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At least 19 recordsLinked to original sources

Gene Cloning, Expression, and Purification of Kunitz Trypsin Inhibitor from Glycine max Using Halo Tag.

Soybean Kunitz Trypsin Inhibitor (SKTI) is one of the most extensively studied protease inhibitors, with applications in pest management, medicine, the food processing industry, and the leather industry. In this study, SKTI was cloned into the pFN29A Flexi vector containing a barnase gene. Genomic DNA was isolated from tender soybean leaves, and SKTI was amplified by PCR to obtain a 671 bp product. After cloning, an internal 380 bp sequence was amplified using specific primers to confirm that the cloned sequence was a functional SKTI, as non-functional SKTI genes also exist in Glycine max. The amplified PCR product, containing an AsiSI site at the 5' end and a PmeI site at the 3' end, was cloned into the pFN29A vector. The resulting colonies were screened by colony PCR, and the insert sequence was confirmed by Sanger sequencing. The recombinant protein, containing a His-tag, Halo-tag, and a TEV protease cleavage site, was expressed in Escherichia coli BL21 cells. Maximum expression was achieved 5 h after induction with 0.5 mM IPTG at 37 °C. The expressed SKTI was purified using affinity chromatography on HaloLink resin, and the bound SKTI was cleaved with HaloTEV protease to obtain pure SKTI. The purified inhibitor effectively inhibited bovine trypsin, with an IC₅₀ of 0.6 ± 0.003 µg/µl, yielding 1.6 mg per gram of bacterial pellet. The 24 kDa inhibitor remained stable up to a temperature of 50 °C. Kinetic analysis revealed that recombinant SKTI competitively inhibits trypsin, with a Kᵢ value of 14 µM.

Cloning, Molecular

Foliar disease resistance phenomics of fungal pathogens: image-based approaches for mapping quantitative resistance in cereal germplasm.

Host plant resistance is the most effective and environmentally sustainable means of reducing yield losses caused by fungal foliar pathogens of cereal species. Cereal genebank collections hold diverse pools of potentially underutilized disease resistance alleles, and cereal genomic resources are well advanced due to large-scale sequencing and genotyping efforts. Genome-Wide Association Studies (GWAS) have emerged as the predominant association genetics technique to initially discover novel disease resistance loci or alleles in these diverse collections. Traditional disease resistance phenotyping methods are reliant on visual estimation of disease symptom severity and have successfully supported genetic mapping studies either via GWAS or QTL mapping in biparental populations facilitating both marker development and gene cloning efforts. Due to foliar pathogens having a high capacity to evolve, there is a need to pyramid disease resistance genes with diverse mechanisms for durable control. Resistance expressed as a quantitative trait, known as quantitative resistance (QR), is hypothesized to be more durable, unlike major R-gene resistance that is race-specific and can be vulnerable to breaking down without gene stewardship. However, assessing QR visually is challenging, particularly when complicated by complex genotype × environment (G × E) effects in the field. High-throughput image-based phenotyping provides accurate and unbiased data that can support foliar disease resistance screening efforts of genebank collections using GWAS. In this review, we discuss image-based disease phenotyping based on macroscopic (visible symptoms) and microscopic features during the host-pathogen interaction. Quantitative image analysis approaches using conventional and artificial intelligence (AI) algorithms are also discussed.

Disease Resistance

Avirulence depletion assay: Combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew.

Wheat production is threatened by multiple fungal pathogens, such as the wheat powdery mildew fungus (Blumeria graminis f. sp. tritici, Bgt). Wheat resistance breeding frequently relies on the use of resistance (R) genes that encode diverse immune receptors which detect specific avirulence (AVR) effectors and subsequently induce an immune response. While R gene cloning has accelerated recently, AVR identification in many pathogens including Bgt lags behind, preventing pathogen-informed deployment of resistance sources. Here we describe a new "avirulence depletion (AD) assay" for rapid identification of AVR genes in Bgt. This assay relies on the selection of a segregating, haploid F1 progeny population on a resistant host, followed by bulk sequencing, thereby allowing rapid avirulence candidate gene identification with high mapping resolution. In a proof-of-concept experiment we mapped the AVR component of the wheat immune receptor Pm3a to a 25 kb genomic interval in Bgt harboring a single effector, the previously described AvrPm3a2/f2. Subsequently, we applied the AD assay to map the unknown AVR effector recognized by the Pm60 immune receptor. We show that AvrPm60 is encoded by three tandemly arrayed, nearly identical effector genes that trigger an immune response upon co-expression with Pm60 and its alleles Pm60a and Pm60b. We furthermore provide evidence that Pm60 outperforms Pm60a and Pm60b through more efficient recognition of AvrPm60 effectors, suggesting it should be prioritized for wheat breeding. Finally, we show that virulence towards Pm60 is caused by simultaneous deletion of all AvrPm60 gene paralogs and that isolates lacking AvrPm60 are especially prevalent in the US thereby limiting the potential of Pm60 in this region. The AD assay is a powerful new tool for rapid and inexpensive AVR identification in Bgt with the potential to contribute to pathogen-informed breeding decisions for the use of novel R genes and regionally tailored gene deployment.

