTRACT FROM AUTHOR]

Phytoalexins are plant defense metabolites that are biosynthesized transiently in response to pathogens. Despite that their biosynthesis is highly restricted in plant tissues, the transcription factors that negatively regulate phytoalexin biosynthesis remain largely unknown. Glyceollins are isoflavonoid-derived phytoalexins that have critical roles in protecting soybean crops from the oomycete pathogen Phytophthora sojae. To identify regulators of glyceollin biosynthesis, we used a transcriptomics approach to search for transcription factors that are co-expressed with glyceollin biosynthesis in soybean and stilbene synthase phytoalexin genes in grapevine. We identified and functionally characterized the WRKY family protein GmWRKY72, which is one of four WRKY72-type transcription factors of soybean. Overexpressing and RNA interference silencing of GmWRKY72 in the soybean hairy root system decreased and increased expression of glyceollin biosynthetic genes and metabolites, respectively, in response to wall glucan elicitor from P. sojae. A translational fusion with green fluorescent protein demonstrated that GFP-GmWRKY72 localizes mainly to the nucleus of soybean cells. The GmWRKY72 protein directly interacts with several glyceollin biosynthetic gene promoters and the glyceollin transcription factor proteins GmNAC42-1 and GmMYB29A1 in yeast hybrid systems. The results show that GmWRKY72 is a negative regulator of glyceollin biosynthesis that may repress biosynthetic gene expression by interacting with transcription factor proteins and the DNA of glyceollin biosynthetic genes. [ABSTRACT FROM AUTHOR]

The medicinal plants of the Asteraceae family are a valuable source of bioactive secondary metabolites, including polyphenols, phenolic acids, flavonoids, acetylenes, sesquiterpene lactones, triterpenes, etc. Under stressful conditions, the plants develop these secondary substances to carry out physiological tasks in plant cells. Secondary Asteraceae metabolites that are of the greatest interest to consumers are artemisinin (an anti-malarial drug from Artemisia annua L.—sweet wormwood), steviol glycosides (an intense sweetener from Stevia rebaudiana Bert.—stevia), caffeic acid derivatives (with a broad spectrum of biological activities synthesized from Echinacea purpurea (L.) Moench—echinacea and Cichorium intybus L.—chicory), helenalin and dihydrohelenalin (anti-inflammatory drug from Arnica montana L.—mountain arnica), parthenolide ("medieval aspirin" from Tanacetum parthenium (L.) Sch.Bip.—feverfew), and silymarin (liver-protective medicine from Silybum marianum (L.) Gaertn.—milk thistle). The necessity to enhance secondary metabolite synthesis has arisen due to the widespread use of these metabolites in numerous industrial sectors. Elicitation is an effective strategy to enhance the production of secondary metabolites in in vitro cultures. Suitable technological platforms for the production of phytochemicals are cell suspension, shoots, and hairy root cultures. Numerous reports describe an enhanced accumulation of desired metabolites after the application of various abiotic and biotic elicitors. Elicitors induce transcriptional changes in biosynthetic genes, leading to the metabolic reprogramming of secondary metabolism and clarifying the mechanism of the synthesis of bioactive compounds. This review summarizes biotechnological investigations concerning the biosynthesis of medicinally essential metabolites in plants of the Asteraceae family after various elicitor treatments. [ABSTRACT FROM AUTHOR]

Blueberries (Vaccinium spp.) are extremely sensitive to drought stress. Flavonoids are crucial secondary metabolites that possess the ability to withstand drought stress. Therefore, improving the drought resistance of blueberries by increasing the flavonoid content is crucial for the development of the blueberry industry. To explore the underlying molecular mechanism of blueberry in adaptation to drought stress, we performed an integrated analysis of the metabolome and transcriptome of blueberry leaves under drought stress. We found that the most enriched drought-responsive genes are mainly involved in flavonoid biosynthesis and plant hormone signal transduction pathways based on transcriptome data and the main drought-responsive metabolites come from the flavonoid class based on metabolome data. The UDP-glucose flavonoid 3-O-glucosyl transferase (UFGT), flavonol synthase (FLS), and anthocyanidin reductase (ANR-2) genes may be the key genes for the accumulation of anthocyanins, flavonols, and flavans in response to drought stress in blueberry leaves, respectively. Delphinidin 3-glucoside and delphinidin-3-O-glucoside chloride may be the most important drought-responsive flavonoid metabolites. VcMYB1, VcMYBPA1, MYBPA1.2, and MYBPA2.1 might be responsible for drought-induced flavonoid biosynthesis and VcMYB14, MYB14, MYB102, and MYB108 may be responsible for blueberry leaf drought tolerance. ABA responsive elements binding factor (ABF) genes, MYB genes, bHLH genes, and flavonoid biosynthetic genes might form a regulatory network to regulate drought-induced accumulation of flavonoid metabolites in blueberry leaves. Our study provides a useful reference for breeding drought-resistant blueberry varieties. [ABSTRACT FROM AUTHOR]

Aspergillus flavus produces aflatoxin, a carcinogenic fungal toxin that poses a threat to the agricultural and food industries. There is a concern that the distribution of aflatoxin-producing A. flavus is expanding in Japan due to climate change, and it is necessary to understand what types of strains inhabit. In this study, we sequenced the genomes of four Aspergillus strains isolated from agricultural fields in the Ibaraki prefecture of Japan and identified their genetic variants. Phylogenetic analysis based on single-nucleotide variants revealed that the two aflatoxin-producing strains were closely related to A. flavus NRRL3357, whereas the two non-producing strains were closely related to the RIB40 strain of Aspergillus oryzae, a fungus widely used in the Japanese fermentation industry. A detailed analysis of the variants in the aflatoxin biosynthetic gene cluster showed that the two aflatoxin-producing strains belonged to different morphotype lineages. RT-qPCR results indicated that the expression of aflatoxin biosynthetic genes was consistent with aflatoxin production in the two aflatoxin-producing strains, whereas the two non-producing strains expressed most of the aflatoxin biosynthetic genes, unlike common knowledge in A. oryzae, suggesting that the lack of aflatoxin production was attributed to genes outside of the aflatoxin biosynthetic gene cluster in these strains. [ABSTRACT FROM AUTHOR]

Pinus taeda is a key timber species, and extensive research has been conducted on its wood formation. However, a comprehensive investigation into the biosynthetic pathways of lignin, cellulose, and hemicellulose in P. taeda is lacking, resulting in an incomplete understanding of secondary cell wall (SCW) formation in this species. In this study, we systematically analyzed transcriptomic data from previously published sources and constructed detailed pathways for lignin, cellulose, and hemicellulose biosynthesis. We identified 188 lignin-related genes and 78 genes associated with cellulose and hemicellulose biosynthesis. An RT-qPCR highlighted 15 key lignin biosynthesis genes and 13 crucial genes for cellulose and hemicellulose biosynthesis. A STEM analysis showed that most essential enzyme-coding genes clustered into Profile 14, suggesting their significant role in SCW formation. Additionally, we identified seven NAC and six MYB transcription factors (TFs) from atypical evolutionary clades, with distinct expression patterns from those of the previously characterized NAC and MYB genes, indicating potentially unique functions in SCW formation. This research provides the first comprehensive overview of lignin, cellulose, and hemicellulose biosynthetic genes in P. taeda and underscores the importance of non-canonical NAC and MYB TFs, laying a genetic foundation for future studies on SCW regulatory mechanisms. [ABSTRACT FROM AUTHOR]

