Search Results (4,216)

Gibberellic acids (GAs) are a class of tetracyclic diterpene carboxylic acid compounds produced by green plants, fungi, and bacteria, which have a wide range of applications in agricultural production and food ingredients processing. Owing to the continuously growing market demand, enhancing GA yield has become imperative. The biosynthesis of GAs is a multi-enzymatic synergistic process that can be enhanced through genetic and metabolic engineering strategies. In this review, we first summarize recent advances in GA production by Fusarium fujikuroi. We then highlight key metabolic engineering strategies, including biosynthetic pathway engineering, cluster-specific channeling of geranylgeranyl diphosphate biosynthesis, cofactor engineering, as well as regulatory mechanisms involving nitrogen modulation and histone modification. Finally, we discuss promising approaches for constructing high-efficiency microbial cell factories, such as implementation of the CRISPR/Cas9 system, the application of strong promoters, the development of target-specific technologies for small molecules, and the employment of genome-scale metabolic models. Recent metabolic engineering efforts have achieved GA3 titers of up to 3.16 g/L through multi-target nitrogen regulation strategies, highlighting the potential for further yield improvement. Full article

Cannabis sativa L. is an economically significant multi-use crop valued for fiber, seed, and phytochemical production. Compared with other crops, advancement in Cannabis sativa has been slow due to regulatory constraints and genetic resource limitations. Recent advances in technology have transformed the research landscape, supporting a deeper understanding of the genetic architecture underlying key agronomic traits. This review summarizes current progress in Cannabis sativa genetics and genomics, mainly focusing on structural genome organization, including chromosome-level assemblies and emerging pangenomic resources that capture species-wide diversity. We explore the molecular basis of key agronomic traits, including sex determination, cannabinoid biosynthesis, fiber quality, seed composition, disease resistance, and abiotic stress tolerance, highlighting their complex regulatory networks. Functional genomics tools including virus-induced gene silencing, transient expression systems, and CRISPR/Cas9 genome editing are reviewed as approaches enabling direct gene functional validation. We further review integration of these resources with molecular breeding strategies, including marker-assisted and genomic selection, to accelerate elite genotype development. Finally, we address persistent challenges such as genomic complexity, reference bias, and phenotyping limitations while outlining future research directions. Together, these advances position C. sativa as a compelling system for both fundamental plant biology and applied crop improvement. Full article

Genome editing, particularly CRISPR/Cas-based systems, has emerged as a key tool for functional genomics and trait improvement in flax (Linum usitatissimum L.), an important fiber and oilseed crop. This review focuses specifically on flax as an emerging target species and distinguishes experimentally validated applications from approaches adapted from model plants. Recent progress includes the characterization of endogenous U6 promoters, which improved guide RNA expression and contributed to enhanced genome editing performance under optimized conditions. Reported studies demonstrate efficient targeted mutagenesis in flax; however, editing outcomes remain strongly dependent on genotype, construct design, and regeneration capacity, and stable homozygous edited lines are still limited. Target genes include pathways involved in lignin and cellulose biosynthesis, fatty acid metabolism, and stress responses, influencing fiber quality, oil composition, and stress adaptation. Despite current bottlenecks such as low homologous recombination efficiency and regeneration constraints, base editing, prime editing, and multiplex CRISPR systems provide promising avenues for precision breeding in flax. Full article