Triticum

Coordinated regulation of glutathione S-transferases confers metabolic flexibility in multi-insecticide-resistant Frankliniella occidentalis (Pergande).

INTRODUCTION: The evolution of multi-insecticide resistance in insect pests threatens global food security. Although glutathione S-transferases (GSTs) are implicated in detoxification, the coordinated mechanism by which specific gene subfamilies interact to confer broad-spectrum resistance remains inadequately characterized. OBJECTIVE: To dissect the functional allocation and cooperation of GST subfamilies in multi-insecticide-resistant strains of Frankliniella occidentalis. METHODS: We integrated comparative genomics (20 GST genes cloned), transcriptomics (qRT-PCR), RNAi-mediated silencing, molecular docking (AutoDock Vina), and in vitro metabolism assays (UPLC-MS/MS) across susceptible and resistant thrips strains. RESULTS: The two resistant strains (NIL-R and FS-R) exhibited moderate to high resistance to five insecticides (chlorfenapyr, emamectin benzoate, spinetoram, spinosad, and thiamethoxam), accompanied by significantly elevated GSTs activity. Phylogenetic analysis indicates that GSTs include 10 conserved delta and 7 diverse sigma members. The sigma subfamily has undergone a marked expansion due to gene duplication. Delta (FoGSTd1, d4, and d9) and sigma (FoGSTs1, s2, and s6) genes were significantly up-regulated in the resistant strains. RNAi showed specialized functional allocation among GSTs: delta GSTs mediated resistance to spinosad and chlorfenapyr, sigma GSTs were responsible for thiamethoxam resistance, and notably, cooperation between these subfamilies contributed to resistance against emamectin benzoate and spinetoram. Molecular docking and in vitro metabolism assays of FoGSTd9 and FoGSTs1 proteins further supported the functional allocation and cooperative roles of GST subfamilies. CONCLUSION: Our results indicate that F. occidentalis may coordinate GST subfamilies to achieve metabolic flexibility in response to multi-insecticide pressure. This survival strategy, mediated by mechanistic functional allocation and cooperative interactions among subfamilies, may contribute to energy conservation and reduced adaptive costs. Disruption of this coordinated mechanism represents a potential approach for overcoming resistance in agricultural pest populations.

Animals

Genetic Analysis of Genomic and Methylomic Variation and Identification of Multi-Trait Mutants in Rice Carried on Chang'e-5.

Global food security is facing challenges from population growth to diminishing arable land. Space mutation breeding holds promise for overcoming the variation limitations in conventional breeding; however, the mutagenic effects of the deep-space environment on rice and the transgenerational inheritance patterns of induced variations remain unclear. In this study, rice seeds carried by the Chang'e-5 spacecraft were used as materials. Whole-genome sequencing and whole-genome bisulfite sequencing were performed on the first (SP1) and second generations (SP2) of space-mutagenized plants after their return to Earth. The results showed that the number of genomic variants in the SP2 generation increased significantly compared with SP1, and SNPs, homozygous sites, and variants in coding regions were more heritable. The genome-wide methylation level was elevated in the SP2 generation, and among differentially methylated cytosines, those in the CG context exhibited the highest heritability. Furthermore, large-scale screening for nitrogen efficiency, tolerance to PEG-induced stress, and germination-stage cold resistant mutants was conducted in the SP2 generation, and phenotypic validation was performed in the third generation (SP3). By integrating multi-omics analyses of representative mutants to mine candidate genes, a number of heritable elite mutants were obtained, and seven candidate genes for key traits were identified. This study systematically elucidates the transgenerational inheritance patterns of deep-space-induced variation in rice. The multi-trait mutants obtained provide valuable germplasm resources for gene cloning and breeding applications in rice.