Microalgae have demonstrated biostimulant potential owing to their ability to produce various plant growth-promoting substances, such as amino acids, phytohormones, polysaccharides, and vitamins. Most previous studies have primarily focused on the effects of microalgal biostimulants on plant growth. While biomass extracts are commonly used as biostimulants, research on the use of culture supernatant, a byproduct of microalgal culture, is scarce. In this study, we aimed to evaluate the potential of Chlorella vulgaris culture as a biostimulant and assess its effects on the growth and drought tolerance of Arabidopsis thaliana, addressing the gap in current knowledge. Our results demonstrated that the Chlorella cell-free supernatant (CFS) significantly enhanced root growth and shoot development in both seedlings and mature Arabidopsis plants, suggesting the presence of specific growth-promoting compounds in CFS. Notably, CFS appeared to improve drought tolerance in Arabidopsis plants by increasing glucosinolate biosynthesis, inducing stomatal closure, and reducing water loss. Gene expression analysis revealed considerable changes in the expression of drought-responsive genes, such as IAA5, which is involved in auxin signaling, as well as glucosinolate biosynthetic genes, including WRKY63, MYB28, and MYB29. Overall, C. vulgaris culture-derived CFS could serve as a biostimulant alternative to chemical products, enhancing plant growth and drought tolerance. [ABSTRACT FROM AUTHOR]

The flavonoids play important roles in plant salt tolerance. Blueberries (Vaccinium spp.) are extremely sensitive to soil salt increases. Therefore, improving the salt resistance of blueberries by increasing the flavonoid content is crucial for the development of the blueberry industry. To explore the underlying molecular mechanism, we performed an integrated analysis of the metabolome and transcriptome of blueberry leaves under salt stress. We identified 525 differentially accumulated metabolites (DAMs) under salt stress vs. control treatment, primarily including members of the flavonoid class. We also identified 20,920 differentially expressed genes (DEGs) based on transcriptome data; of these, 568 differentially expressed transcription factors (TFs) were annotated, and bHLH123, OsHSP20, and HSP20 TFs might be responsible for blueberry leaf salt tolerance. DEGs involved in the flavonoid biosynthesis pathway were significantly enriched at almost all stages of salt stress. Salt treatment upregulated the expression of most flavonoid biosynthetic pathway genes and promoted the accumulation of flavonols, flavonol glycosides, flavans, proanthocyanidins, and anthocyanins. Correlation analysis suggested that 4-coumarate CoA ligases (4CL5 and 4CL1) play important roles in the accumulation of flavonols (quercetin and pinoquercetin) and flavan-3-ol (epicatechin and prodelphinidin C2) under salt stress, respectively. The flavonoid 3′5′-hydroxylases (F3′5′H) regulate anthocyanin (cyanidin 3-O-beta-D-sambubioside and delphinidin-3-O-glucoside chloride) biosynthesis, and leucoanthocyanidin reductases (LAR) are crucial for the biosynthesis of epicatechin and prodelphinidin C2 during salt stress. Taken together, it is one of the future breeding goals to cultivate salt-resistant blueberry varieties by increasing the expression of flavonoid biosynthetic genes, especially 4CL, F3′5′H, and LAR genes, to promote flavonoid content in blueberry leaves. [ABSTRACT FROM AUTHOR]

Potato (Solanum tuberosum L.) is sensitive to drought, which severely impacts tuber yield and quality. In this study, we characterized a XERICO gene, encoding a RING-H2 type E3 ubiquitin ligase, StXERICO1, from a diploid potato, investigated its role in enhancing drought resistance and ABA accumulation, and identified its interaction with the miRNA novel-miR1730-3p, as well as its protein interactions with StUBC and StTLP. StXERICO1, with a complete Open Reading Frame (ORF) of 459 bp encoding 152 amino acids, was highly responsive to drought, ABA treatment, and abiotic stresses in potato plants. Overexpression of the StXERICO1 significantly enhanced drought resistance and ABA accumulation in transgenic potato and tobacco plants and exhibited greater sensitivity to ABA treatment, which was associated with the upregulation of expression of ABA biosynthetic genes NCED and CYP707A. Furthermore, our results revealed that StXERICO1 and its encoding protein interacted with miRNAs and other proteins. 5′ RLM-RACE (cDNA terminal rapid amplification) experiment showed that the miRNA novel-miR1730-3p targets 5′ UTR region of the StXERICO1 gene. Dual luciferase assay and virus-based miRNA silencing experiment showed that the novel-miR1730-3p negatively regulates StXERICO1 expression. Moreover, yeast two-hybrid assay indicated that StXERICO1 interacts with StUBC (an E2 ubiquitin ligase) and StTLP (a Tubby-like protein), suggesting that StXERICO1 might function on ABA homeostasis at the post-translational level. These findings elucidate the molecular mechanisms by which StXERICO1, a RING-H2 type E3 ubiquitin ligase, enhances drought resistance through increased ABA accumulation, how its expression is regulated by miRNA, and how it exerts its function through interactions with other proteins. The results also provide a potential candidate gene for subsequent precision molecular breeding aimed at improving crop drought resistance. [ABSTRACT FROM AUTHOR]

Basic leucine zipper (bZIP) transcription factors (TFs) play a crucial role in anthocyanin accumulation in plants. In addition to bZIP TFs, abscisic acid (ABA) increases anthocyanin biosynthesis. Therefore, this study aimed to investigate whether bZIP TFs are involved in ABA-induced anthocyanin accumulation in sweet cherry and elucidate the underlying molecular mechanisms. Specifically, the BLAST method was used to identify bZIP genes in sweet cherry. Additionally, we examined the expression of ABA- and anthocyanin-related genes in sweet cherry following the overexpression or knockdown of a bZIP candidate gene. In total, we identified 54 bZIP-encoding genes in the sweet cherry genome. Basic leucine zipper 6 (bZIP6) showed significantly increased expression, along with increased anthocyanin accumulation in sweet cherry. Additionally, yeast one-hybrid and dual-luciferase assays indicated that PavbZIP6 enhanced the expression of anthocyanin biosynthetic genes (PavDFR, PavANS, and PavUFGT), thereby increasing anthocyanin accumulation. Moreover, PavbZIP6 interacted directly with the PavBBX6 promoter, thereby regulating PavNCED1 to promote abscisic acid (ABA) synthesis and enhance anthocyanin accumulation in sweet cherry fruit. Conclusively, this study reveals a novel mechanism by which PavbZIP6 mediates anthocyanin biosynthesis in response to ABA and contributes to our understanding of the mechanism of bZIP genes in the regulation of anthocyanin biosynthesis in sweet cherry. [ABSTRACT FROM AUTHOR]

The bHLH transcription factors are important plant regulators against abiotic stress and involved in plant growth and development. In this study, SlALC, a gene coding for a prototypical DNA-binding protein in the bHLH family, was isolated, and SlALC-overexpression tomato (SlALC-OE) plants were generated by Agrobacterium-mediated genetic transformation. SlALC transgenic lines manifested higher osmotic stress tolerance than the wild-type plants, estimated by higher relative water content and lower water loss rate, higher chlorophyll, reducing sugar, starch, proline, soluble protein contents, antioxidant enzyme activities, and lower MDA and reactive oxygen species contents in the leaves. In SlALC-OE lines, there were more significant alterations in the expression of genes associated with stress. Furthermore, SlALC-OE fruits were more vulnerable to dehiscence, with higher water content, reduced lignin content, SOD/POD/PAL enzyme activity, and lower phenolic compound concentrations, all of which corresponded to decreased expression of lignin biosynthetic genes. Moreover, the dual luciferase reporter test revealed that SlTAGL1 inhibits SlALC expression. This study revealed that SlALC may play a role in controlling plant tolerance to drought and salt stress, as well as fruit lignification, which influences fruit dehiscence. The findings of this study have established a foundation for tomato tolerance breeding and fruit quality improvement. [ABSTRACT FROM AUTHOR]