Soybean is a strategic crop for global protein and vegetable oil supply chains; however, genetic improvement remains constrained by genotype-dependent regeneration, variable transformation efficiency, and regulatory concerns regarding stable transgene integration. This review synthesizes emerging DNA-free and genotype-independent genome-editing frameworks for soybean, where genotype independence is defined as the ability to recover fertile, non-chimeric edited plants across elite germplasm. We critically examine the soybean genome-editing toolbox, including CRISPR-Cas9, Cas12a, multiplex editing systems, base editing, and prime editing, and discuss persistent bottlenecks associated with target selection, off-target assessment, editability, and plant recovery. Particular emphasis is placed on artificial intelligence (AI)-assisted approaches that integrate genomic, epigenomic, chromatin-accessibility, and multi-omics datasets to improve target prioritization, guide RNA design, off-target prediction, and locus- and genotype-specific editability assessment. We further evaluate DNA-free genome-editing technologies, including CRISPR-Cas ribonucleoproteins, transient RNA-based systems, and nanocarrier-mediated delivery platforms, highlighting their potential to generate non-integrative edits while reducing prolonged nuclease exposure. In addition, we discuss regeneration reprogramming strategies based on developmental regulators and morphogenic modules, including BBM-WUS, GRF-GIF, de novo meristem induction, and somatic embryogenesis, as enabling technologies for overcoming cultivar-dependent regeneration barriers. Importantly, this review proposes an integrated AI-to-field framework that connects target discovery, editability prediction, DNA-free editing, regeneration reprogramming, phenotypic validation, and breeding deployment into a unified soybean improvement pipeline. We further highlight emerging opportunities in multi-omics-guided target discovery, genotype-aware prediction models, regeneration-aware editing strategies, and closed-loop machine-learning systems that continuously improve editing decisions through experimental feedback. Collectively, these convergent innovations provide a practical foundation for accelerating the development of climate-resilient, nutritionally enhanced, and industry-ready soybean cultivars. Full article

Nanotechnology has become an important platform in the fields of gene therapy and genome editing, providing delivery strategies that address persistent therapeutic challenges by improving the precision, efficiency, and safety of genetic modifications. This review highlights the central role of nanomaterials in overcoming persistent barriers to genetic interventions, including inefficient delivery, instability of genetic cargo, and off-target effects. Specifically, we emphasize the combined use of nanomaterials with clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) systems, which can improve editing specificity and therapeutic efficacy. Beyond the classical CRISPR/Cas9 platform, this review also discusses next-generation modalities such as base editors, Cas13, prime editing, and the recently described Tandem Interspaced Guide RNA and TIGR-associated protein (TIGR-Tas) system, while considering their therapeutic potential and distinct delivery challenges. By using nanomaterials, the stability and intracellular delivery of genome-editing systems are improved, enabling more effective treatments for genetic disorders and acquired diseases such as cancer and infectious diseases. In addition, nanocarriers provide controlled release, protection from degradation, and better biocompatibility, thereby improving the safety and reliability of gene-editing therapies. Despite these advances, important translational challenges remain, including immunotoxicity, large-scale manufacturing, and regulatory integration. Overall, the continued convergence of nanotechnology and genome engineering may support the development of personalized medicine strategies that adapt genetic engineering tools for patient-specific applications. Full article

Apolipoprotein A1 (APOA1) and paraoxonase 1 (PON1) are key proteins of high-density lipoproteins (HDL). The aim of the present study was to obtain and characterize an in vitro model for endogenous APOA1 and PON1 longstanding upregulation in hepatocytes that can be further used to decipher the mechanisms of their protective action. Cultured human hepatocytes (HuH-7 cell line) were transfected with CRISPR/dCas9 activation plasmids targeting APOA1/PON1 genes. Following selection with specific antibiotics, RNA sequencing was used for the transcriptomic characterization of the transfected hepatocytes. The functionality of the secreted APOA1/PON1 was evaluated as the capacity of the conditioned medium (CM) from transfected HuH-7 to modulate the oxidative and inflammatory stress in TNFα-activated primary human umbilical endothelial cells (HUVEC). The results showed that: (1) a robust, longstanding upregulation (46 days) of endogenous APOA1/PON1 was obtained after CRISPR/dCas9 transfection and antibiotics selection; (2) APOA1/PON1 upregulation led to a modified transcriptomic profile and increased the expression of several antioxidant genes in transfected hepatocytes as demonstrated by RNAseq analysis; (3) secreted APOA1/PON1 were functional as demonstrated by the CM ability to reduce the levels of reactive oxygen species and inflammatory markers (VCAM-1, MCP-1) in TNFα-activated HUVEC. In conclusion, we achieved an experimental model of successful longstanding upregulation of endogenous APOA1 and PON1 in human hepatocytes. The targeted proteins are secreted in a functional form and can be used for deciphering their complex mechanism of protective action in various pathological conditions. Full article