DNA methylation

Cloning, Transformation, and Reporter Gene Analysis of the SalT Promoter in Barley (Hordeum vulgare).

Constitutive gene expression can lead to pleiotropic effects. Therefore, spatial or temporal restriction of expression via specific promoters provides a more targeted approach. This study aimed to clone the SalT promoter and analyze its activity in transgenic barley using GFP and GUS reporter genes. The T-DNA constructs carrying the SalT promoter were introduced into barley cv. Golden Promise, and transgenic plants were confirmed through PCR, hygromycin selection, and Southern hybridization. Both constructs, SalT-GFP and SalT-GUS, were transformed in barley cv. Golden Promise. Here, we characterized the expression pattern of the SalT promoter in barley and utilized it to drive the expression of reporter genes GFP and GUS. The SalT promoter was isolated from rice genomic DNA, cloned into the pNos-AB-M vector, and confirmed through PCR and restriction analysis. Subsequently, GFP and GUS genes were cloned under the SalT promoter in the same vector. The constructs were then subcloned into the p6U vector for plant expression. Agrobacterium-mediated genetic transformation of barley cultivar "Golden Promise" was conducted, resulting in successful integration of the transgenes. Callus induction, regeneration, and root formation efficiency were assessed, demonstrating the potential of the SalT promoter to drive gene expression during various stages of plant development. Molecular analyses, including PCR and Southern hybridization, confirmed the presence and integration of transgenes in the barley genome. Furthermore, GFP fluorescence and GUS staining analyses revealed strong expression of the respective genes under control of the SalT promoter in different plant tissues. This study provides insights into the application of the SalT promoter for genetic manipulation and functional characterization in barley, offering opportunities for crop improvement and biotechnological applications.

Hordeum

Development of linezolid and daptomycin resistance in vancomycin resistant Enterococcus faecium during antibiotic treatment.

The increasing incidence of vancomycin-resistant enterococci (VRE) over the past decade has reduced treatment options largely to linezolid and daptomycin. However, the emergence of resistance to both agents further complicates the management of VRE infections. While the mechanisms of linezolid resistance are relatively well understood, those underlying daptomycin resistance remain less clearly defined. In this study, we analyzed genomic changes associated with the development of linezolid and daptomycin resistance in initially susceptible isolates following treatment at a Danish university hospital. Phenotypic susceptibility testing and whole-genome sequencing were performed on eight isolates obtained from the same patient. We identified two distinct Enterococcus faecium clones with different mechanisms of linezolid resistance. Linezolid resistance was associated with a G2576T mutation in the 23S rRNA gene (ST80 clone) and the presence of the poxtA gene (ST3082 clone). The ST80 clone also developed daptomycin resistance during therapy. We found that daptomycin resistance might result from either a G173R substitution in a gene annotated as an "ABC transporter ATP-binding protein (LolD)" or a nonsense mutation (Q58*) in phosphoketolase, with both alterations potentially acting synergistically, but further studies are warranted to confirm if these mutations can confer resistance. Together with these findings, the study demonstrates that a single patient may harbor multiple E. faecium clones simultaneously, highlighting the risk of treatment failure if all clones are not accurately identified.

Daptomycin

Cloning of two Hsp70 genes and association analysis between SNP haplotypes and high temperature tolerance trait in red swamp crayfish (Procambarus clarkii).