The biosynthesis of antibiotics and other secondary metabolites (also named special metabolites) is regulated by multiple regulatory networks and cascades that act by binding transcriptional factors to the promoter regions of different biosynthetic gene clusters. The binding affinity of transcriptional factors is frequently modulated by their interaction with specific ligand molecules. In the last decades, it was found that the biosynthesis of penicillin is induced by two different molecules, 1,3-diaminopropane and spermidine, but not by putrescine (1,4-diaminobutane) or spermine. 1,3-diaminopropane and spermidine induce the expression of penicillin biosynthetic genes in Penicillium chrysogenum. Proteomic studies clearly identified two different proteins that respond to the addition to cultures of these inducers and are involved in β-alanine and pantothenic acid biosynthesis. These compounds are intermediates in the biosynthesis of phosphopantetheine that is required for the activation of non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. These large-size multidomain enzymes are inactive in the "apo" form and are activated by covalent addition of the phosphopantetheine prosthetic group by phosphopantetheinyl transferases. Both 1,3-diaminopropane and spermidine have a similar effect on the biosynthesis of cephalosporin by Acremonium chrysogenum and lovastatin by Aspergillus terreus, suggesting that this is a common regulatory mechanism in the biosynthesis of bioactive secondary metabolites/natural products. [ABSTRACT FROM AUTHOR]

Burkholderia is the second largest source of natural product bacteria after Actinomyces and can produce many secondary metabolites including pyrrolnitrin (PRN). Natural products of microbial origin are usually found in trace amounts, so in metabolic engineering, promoter engineering is often used to regulate gene expression to increase yield. In this study, an endogenous strong promoter was identified based on RNA-seq to overexpress biosynthetic genes to increase the production of PRN. By analyzing the transcriptomic data of the antagonistic bacterium Burkholderia sp. JP2-270 in three different development periods, we screened 50 endogenous promoters with high transcriptional activity, nine of which were verified by an obvious fluorescent signal via fluorescence observation. Then, combined with RT-qPCR analysis, Php, the promoter of a hypothetical protein, was found to be significantly expressed in all three periods. In order to increase the suitability of endogenous promoters, the promoter Php was shortened at different lengths, and the results show that a sequence length of 173 bp was necessary for its activity. Moreover, this promoter was used to overexpress the PRN biosynthesis genes (prnA, prnB, prnC and prnD) in JP2-270, resulting in a successful increase in gene expression levels by 40–80 times. Only the overexpression of the prnB gene successfully increased PRN production to 1.46 times that of the wild type. Overall, the endogenous strong promoters screened in this study can improve gene expression and increase the production of secondary metabolites in JP2-270 and other strains. [ABSTRACT FROM AUTHOR]

Cold stress severely impairs plant growth, development, and yields. L-ascorbic acid (ASA), a crucial antioxidant, is pivotal in mitigating stress-induced damage. Previous research found that 2-keto-L-gulonic acid (2KGA), a precursor of ASA in its industrial production, effectively enhances the endogenous ASA content in plants. We hypothesized that 2KGA might alleviate chilling stress and tried to verify it through a cultivation experiment of Arabidopsis thaliana. The results demonstrate that the application of 2KGA significantly increased ASA content (24.58%) and up-regulated ASA biosynthetic genes in Arabidopsis at 4 °C for 24 h. Furthermore, 2KGA alleviated the decrease in fresh weight (17.05%) and total chlorophyll content (15.85%) caused by low temperatures. The contents of proline, soluble sugar (SS), soluble protein (SP), and the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) were significantly increased under the 2KGA treatment at low temperatures, while the malondialdehyde (MDA) content was reduced. Moreover, 2KGA up-regulated the ICE-CBF-COR signaling pathway in response to cold stress. These collective findings strongly support the involvement of 2KGA in enhancing cold tolerance in Arabidopsis, presenting an innovative approach for agricultural practices aimed at enhancing crop resilience to environmental stresses. [ABSTRACT FROM AUTHOR]

Simple Summary: Ochratoxin A (OTA), a nephrotoxic mycotoxin categorized as a possible carcinogenic agent, is a current problem in the cheese manufacturing industry. The main OTA producers are Penicillium nordicum and Penicillium verrucosum. Therefore, we aimed to investigate different cheese ripening phases to hinder OTA production. We elaborated cheese analogues, inoculated both fungal species, and performed two different ripening phases, at 10 and 15 °C. Despite the fact that both were able to grow, they did not express genes related to OTA production, and no OTA was detected during two weeks of ripening. Therefore, we show that, when the first phases of ripening are maintained at <15 °C, the possibility of OTA production is dramatically minimized. This information is of utmost importance for industries to enhance the safety of their cheese products, which positively impacts human health. A lack of control of the technological abiotic parameters apparent during cheese manufacture, including temperature and relative humidity, results in this dairy product being prone to mold contamination. Sometimes, inoculant molds are used to obtain the characteristic sensory properties of this type of product. However, during the maturation process, some unwanted molds can colonize the ripening cheese and produce mycotoxins. Mycotoxigenic molds such as Penicillium nordicum and Penicillium verrucosum can colonize ripened cheeses, contaminating them with ochratoxin A (OTA), a nephrotoxic 2B toxin. Thus, the presence of OTA in cheeses could represent a hazard to consumers' health. This study has evaluated the growth and OTA production of P. nordicum and P. verrucosum on a cheese analogue under simulated ripening conditions of 10 and 15 °C and 0.96 water activity (aw). Ecophysiological, molecular, and analytical tools assessed the mold growth, gene expression, and OTA production under these environmental conditions. Both species were able to effectively colonize the cheese under these ripening conditions. However, neither species expressed the otapks and otanps biosynthetic genes or produced phenotypic OTA. Therefore, these results suggest a relatively low risk of exposure to OTA for consumers of this type of cheese product. The conditions used were thus appropriate for cheese ripening to minimize the potential for contamination with such mycotoxins. An appropriate adjustment of the technological ripening parameters during such cheese manufacture could contribute to OTA-free cheeses. [ABSTRACT FROM AUTHOR]

Abiotic stress, especially drought stress, poses a significant threat to terrestrial plant growth, development, and productivity. Although mulberry has great genetic diversity and extensive stress-tolerant traits in agroforestry systems, only a few reports offer preliminary insight into the biochemical responses of mulberry leaves under drought conditions. In this study, we performed a comparative metabolomic and transcriptomic analysis on the "drooping mulberry" (Morus alba var. pendula Dippel) under PEG-6000-simulated drought stress. Our research revealed that drought stress significantly enhanced flavonoid accumulation and upregulated the expression of phenylpropanoid biosynthetic genes. Furthermore, the activities of superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) content were elevated. In vitro enzyme assays and fermentation tests indicated the involvement of flavonol synthase/flavanone 3-hydroxylase (XM_010098126.2) and anthocyanidin 3-O-glucosyltransferase 5 (XM_010101521.2) in the biosynthesis of flavonol aglycones and glycosides, respectively. The recombinant MaF3GT5 protein was found to recognize kaempferol, quercetin, and UDP-glucose as substrates but not 3-/7-O-glucosylated flavonols and UDP-rhamnose. MaF3GT5 is capable of forming 3-O- and 7-O-monoglucoside, but not di-O-glucosides, from kaempferol. This implies its role as a flavonol 3, 7-O-glucosyltransferase. The findings from this study provided insights into the biosynthesis of flavonoids and could have substantial implications for the future diversified utilization of mulberry. [ABSTRACT FROM AUTHOR]