Ischemic vascular diseases remain a leading cause of morbidity and mortality worldwide and are frequently associated with irreversible tissue damage. Although stem cell-based therapies have shown promise for vascular regeneration, their clinical translation has been limited by poor survival, insufficient engraftment, functional heterogeneity, and immune rejection. Recent advances in genome-editing technologies, including CRISPR/Cas9, base editing, and prime editing, have provided powerful tools for overcoming these limitations through precise genetic modification of stem cells. Gene editing can enhance angiogenic potential, improve resistance to ischemic stress, augment paracrine activity, promote endothelial maturation, and reduce immunogenicity. In this review, we outline the current genome-editing toolbox and its application to stem cell engineering for vascular regeneration in ischemic disease. We also examine emerging therapeutic concepts, universal donor cell platforms, and key issues in safety and ethics, with a focus on translational pathways. Taken together, advances at the interface of genome editing and stem cell biology are likely to accelerate the development of regenerative therapies that deliver more durable vascular repair in ischemic vascular disease. Full article

Chilli peppers (Capsicum species) have been widely used around the world because of their economic value and distinctive sensory characteristics. They contain abundant functional metabolites, especially a group of vanillylamide compounds belonging to the family of capsaicinoids, which have been exploited for medicinal, nutritional, agricultural, and cosmetic uses. The demand for capsaicinoid molecules is increasing day by day due to their high economic value and wide range of applications. Therefore, increasing bioactive metabolites, especially capsaicinoids in chilli peppers, is a major priority in the current scenario. Multi-omics approaches such as genomics, transcriptomics, proteomics, and metabolomics have substantially contributed to understanding the complex regulatory networks governing capsaicinoid biosynthesis. Key structural genes, transcription factors, and signaling pathways involved in the phenylpropanoid and branched-chain fatty acid pathways have been identified, providing valuable targets for metabolic engineering in chilli pepper. Despite these advances, the integration of genetic modification approaches for the targeted enhancement of capsaicinoid production remains limited in chilli pepper. Recent developments in biotechnology, particularly CRISPR/Cas-mediated genome-editing, enable the precise genetic modification of metabolic pathways and regulatory networks in plants. Therefore, it can contribute to the precise modification of key genes involved in the capsaicinoid biosynthesis pathway, offering potential strategies to enhance the capsaicinoid content in chilli pepper. However, CRISPR/Cas-mediated genome editing in chilli pepper is still in its early stages. There are currently no reports available on the successful enhancement of capsaicinoid content in chilli peppers through CRISPR/Cas-mediated genome editing. To date, no comprehensive review has evaluated the CRISPR-Cas-mediated genome-editing approaches for capsaicinoid metabolic engineering in chilli pepper. This review critically evaluates the recent advances in CRISPR/Cas–mediated metabolic engineering in chilli peppers, with particular emphasis on regulatory genes involved in capsaicinoid biosynthesis. Furthermore, multi-omics approaches are expected to complement these strategies by enabling the identification of key regulatory genes, the optimization of genome-editing targets, and the prediction of metabolic outcomes for enhanced capsaicinoid production. Overall, this review provides insights into improving capsaicinoid accumulation in chilli peppers through advanced genome-editing technologies. Full article

The non-specific lipid transfer proteins (nsLTPs) are able to bind various hydrophobic compounds and facilitate the transport of fatty acids between intracellular membranes, and nsLTPs are found in rice endosperm and embryo during seed development. However, whether nsLTPs function as lipid carriers and thereby affect lipid metabolism in rice grains remains unclear. To elucidate whether nsLTPs influence fatty acid distribution in rice, we generated OsLTP10-OE (OsLTP10 overexpression) and OsLTP10-CR (OsLTP10 CRISPR/Cas9) lines. Phenotypic and metabolic analyses indicated that OsLTP10 expression is closely associated with fatty acid (FA) profiles and grain appearance. In general, total fatty acid content in the brown rice of OsLTP10-OE was higher than that in wildtype, but OsLTP10-CR was lower than wildtype. While FA accumulation was altered in both tissues, the endosperm (milled grain) was more severely affected than the bran, with individual FAs in the milled grains of OsLTP10-OE expanding by 31.87–52.00%. Additionally, key grain quality traits were substantially altered; OsLTP10-CR lines displayed a significantly enlarged white-belly chalkiness area alongside a 19.50% reduction in amylose content, whereas OsLTP10-OE lines showed decreased chalkiness and a 7.80% increase in amylose. Overall, the fatty acid content and composition, chalkiness, brown rice size, and amylose were influenced by OsLTP10. Full article