Carotenoids are naturally occurring tetraterpenoids that play a key role in fruit coloration, and yellow peaches are one of the best sources of carotenoid intake. MYB transcription factors are one of the largest families in plants and play an important role in the regulation of plant secondary metabolite biosynthesis. However, peach MYB family genes have not been fully analyzed, and in particular, MYBs that regulate carotenoid biosynthesis have not been fully characterized. In this study, 190 peach MYB genes, containing 68 1R-MYBs, 118 2R-MYBs, 3 3R-MYBs, and 1 4R-MYB, were identified at the genome level using bioinformatics methods. These 190 MYBs were classified into 27 subfamilies based on their phylogenetic relationships with Arabidopsis thaliana MYB family members, and they were unevenly distributed across eight chromosomes. MYB genes of the same subfamily exhibit similar but not identical gene structures and conserved motifs. The promoter regions contain cis-acting elements associated with stress response, hormone response, and plant growth and development. There were 54 collinear pairs of MYB genes in the peach genome, compared with 233 and 221 collinear pairs with Rosa chinensis and Arabidopsis, respectively. Thirteen differentially expressed genes in the carotenoid biosynthesis pathway in yellow peach were identified by transcriptome sequencing and contained MYB binding sites on their promoters. Based on a phylogenetic analysis, we identified 13 PpMYBs that may be involved in carotenoid biosynthesis, and a correlation analysis revealed that they regulate carotenoid accumulation by positively or negatively regulating the expression of carotenoid biosynthetic genes. Further degradome sequencing screened that mdm-miR858 was able to target PpMYB17 and PpMYB126 involved in the regulation of carotenoid biosynthesis. Our findings provide new insights into the potential role of MYB transcription factors in carotenoid biosynthesis and provide a theoretical basis for their molecular mechanisms. [ABSTRACT FROM AUTHOR]

Polyhydroxyalkanoates (PHA) have received attention owing to their biodegradability and biocompatibility, with studies exploring PHA-producing bacterial strains. As vegetable oil provides carbon and monomer precursors for poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P(3HB-co-3HHx)), oil-utilizing strains may facilitate PHA production. Herein, Cupriavidus necator BM3-1, which produces 11.1 g/L of PHB with 5% vegetable oil, was selected among various novel Cupriavidus necator strains. This strain exhibited higher preference for vegetable oils over sugars, with soybean oil and tryptone determined to be optimal sources for PHA production. BM3-1 produced 33.9 g/L of exopolysaccharides (EPS), which was three-fold higher than the amount produced by H16 (10.1 g/L). EPS exhibited 59.7% of emulsification activity (EI24), higher than that of SDS and of EPS from H16 with soybean oil. To evaluate P(3HB-co-3HHx) production from soybean oil, BM3-1 was engineered with P(3HB-co-3HHx) biosynthetic genes (phaCRa, phaARe, and phaJPa). BM3-1/pPhaCJ produced 3.5 mol% of 3HHx and 37.1 g/L PHA. BM3-1/pCB81 (phaCAJ) produced 32.8 g/L PHA, including 5.9 mol% 3HHx. Physical and thermal analyses revealed that P(3HB-co-5.9 mol% 3HHx) was better than PHB. Collectively, we identified a novel strain with high vegetable oil utilization capacity for the production of EPS, with the option to engineer the strain for P(3HB-co-3HHx). [ABSTRACT FROM AUTHOR]

Seed infection caused by Fusarium spp. is one of the major threats to the seed quality and yield of agricultural crops, including garden peas. The use of Bacillus spp. with multiple antagonistic and plant growth-promoting (PGP) abilities represents a potential disease control strategy. This study was performed to evaluate the biocontrol potential of new Bacillus spp. rhizosphere isolates against two Fusarium strains affecting garden peas. Six Bacillus isolates identified by 16S rDNA sequencing as B. velezensis (B42), B. subtilis (B43), B. mojavensis (B44, B46), B. amyloliquefaciens (B50), and B. halotolerans (B66) showed the highest in vitro inhibition of F. proliferatum PS1 and F. equiseti PS18 growth (over 40%). The selected Bacillus isolates possessed biosynthetic genes for endoglucanase (B42, B43, B50), surfactin (B43, B44, B46), fengycin (B44, B46), bacillomycin D (B42, B50), and iturin (B42), and were able to produce indole-3-acetic acid (IAA), siderophores, and cellulase. Two isolates, B. subtilis B43 and B. amyloliquefaciens B50, had the highest effect on final germination, shoot length, root length, shoot dry weight, root dry weight, and seedling vigor index of garden peas as compared to the control. Their individual or combined application reduced seed infection and increased seed germination in the presence of F. proliferatum PS1 and F. equiseti PS18, both after seed inoculation and seed bio-priming. The most promising results were obtained in the cases of the bacterial consortium, seed bio-priming, and the more pathogenic strain PS18. The novel Bacillus isolates may be potential biocontrol agents intended for the management of Fusarium seed-borne diseases. [ABSTRACT FROM AUTHOR]

The discovery and biotechnological application of new antimicrobial peptides are impeded by a lack of sensitive methods for peptide quantification. Paenibacillin is an emerging antimicrobial lantibiotic that was discovered in Paenibacillus polymyxa OSY-DF ATCC PTA-7852, isolated from the fermented vegetable Kimchee. This lantibiotic has potency against many foodborne pathogenic and spoilage bacteria. To advance the research and application of paenibacillin, a rapid, specific, and sensitive detection and quantification immunoassay was developed. After anti-paenibacillin polyclonal antibodies (pAbs) were generated and purified, a competitive enzyme-linked immunosorbent assay (cELISA) was developed and optimized for paenibacillin quantification. The dynamic range of the cELISA was determined by using a three-parameter nonlinear regression model, achieving a correlation (R2) value of 0.95. The cELISA displayed high sensitivity, with the ability to detect paenibacillin at levels as low as 15.6 ng/mL, which is significantly lower than the limit of detection of the conventional antimicrobial assay (20 µg/mL paenibacillin). The cELISA successfully differentiated paenibacillin concentrations in cell-free crude supernatants of P. polymyxa wild type and its mutant strain when grown at 30 °C and 37 °C; higher paenibacillin levels were found in the mutant (0.248–0.276 µg/mL) than in the wild type (0.122–0.212 µg/mL) culture. These findings were validated by the transcriptional analysis of 11 paenibacillin biosynthetic genes, which were significantly upregulated (≥2-fold increase) in the mutant compared with the wild strain. Additionally, the cELISA exhibited high sensitivity by recovery of paenibacillin titers spiked at 2.5 and 10 µg/mL in de Man, Rogosa, and Sharpe (MRS) broth and diluted skim milk. These results suggest that the anti-paenibacillin pAbs and the developed cELISA could be valuable in quantifying paenibacillin in complex matrices and in aiding the discovery of paenibacillin-producing natural microbiota. [ABSTRACT FROM AUTHOR]

Green leaf volatiles (GLVs) are important in giving grape a fresh and green aroma. But the changes in GLVs during the phenological development of grapevines are not well known. This study analyzed the GLVs and transcription levels of associated biosynthetic genes in six grape species from the Loess Plateau region at five stages of maturation. Thirteen GLVs were detected, showing unique patterns for each grape type at various growth phases. The primary components in six grapes were (E)-2-hexenal, (E)-2-hexen-1-ol, and hexanal. With the exception of Cabernet Franc in 2019, the overall GLV contents of the six types generally increased during growth and development, peaking or stabilizing at harvest. And Sauvignon Blanc, Cabernet Gernischt, and Cabernet Sauvignon exhibited higher total contents among the varieties. PLS-DA analysis revealed 3-hexenal's high VIP scores across two years, underscoring its critical role in grape variety classification. Correlation analysis revealed a strong positive correlation between the levels of hexanal, 1-hexanol, (E)-2-hexen-1-ol, (Z)-3-hexenyl acetate, nonanal, and (E, E)-2,6-nonadienal and the expression of VvHPL and VvAAT genes in the LOX-HPL pathway. Specifically, VvHPL emerges as a potential candidate gene responsible for species–specific differences in GLV compounds. Comprehending the changing patterns in the biosynthesis and accumulation of GLVs offers viticulturists and enologists the opportunity to devise targeted strategies for improving the aromatic profile of grapes and wines. [ABSTRACT FROM AUTHOR]

The SnRK gene family is the chief component of plant stress resistance and metabolism through activating the phosphorylation of downstream proteins. S. miltiorrhiza is widely used for the treatment of cardiovascular diseases in Asian countries. However, information about the SnRK gene family of S. miltiorrhiza is not clear. The aim of this study is to comprehensively analyze the SnRK gene family of S. miltiorrhiza and its response to phytohormone. Here, 33 SmSnRK genes were identified and divided into three subfamilies (SmSnRK1, SmSnRK2 and SmSnRK3) according to phylogenetic analysis and domain. SmSnRK genes within same subgroup shared similar protein motif composition and were unevenly distributed on eight chromosomes of S. miltiorrhiza. Cis-acting element analysis showed that the promoter of SmSnRK genes was enriched with ABRE motifs. Expression pattern analysis revealed that SmSnRK genes were preferentially expressed in leaves and roots. Most SmSnRK genes were induced by ABA and MeJA treatment. Correlation analysis showed that SmSnRK3.15 and SmSnRK3.18 might positively regulate tanshinone biosynthesis; SmSnRK3.10 and SmSnRK3.12 might positively regulate salvianolic acid biosynthesis. RNAi-based silencing of SmSnRK2.6 down-regulated the biosynthesis of tanshinones and biosynthetic genes expression. An in vitro phosphorylation assay verified that SmSnRK2.2 interacted with and phosphorylated SmAREB1. These findings will provide a valuable basis for the functional characterization of SmSnRK genes and quality improvement of S. miltiorrhiza. [ABSTRACT FROM AUTHOR]

Cyanogenic glucosides are specialized metabolites produced by over 3000 species of higher plants from more than 130 families. The deployment of cyanogenic glucosides is influenced by biotic and abiotic factors in addition to being developmentally regulated, consistent with their roles in plant defense and stress mitigation. Despite their ubiquity, very little is known regarding the molecular mechanisms that regulate their biosynthesis. The biosynthetic pathway of dhurrin, the cyanogenic glucoside found in the important cereal crop sorghum (Sorghum bicolor (L.) Moench), was described over 20 years ago, and yet no direct regulator of the biosynthetic genes has been identified. To isolate regulatory proteins that bind to the promoter region of the key dhurrin biosynthetic gene of sorghum, SbCYP79A1, yeast one-hybrid screens were performed. A bait fragment containing 1204 base pairs of the SbCYP79A1 5′ regulatory region was cloned upstream of a reporter gene and introduced into Saccharomyces cerevisiae. Subsequently, the yeast was transformed with library cDNA representing RNA from two different sorghum developmental stages. From these screens, we identified SbGATA22, an LLM domain B-GATA transcription factor that binds to the putative GATA transcription factor binding motifs in the SbCYP79A1 promoter region. Transient assays in Nicotiana benthamiana show that SbGATA22 localizes to the nucleus. The expression of SbGATA22, in comparison with SbCYP79A1 expression and dhurrin concentration, was analyzed over 14 days of sorghum development and in response to nitrogen application, as these conditions are known to affect dhurrin levels. Collectively, these findings suggest that SbGATA22 may act as a negative regulator of SbCYP79A1 expression and provide a preliminary insight into the molecular regulation of dhurrin biosynthesis in sorghum. [ABSTRACT FROM AUTHOR]

Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein–protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds. [ABSTRACT FROM AUTHOR]

A highly active alkaline phosphatase (ALP) of the protein structural family PhoA, from a mussel gut-associated strain of the marine bacterium Cobetia amphilecti KMM 296 (CmAP), was found to effectively dephosphorylate lipopolysaccharides (LPS). Therefore, the aim of this work was to perform a comprehensive bioinformatics analysis of the structure, and to suggest the physiological role of this enzyme in marine bacteria of the genus Cobetia. A scrutiny of the CmAP-like sequences in 36 available Cobetia genomes revealed nine homologues intrinsic to the subspecies C. amphilecti, whereas PhoA of a distant relative Cobetia crustatorum JO1T carried an inactive mutation. However, phylogenetic analysis of all available Cobetia ALP sequences showed that each strain of the genus Cobetia possesses several ALP variants, mostly the genes encoding for PhoD and PhoX families. The C. amphilecti strains have a complete set of four ALP families' genes, namely: PhoA, PafA, PhoX, and two PhoD structures. The Cobetia marina species is distinguished by the presence of only three PhoX and PhoD genes. The Cobetia PhoA proteins are clustered together with the human and squid LPS-detoxifying enzymes. In addition, the predicted PhoA biosynthesis gene cluster suggests its involvement in the control of cellular redox balance, homeostasis, and cell cycle. Apparently, the variety of ALPs in Cobetia spp. indicates significant adaptability to phosphorus-replete and depleted environments and a notable organophosphate destructor in eco-niches from which they once emerged, including Zostera spp. The ALP clusterization and degree of similarity of the genus-specific biosynthetic genes encoding for ectoine and polyketide cluster T1PKS, responsible for sulfated extracellular polysaccharide synthesis, coincide with a new whole genome-based taxonomic classification of the genus Cobetia. The Cobetia strains and their ALPs are suggested to be adaptable for use in agriculture, biotechnology and biomedicine. [ABSTRACT FROM AUTHOR]

Andrographis paniculata is a medicinal plant traditionally used to produce diterpene lactones and flavonoids, which possess various biological activities. Widely distributed in China, India, and other Southeast Asia countries, A. paniculata has become an important economic crop, significantly treating SARS-CoV-2, and is being cultivated on a large scale in southern China. The biosynthesis of active ingredients in A. paniculata are regulated and controlled by genes, but their specific roles are still not fully understood. To further explore the growth regulation factors and utilization of its medicinal parts of this industrial crop, chemical and transcriptome analyses were conducted on the roots, stems, and leaves of A. paniculata to identify the biosynthesis pathways and related candidate genes of the active ingredients. The chemical analysis revealed that the main components of A. paniculata were diterpene lactones and flavonoids, which displayed potential ability to treat SARS-CoV-2 through molecular docking. Moreover, the transcriptome sequencing annotated a total of 40,850 unigenes, including 7962 differentially expressed genes. Among these, 120 genes were involved in diterpene lactone biosynthesis and 60 genes were involved in flavonoid biosynthesis. The expression of diterpene lactone-related genes was the highest in leaves and the lowest in roots, consistent with our content determination results. It is speculated that these highly expressed genes in leaves may be involved in the biosynthesis pathway of diterpenes. Furthermore, two class Ⅰ terpene synthases in A. paniculata transcriptome were also annotated, providing reference for the downstream pathway of the diterpene lactone biosynthesis. With their excellent market value, our experiments will promote the study of the biosynthetic genes for active ingredients in A. paniculata and provide insights for subsequent in vitro biosynthesis. [ABSTRACT FROM AUTHOR]

Tea is a popular beverage with characteristic functional and flavor qualities, known to be rich in bioactive metabolites such as tea polyphenols and theanine. Recently, tea varieties with variations in leaf color have been widely used in agriculture production due to their potential advantages in terms of tea quality. Numerous studies have used genome, transcriptome, metabolome, proteome, and lipidome methods to uncover the causes of leaf color variations and investigate their impacts on the accumulation of crucial bioactive metabolites in tea plants. Through a comprehensive review of various omics investigations, we note that decreased expression levels of critical genes in the biosynthesis of chlorophyll and carotenoids, activated chlorophyll degradation, and an impaired photosynthetic chain function are related to the chlorina phenotype in tea plants. For purple-leaf tea, increased expression levels of late biosynthetic genes in the flavonoid synthesis pathway and anthocyanin transport genes are the major and common causes of purple coloration. We have also summarized the influence of leaf color variation on amino acid, polyphenol, and lipid contents and put forward possible causes of these metabolic changes. Finally, this review further proposes the research demands in this field in the future. [ABSTRACT FROM AUTHOR]