Background:Pectobacterium brasiliense-mediated soft rot severely threatens the production of diverse cash crops worldwide and brings severe yield reduction risks. A virulent strain BS1113 was separated from diseased cigar tobacco plants collected in Yunnan, yet its virulence regulatory genes and copper resistance-related genetic background have not been fully analyzed so far. This study aims to decipher the genomic features of BS1113 and clarify its pathogenic and copper-tolerant characteristics via whole-genome sequencing, comparative genomics and indoor phenotype verification. Methods: Hybrid sequencing strategies combining Illumina short reads and PacBio long reads were adopted to obtain the complete circular genome sequence of strain BS1113. Subsequent comparative genomic analysis and multiple phenotypic identification experiments were conducted to characterize its genetic architecture and physiological traits. Results: Genome assembly results showed that the circular chromosome of BS1113 spans 4,916,962 bp with a GC content of 51.96%, which encodes a total of 4369 functional protein-coding genes. Genomic comparison revealed that BS1113 completely lacks the T3SS gene cluster, while it conserves intact T2SS, T6SS and I-F CRISPR-Cas systems; the chromosomal copper resistance operon copRSAB was also detected in this isolate. Pathogenicity tests validated that BS1113 satisfies all criteria of Koch’s postulates on cigar tobacco hosts. In addition, BS1113 displayed prominent tolerance against eight mainstream copper bactericides widely used for tobacco disease management. Conclusions: This research generates the first complete high-quality genome of P. brasiliense isolated from cigar tobacco hosts. The genomic data explain the infection mechanism of this pathogen independent of intact T3SS, and also reveal the genetic basis supporting its persistent survival under long-term copper fungicide pressure in field cultivation environments. Full article

Drosophila melanogaster, widely known as the fruit fly, has emerged as a pivotal model organism for studying development and signaling transduction. Its fully sequenced genome, short generation time, and powerful genetic toolkit—including the Gal4/UAS system, RNA interference, and CRISPR-Cas9—enable precise, tissue-specific manipulation and high-throughput functional analyses. Despite differences in anatomy, the internal organ systems of Drosophila melanogaster, including the nervous system, heart, fat body, oenocytes, and nephrocytes, exhibit conserved molecular pathways and physiological functions comparable to those of humans. The morphological differences between invertebrates and vertebrates have long led researchers to undervalue the studies of insects in underlying the pathogenesis of human diseases. Over the past decades, the fruit fly has been widely validated for modeling the pathogenesis of neurodegenerative, cardiovascular, metabolic, renal, and muscular disorders. In this review, we systematically summarize the conserved molecular pathways and organ functions between the fruit fly and human, and provide examples of recent studies that use the fruit fly as a model system to answer questions associated with human diseases. We also discuss how Drosophila help researchers to fulfill the gap from mechanistic study toward translational research, and provide methodological considerations regarding the utility of Drosophila models in drug screening. Full article

Pre-harvest sprouting (PHS), the premature germination of grains on the mother plant, causes substantial yield loss and grain-quality deterioration in rice under humid conditions. Although seed dormancy and germination are largely controlled by hormonal balance, the transcriptional mechanisms linking hormone signaling with metabolic adaptation during PHS remain unclear. In this study, we investigated the roles of two ethylene-responsive factor transcription factors, OsERF1 and OsERF94, in rice PHS regulation using CRISPR/Cas9-mediated knockout lines, together with physiological, gene-expression, and metabolite analyses. The oserf1-KO mutant showed reduced seed dormancy and increased germination under PHS-inducing conditions, accompanied by altered expression of abscisic acid- and gibberellin-related genes. In contrast, the oserf94-KO mutant exhibited enhanced dormancy and reduced germination, with decreased expression of hypoxia-responsive fermentation genes and impaired carbohydrate mobilization, as indicated by reduced soluble sugar and ethanol accumulation and increased starch content. These results suggest that OsERF1 contributes primarily to hormone-mediated dormancy maintenance, whereas OsERF94 supports metabolic activation required for germination under high-moisture conditions. Collectively, this study proposes a dual regulatory framework in which hormonal control and hypoxia-associated carbon metabolism coordinately determine rice PHS susceptibility. Full article

Phytophthora and allied oomycete pathogens pose a perennial challenge to global food security through their devastating impact on crop systems. While metalaxyl has demonstrated remarkable efficacy in controlling Phytophthora diseases since its introduction decades ago, the persistent emergence of metalaxyl-resistant strains has severely compromised its field efficacy. Elucidating the genetic determinants underlying resistance mechanisms is critical to developing surveillance strategies and sustainable countermeasures against evolving oomycete resistance. Through experimental evolution, we generated six metalaxyl-resistant Phytophthora sojae mutants exhibiting extreme resistance levels (resistance factor > 2000). Comparative whole-genome re-sequencing of resistant mutants versus the wild-type parental strain identified 64 candidate genes containing conserved nonsynonymous mutations across all resistant lineages. Among these, PsALG8, encoding a putative alpha-1,3-glucosyltransferase, was identified as the primary determinant, carrying a recurrent homozygous missense mutation across all resistant lineages. CRISPR/Cas9-mediated knockout of PsALG8 in both wild-type and resistant backgrounds significantly reduced metalaxyl tolerance (p < 0.01), confirming its functional involvement in resistance modulation. These results suggest that PsALG8 is associated with metalaxyl sensitivity and mycelial growth in P. sojae under laboratory conditions. The conservation of ALG8 homologs suggests that PsALG8 may have a conserved cellular function related to protein glycosylation across eukaryotes. Although this glucosyltransferase is universally conserved among oomycete species, whether its association with metalaxyl sensitivity constitutes a shared resistance adaptation pathway still requires extensive functional validation in diverse Phytophthora pathogens, which may offer insights into future fungicide resistance management strategies in P. sojae. Full article

Cytogenomics, including karyotyping, FISH, chromosomal microarrays, and optical genome mapping, has yielded significant results for clinical phenotypes in constitutional and cancer genetics, including intellectual disability, autism spectrum disorders, dysmorphic features, and hematological and solid-tissue neoplasia. However, some of these assays have yielded results of unclear significance because the abnormalities detected were often located in intergenic regions of the genome. Because these abnormalities are within the “dark matter” of the genome, their clinical significance has been a matter of speculation. However, functional genomics can explore the clinical implications of such abnormalities more robustly, whether the abnormalities disrupt topologically associating domains (TADs), delete regulatory regions, etc. Some human genetic diseases associated with these intergenic abnormalities and characterized by functional genomics include preaxial polydactyly (SHH gene), Pierre Robin syndrome (SOX9), and 5q14.3 microdeletion syndrome (MEF2C). While functional genomics is a broad research topic, this review focuses on prior and current efforts to leverage functional genomics within the intergenic regions for human health. Full article

Over a decade of advances in Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9)-based technologies have culminated in the first-ever FDA-approved CRISPR/Cas-based therapy. Aside from this approved therapy for sickle cell anemia, several CRISPR/Cas-based therapies are currently under development or testing for a range of chronic diseases, including viral diseases like human immunodeficiency virus type 1 (HIV-1) infection, genetic diseases like familial hypercholesterolemia, and cancer. The success of these therapies hinges on the effective delivery of CRISPR/Cas9 components to target regions, efficient Cas endonuclease editing, repair profiles generated, and their resulting outcomes. Here, we discuss the factors that influence the generation of CRISPR/Cas9-generated repair edits, the overall profiles, and outcome prediction(s), as well as the analytical tools that have been developed to date. Finally, how this technology has been used towards a functional HIV-1 cure is discussed. Full article