Alternaria spp. and its toxins are the main contaminants in processing tomato. Based on our earlier research, the current study looked into the anti-fungal capacity of crude lipopeptides from B. amyloliquefaciens XJ-BV2007 against A. alternata. We found that the crude lipopeptides significantly inhibited A. alternata growth and reduced tomato black spot disease incidence. SEM analysis found that the crude lipopeptides could change the morphology of mycelium and spores of A. alternata. Four main Alternaria toxins were detected using UPLC-MS/MS, and the findings demonstrated that the crude lipopeptides could lessen the accumulation of Alternaria toxins in vivo and in vitro. Meanwhile, under the stress of crude lipopeptides, the expression of critical biosynthetic genes responsible for TeA, AOH, and AME was substantially down-regulated. The inhibitory mechanism of the crude lipopeptides was demonstrated to be the disruption of the mycelial structure of A. alternata, as well as the integrity and permeability of the membrane of A. alternata sporocytes. Taken together, crude lipopeptides extracted from B. amyloliquefaciens XJ-BV2007 are an effective biological agent for controlling tomato black spot disease and Alternaria toxins contamination. [ABSTRACT FROM AUTHOR]

It is important to improve the production of bioactive secondary products for drug development. The Escherichia coli—Streptomyces shuttle vector pSET152 and its derived vector pIB139 containing a strong constitutive promoter ermEp* are commonly used as integrative vectors in actinomycetes. Four new integrative vectors carrying the strong constitutive promoter kasOp*, hrdBp, SCO5768p, and SP44, respectively, were constructed and proven to be functional in different mangrove-derived Streptomyces host strains by using kanamycin resistance gene neo as a reporter. Some biosynthetic genes of elaiophylins, azalomycin Fs, and armeniaspirols were selected and inserted into these vectors to overexpress in their producers including Streptomyces sp. 219807, Streptomyces sp. 211726, and S. armeniacus DSM 43125, resulting in an approximately 1.1–1.4-fold enhancement of the antibiotic yields. [ABSTRACT FROM AUTHOR]

Nitric oxide (NO) is a natural reactive nitrogen species (RNS) that alters proteins, DNA, and lipids and damages biological activities. Although microorganisms respond to and detoxify NO, the regulation of the cellular metabolic mechanisms that cause cells to tolerate RNS toxicity is not completely understood. We found that the proline and arginine auxotrophic proA5 and argB2 mutants of the fungus Aspergillus nidulans require more arginine and proline for normal growth under RNS stress that starves cells by accumulating fewer amino acids. Fungal transcriptomes indicated that RNS stress upregulates the expression of the biosynthetic genes required for global amino acids, including proline and arginine. A mutant of the gene disruptant, cpcA, which encodes the transcriptional regulation of the cross-pathway control of general amino acid synthesis, did not induce these genes, and cells accumulated fewer amino acids under RNS stress. These results indicated a novel function of CpcA in the cellular response to RNS stress, which is mediated through amino acid starvation and induces the transcription of genes for general amino acid synthesis. Since CpcA also controls organic acid biosynthesis, impaired intermediates of such biosynthesis might starve cells of amino acids. These findings revealed the importance of the mechanism regulating amino acid homeostasis for fungal responses to and survival under RNS stress. [ABSTRACT FROM AUTHOR]

The correction notice in the International Journal of Molecular Sciences addresses an error in a reference citation in a previous publication regarding the differential expression of anthocyanin biosynthetic genes in Litchi Chinensis Sonn. The corrected reference is provided, and it is stated that this correction does not impact the scientific conclusions of the original publication. The authors of the study confirm that the order of other references does not need adjustment, and the correction has been approved by the Academic Editor. [Extracted from the article]

Plants have evolved complicated defense and adaptive systems to grow in various abiotic stress environments such as drought, cold, and salinity. Anthocyanins belong to the secondary metabolites of flavonoids with strong antioxidant activity in response to various abiotic stress and enhance stress tolerance. Anthocyanin accumulation often accompanies the resistance to abiotic stress in plants to scavenge reactive oxygen species (ROS). Recent research evidence showed that many regulatory pathways such as osmoregulation, antioxidant response, plant hormone response, photosynthesis, and respiration regulation are involved in plant adaption to stress. However, the molecular regulatory mechanisms involved in controlling anthocyanin biosynthesis in relation to abiotic stress response have remained obscure. Here, we summarize the current research progress of specific regulators including small RNAs, and lncRNAs involved in the molecular regulation of abiotic stress-induced anthocyanin biosynthesis. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by microRNAs (miRNAs), long non-coding RNAs (lncRNAs), transcription factors, and stress response factors is also discussed. Understanding molecular mechanisms of anthocyanin biosynthesis for ROS scavenging in various abiotic stress responses will benefit us for resistance breeding in crop plants. [ABSTRACT FROM AUTHOR]

Background:Dendrobium officinale glycolipids (DOG), often left as residues after hot water extraction for polysaccharide production, are often discarded. Methods: This study investigates the optimal extraction of DOG using response surface methodology, focusing on liquid–solid ratios, ethanol concentrations, extraction temperatures, and extraction times, while preliminarily analyzing DOG's structural properties. Additionally, the differences in antioxidant effects between DOG and ascorbic acid based on intestinal flora metabolism were further evaluated. Results: The optimal parameters for DOG extraction were determined as follows: liquid–solid ratio of 20 mL/g, ethanol concentration of 70%, extraction temperature of 70 °C, and extraction time of 2.5 h, yielding 2.64 ± 0.18%. In addition, DOG was identified as a diglyceride, mainly composed of glucose, mannose, linoleic acid, 9,12,15-octadecatrienoic acid, and presented certain direct free radicals scavenging effects. In animal experiments, unlike the direct free scavenging effects of ascorbic acid, DOG increased intestinal Bacteroides acidifaciens abundance in mice, up-regulated piceatannol expression, and down-regulated 1-naphthol expression, which contributed to antioxidant effects by enhancing the activities of SOD and GSH-Px while reducing MDA content. Conclusions: DOG was a diglyceride isolated from D. officinale residues after hot water extraction, and presented strong antioxidant effects by regulating intestinal flora metabolism. These findings could promote the efficient utilization of D. officinale and support further development of DOG in functional food applications. [ABSTRACT FROM AUTHOR]

Chinese cabbage is rich in vitamins, fibre, and nutrients and is one of the primary vegetables consumed in autumn and winter in South Asia. 'Purple pak choi' sprouts are particularly rich in anthocyanins and are favoured by consumers. However, reports on the regulation of anthocyanin synthesis in purple pak choi sprouts do not exist. In this study, we examined the phenotypic development of purple pak choi sprouts after germination. The total anthocyanin content increased from 0.02 to 0.52 mg/g FW from days 0 to 6. RNA-seq data analysis revealed an increase in differentially expressed genes corresponding to the development of purple pak choi sprouts. Expression pattern analysis of genes associated with the anthocyanin biosynthesis pathway revealed a significant upregulation of structural genes during the purple phase, suggesting that the transcription factors PAP2 and MYBL2 may play crucial regulatory roles. BraPAP2.A03, BraTT8.A09, and BraMYBL2.A07 exhibited strong interactions with key genes in the anthocyanin biosynthesis pathway, specifically BraDFR.A09. Furthermore, the expression of BraPAP2.A03 aligned with the expression patterns of most anthocyanin biosynthesis-related genes, whereas those of BraTT8.A09 and BraMYBL2.A07 corresponded with the expression pattern of BraDFR.A09. These results provide valuable insights into regulatory mechanisms underlying anthocyanin synthesis in purple pak choi sprouts. [ABSTRACT FROM AUTHOR]

Sweet potato (Ipomoea batatas) is an important food crop that plays a pivotal role in preserving worldwide food security. Due to its polyploid genome, high heterogeneity, and phenotypic plasticity, sweet potato genetic characterization and breeding is challenging. Genome-wide association studies (GWASs) can provide important resources for breeders to improve breeding efficiency and effectiveness. GWASpoly was used to identify 28 single nucleotide polymorphisms (SNPs), comprising 21 unique genetic loci, associated with sweet potato storage root traits including dry matter (4 loci), subjective flesh color (5 loci), flesh hue angle (3 loci), and subjective skin color and skin hue angle (9 loci), in 384 accessions from the USDA sweet potato germplasm collection. The I. batatas 'Beauregard' and I. trifida reference genomes were utilized to identify candidate genes located within 100 kb from the SNPs that may affect the storage traits of dry matter, flesh color, and skin color. These candidate genes include transcription factors (especially Myb, bHLH, and WRKY family members), metabolite transporters, and metabolic enzymes and associated proteins involved in starch, carotenoid, and anthocyanin synthesis. A greater understanding of the genetic loci underlying sweet potato storage root traits will enable marker-assisted breeding of new varieties with desired traits. This study not only reinforces previous research findings on genes associated with dry matter and β-carotene content but also introduces novel genetic loci linked to these traits as well as other root characteristics. [ABSTRACT FROM AUTHOR]

Grapevine (Vitis vinifera L.) is a globally significant economic crop. However, its widely cultivated varieties are highly susceptible to white rot disease. To elucidate the mechanisms of resistance in grapevine against this disease, we utilized time-ordered gene co-expression network (TO-GCN) analysis to investigate the molecular responses in the grapevine varieties 'Guifeimeigui' (GF) and 'Red Globe' (RG). An assessment of their resistance demonstrated that GF is highly resistant to white rot, whereas RG is highly susceptible. We conducted transcriptome sequencing and a TO-GCN analysis on leaf samples from GF and RG at seven time points post-infection. Although a significant portion of the differentially expressed genes related to disease resistance were shared between GF and RG, the GF variety rapidly activated its defense mechanisms through the regulation of transcription factors during the early stages of infection. Notably, the gene VvLOX3, which is a key enzyme in the jasmonic acid biosynthetic pathway, was significantly upregulated in GF. Its upstream regulator, Vitvi08g01752, encoding a HD-ZIP family transcription factor, was identified through TO-GCN and yeast one-hybrid analyses. This study provides new molecular insights into the mechanisms of grapevine disease resistance and offers a foundation for breeding strategies aimed at enhancing resistance. [ABSTRACT FROM AUTHOR]

Many phytopathogens' gene products that contribute to plant–pathogen interactions remain unexplored. In one of the most harmful phytopathogenic bacterium Pectobacterium atrosepticum (Pba), phosphonate-related genes have been previously shown to be among the most upregulated following host plant colonization. However, phosphonates, compounds characterized by a carbon–phosphorus bond in their composition, have not been described in Pectobacterium species and other phytopathogenic bacteria, with the exception of Pseudomonas syringae and Pantoea ananatis. Our study aimed to determine whether Pba synthesizes extracellular phosphonates and, if so, to analyze their physiological functions. We demonstrated that Pba produces two types of extracellular phosphonates: 2-diethoxyphosphorylethanamine and phenylphosphonic acid. Notably, such structures have not been previously described among natural phosphonates. The production of Pba phosphonates was shown to be positively regulated by quorum sensing and in the presence of pectic compounds. Pba phosphonates were found to have a positive effect on Pba stress resistance and a negative effect on Pba virulence. The discovered Pba phosphonates are discussed as metabolites that enable Pba to control its "harmful properties", thereby maintaining its ecological niche (the host plant) in a relatively functional state for an extended period. [ABSTRACT FROM AUTHOR]

Genes involved in iron deficiency responses have been well characterized in Arabidopsis thaliana, but their roles in crop species have not been well explored. Reliance on model species may fail to identify novel iron stress mechanisms present within crop species, likely selected by hundreds of years of selection. Fiskeby III (PI 438471) is a soybean line from Sweden that demonstrates high levels of resilience to numerous stresses. Earlier Fiskeby III studies have identified a suite of genes responding to iron deficiency stress in Fiskeby III that are also associated with Arabidopsis iron deficiency responses. We were interested in determining how canonical iron genes function in Fiskeby III under normal and iron stress conditions. To investigate this, we used virus-induced gene silencing to knock down gene expression of three iron deficiency response genes (FER-like iron deficiency induced transcription factor (FIT), elongated hypocotyl 5 (HY5) and popeye (PYE)) in Fiskeby III. Analyses of RNAseq data generated from silenced plants in iron-sufficient and -deficient conditions found silencing FIT and HY5 altered general stress responses but did not impact iron deficiency tolerance, confirming Fiskeby III utilizes novel mechanisms to tolerate iron deficiency stress. [ABSTRACT FROM AUTHOR]

A number of consequences of climate change, notably salinity, put global food security at risk by impacting the development and production of lentils. Salinity-induced stress alters lentil genetics, resulting in severe developmental issues and eventual phenotypic damage. Lentils have evolved sophisticated signaling networks to combat salinity stress. Lentil genomics and transcriptomics have discovered key genes and pathways that play an important role in mitigating salinity stress. The development of saline-smart cultivars can be further revolutionized by implementing proteomics, metabolomics, miRNAomics, epigenomics, phenomics, ionomics, machine learning, and speed breeding approaches. All these cutting-edge approaches represent a viable path toward creating saline-tolerant lentil cultivars that can withstand climate change and meet the growing demand for high-quality food worldwide. The review emphasizes the gaps that must be filled for future food security in a changing climate while also highlighting the significant discoveries and insights made possible by omics and other state-of-the-art biotechnological techniques. [ABSTRACT FROM AUTHOR]

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes—PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15—under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family's functional characteristics and stress resistance regulation in P. bournei. [ABSTRACT FROM AUTHOR]

Pitaya (Hylocereus undatus) fruit is an attractive, nutrient-rich tropical fruit with commercial value. However, low-temperature stress severely affects the yield and quality of pitaya. The relevant mechanisms involved in the response of pitaya to low-temperature stress remain unclear. To study whether the SWEET gene family mediates the response of H. undatus to low-temperature stress and the related mechanisms, we performed genome-wide identification of the SWEET gene family in pitaya, and we used 'Baiyulong' tissue-cultured plantlets as material in the present study. We identified 28 members of the SWEET gene family from the H. undatus genome and divided these family members into four groups. Members of this gene family presented some differences in the sequences of introns and exons, but the gene structure, especially the motifs, presented relatively conserved characteristics. The promoter regions of most HuSWEETs have multiple stress- or hormone-related cis-elements. Three duplicated gene pairs were identified, including one tandem duplication gene and two fragment duplication gene pairs. The results revealed that the SWEET genes may regulate the transport and distribution of soluble sugars in plants; indirectly regulate the enzyme activities of CAT, POD, and T-SOD through its expression products; and are involved in the response of pitaya to low-temperature stress and play vital roles in this process. After ABA and MeJA treatment, the expression of HuSWEETs changed significantly, and the cold stress was also alleviated. This study elucidated the molecular mechanism and physiological changes in the SWEET gene in sugar metabolism and distribution of pitaya when it experiences low-temperature stress and provided a theoretical basis for cold-resistant pitaya variety breeding. [ABSTRACT FROM AUTHOR]

Camellia (Camellia japonica) is a semi-shaded plant that is highly vulnerable to heat stress. To investigate the mechanisms underlying heat stress in C. japonica, two C. japonica cultivars, "Xiaotaohong" and "Zhuapolian", which exhibit significant differences in heat tolerance, were selected from four common cultivars. The selection methods included phenotypic observations and physiological index detection, including relative electric conductivity (REC), malondialdehyde (MDA) content, superoxide dismutase (SOD) enzyme activity, relative water content (RWC), and chlorophyll content. RNA-seq analysis yielded 980 million reads and identified 68,455 differentially expressed genes (DEGs) in the two C. japonica cultivars during heat stress compared to the control samples. Totals of 12,565 and 16,046 DEGs were differentially expressed at 16 h and 32 h, respectively, in "Xiaotaohong" during heat stress. In "Zhuapolian", 40,280 and 37,539 DEGs were found at 16 h and 32 h, respectively. KEGG enrichment analysis revealed that both cultivars were enriched in the "plant hormone signal transduction" and "circadian rhythm" pathways at two stages, indicating the critical role these pathways play in the heat stress response. The differences in the tolerance between the two cultivars are likely linked to pathways such as "plant hormone signal transduction", "photosynthesis", and "circadian rhythm". Some members of heat shock proteins (HSPs) are associated with the heat stress response. It is speculated that transcription factor families contributing to the tolerance differences include AP2/ERF, C3H, bHLH, bZIP, and MYB-related with a small number of heat shock factors (HSFs) also induced by the stress. In conclusion, these results reveal the changes in the physiological indices and molecular networks of two C. japonica cultivars under heat stress. This study lays the foundation for the breeding of superior heat-resistant C. japonica cultivars and for further molecular research. [ABSTRACT FROM AUTHOR]

Microtubule-associated proteins (MAPs) play a pivotal role in the assembly and stabilization of microtubules, which are essential for plant cell growth, development, and morphogenesis. A class of plant-specific MAPs, MAP65, plays largely unexplored roles in moso bamboo (Phyllostachys edulis). This study identified 19 PeMAP65 genes in moso bamboo, systematically examining their phylogenetic relationships, conserved motifs, gene structures, collinearity, and cis-acting elements. Analysis of gene expression indicated that PeMAP65s exhibit tissue-specific expression patterns. Functional differentiation was investigated among the members of different PeMAP65 subfamilies according to their expression patterns in different development stages of bamboo shoots. The expression of PeMAP65-18 was positively correlated with the expression of genes involved in secondary cell wall (SCW) biosynthesis. Y1H and Dual-LUC assays demonstrated that the transcription of PeMAP65-18 was upregulated by PeMYB46, a key transcription factor of SCW biosynthesis. The result of subcellular localization showed that PeMAP65-18 was located in cortical microtubules. We speculate that PeMAP65-18 may play a crucial role in the SCW deposition of moso bamboo. This comprehensive analysis of the MAP65 family offers novel insights into the roles of PeMAP65s in moso bamboo, particularly in relation to the formation of SCWs. [ABSTRACT FROM AUTHOR]

Long-term exposure to ultraviolet (UV) rays can result in skin photoaging, which is primarily characterized by dryness, roughness, pigmentation, and a loss of elasticity. However, the clinical drugs commonly employed to treat photoaged skin often induce adverse effects on the skin. Anthocyanins (ACNs) are water-soluble pigments occurring abundantly in various flowers, fruits, vegetables, and grains and exhibiting a range of biological activities. Studies have demonstrated that ACNs contribute to the repair of photoaged skin due to their diverse biological characteristics and minimal side effects. Evidence suggests that the stability of ACNs can be enhanced through encapsulation or combination with other substances to improve their bioavailability and permeability, ultimately augmenting their efficacy in repairing photoaged skin. A growing body of research utilizing cell lines, animal models, and clinical studies has produced compelling data demonstrating that ACNs mitigate skin photoaging by reducing oxidative stress, alleviating the inflammatory response, improving collagen synthesis, alleviating DNA damage, and inhibiting pigmentation. This review introduces sources of ACNs while systematically summarizing their application forms as well as mechanisms for repairing photoaged skin. Additionally, it explores the potential role of ACNs in developing functional foods. These findings may provide valuable insight into using ACNs as promising candidates for developing functional products aimed at repairing photoaged skin. [ABSTRACT FROM AUTHOR]

Polyphenols are important functional components that have anti-cancer and anti-inflammatory effects. Apple fruit is rich in polyphenols and is one of the dietary sources of polyphenols. The polyphenol components and contents of the peel and pulp of 74 Malus sieversii (Led.) Roem. and 26 Chinese Malus germplasm resources were determined using ultra-high-phase chromatography (UPLC) and liquid chromatography–mass spectrometry (LC–MS). The results showed that 34 components were detected in the peel and 30 in the flesh, and that the polyphenol components and contents of the different germplasm resources were significantly different; the polyphenol content of Malus sieversii (Led.) Roem. was significantly higher than that of the other local varieties, and the polyphenol content in the peel was also higher than that in the flesh. Rutin, quercetin 3-O-arabopyranoside, kaempferol 3-O-rutinoside, and peonidin 3-O-galactoside were detected only in the peel. The total polyphenol content in the peel ranged from 949.76 to 5840.06 mg/kg, and the polyphenol content in the pulp ranged from 367.31 to 5123.10 mg/kg. The cluster analysis of polyphenol components and contents in peel and pulp showed that 100 Malus germplasm resources could be grouped into four categories. Principal component analysis of 34 kinds and 30 kinds of polyphenols in peel and pulp of 100 resources was performed. If the eigenvalue is greater than 1, eight and seven principal components are extracted, respectively. Five Malus resources with high polyphenol content in the peel and pulp were selected: 'XY-77' (peel: 5840.06 mg/kg, pulp: 5123.10 mg/kg; 'LF-09' (peel: 4692.63 mg/kg, pulp: 3729.79 mg/kg); '2012-5' (peel: 4377.61 mg/kg, pulp: 3847.54 mg/kg); '29028' (peel: 5088.05 mg/kg, pulp: 3994.61 mg/kg); and '11-01' (peel: 5154.45 mg/kg, pulp: 3616.15 mg/kg). These results provide us with information regarding the polyphenol composition and content of the wild apple resources and local cultivars. The high polyphenol content resources obtained by screening can be used as raw materials for the extraction of polyphenol components and functional fruit juice processing and can also be used as parents for functional fruit creation and variety breeding. [ABSTRACT FROM AUTHOR]

Panax japonicus C. A. Meyer is renowned for its significant therapeutic effects and is commonly used worldwide. Its active ingredients, triterpenoid saponins, show variation in content among different tissues. The tissue-specific distribution of saponins is potentially related to the expression of vital genes in the biosynthesis pathway. In this study, the contents of five saponins (ginsenoside Ro, chikusetsusaponin IV, chikusetsusaponin IVa, ginsenoside Rg1, and ginsenoside Rb1) in three different tissues were determined by HPLC. Transcriptome sequencing analysis identified differentially expressed genes (DEGs) involved in triterpenoid saponin biosynthesis, highlighting significant correlations between saponin contents and the expression levels of 10 cytochrome p450 monooxygenase (CYP) and 3 UDP-glycosyltransferase (UGT) genes. Cloning, sequencing, and prokaryotic expression of UGT genes confirmed the molecular weights of UGT proteins. Gene sequence alignment and phylogenetic analysis provided preliminary insights into UGT gene functions. Meanwhile, the function of one UGT gene was characterized in the yeast. These findings advance our understanding of the triterpenoid saponin biosynthesis in P. japonicus and support future research in traditional Chinese medicine (TCM) and synthetic biology. [ABSTRACT FROM AUTHOR]