Aquaculture is suffering the challenge from high temperature climate. Two Hsp70 genes, PcHsp70-1 and PcHsp70-2, as key genes involved in the high temperature tolerance of red swamp crayfish (Procambarus clarkii) were identified and cloned in this study. Their molecular features and expression patterns were characterized, revealing the distinct tissue-specific upregulation expression under high temperature stress (33 °C). Two SNPs, PcHsp70-1 (SNP258) and PcHsp70-2 (SNP555) were examined to associate with high temperature tolerance in three populations (n = 675). The genotypes of PcHsp70-1-SNP258 (GA) and PcHsp70-2-SNP555 (TT) were significantly associated with stronger high temperature tolerance. Notably, individuals carrying the haplotype of Hap I (GG + TT) showed a survival rate exceeding 70% under high temperature stress, whereas, the Hap VIII (AA + CT) showed it at 5.2%. RNA interference of PcHsp70-1 resulted in a significant decrease expression of the gene GSH-Px and its encoding protein (glutathione peroxidase) activity, and damage in intestinal tissue under high temperature stress. The transcriptome result revealed that PcHsp70-1 participates in regulation of the pathways related to cytoskeletal construction, immune response, apoptosis, and antioxidant defense. These findings indicate that PcHsp70 genes are crucial for the cellular stress response under high temperature stress. The developed Kompetitive Allele Specific PCR (KASP) markers provide valuable tools for the marker-assisted selection of high temperature tolerant crayfish varieties, supporting the sustainable development of aquaculture under the challenge of global warming.

Animals

1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis.

Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilization of a CGH has been limited by the lack of well characterized, high-resolution clone sets optimized for consistent performance in aCGH assays and specifically designed analytic software. We have assembled a set of approximately 4100 publicly available human bacterial artificial chromosome (BAC) clones evenly spaced at approximately 1-Mb resolution across the genome, which includes direct coverage of approximately 400 known cancer genes. This aCGH-optimized clone set was compiled from five existing sets, experimentally refined, and supplemented for higher resolution and enhancing mapping capabilities. This clone set is associated with a public online resource containing detailed clone mapping data, protocols for the construction and use of arrays, and a suite of analytical software tools designed specifically for aCGH analysis. These resources should greatly facilitate the use of aCGH in gene discovery.

Cell Line, Tumor

Binding analysis of the response regulator NarL protein to the promoter of the O6-methylguanine-DNA methyltransferase (ogt) gene in Salmonella Typhimurium.

BACKGROUND: Salmonella Typhimurium (STM) is a gram-negative bacterium that causes severe gastrointestinal disorders in both animals and humans. The regulation of DNA repair genes is critical for maintaining genomic stability of the bacteria. O6-methylguanine DNA methyltransferase (Ogt), plays a vital role in repairing alkylated DNA in STM; however, the transcriptional regulation of ogt gene remains poorly characterized. Furthermore, NarL is a transcriptional regulator, involved in the pathogenesis of STM under anaerobic condition. Therefore, this study investigated the interaction between NarL protein and the promoter region of the ogt gene. METHODS: In this study, narl gene was cloned in pET32a vector and NarL protein was expressed in Escherichia coli BL21 (DE3). Subsequently, the ogt gene promoter (pogt) was selected, amplified, cloned and its activity was evaluated. Electrophoretic mobility shift assay (EMSA), isothermal titration calorimetry (ITC), molecular docking were employed to elucidate the interaction between NarL protein and ogt promoter. Furthermore, the regulatory role of NarL in ogt gene expression was validated in vivo using RT-qPCR and β-galactosidase assay. RESULTS: This study resulted that NarL protein interacts specifically with the ogt promoter, as confirmed by EMSA and ITC, with ΔG of - 9.42 kcal mol⁻¹. Furthermore, RT-qPCR and β-galactosidase assays demonstrated that deletion of narl significantly (P ≤ 0.01) decreased ogt transcript levels and promoter activity than wild Salmonella Typhimurium, whereas exogenous supplementation of recombinant NarL protein restored the expression. These findings suggest that NarL plays a potential regulatory role in ogt gene expression in response to environmental signals. CONCLUSION: These findings highlight an interaction between NarL protein and the promoter region of ogt gene in Salmonella Typhimurium, linking nitrogen metabolism with the DNA repair pathway in STM, which may contribute to the bacterial survival under nitrosative stress.

Salmonella typhimurium

Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse.

Rapid expansion of available data, both phenotypic and genotypic, for multiple strains of mice has enabled the development of new methods to interrogate the mouse genome for functional genetic perturbations. In silico mapping provides an expedient way to associate the natural diversity of phenotypic traits with ancestrally inherited polymorphisms for the purpose of dissecting genetic traits. In mouse, the current single nucleotide polymorphism (SNP) data have lacked the density across the genome and coverage of enough strains to properly achieve this goal. To remedy this, 470,407 allele calls were produced for 10,990 evenly spaced SNP loci across 48 inbred mouse strains. Use of the SNP set with statistical models that considered unique patterns within blocks of three SNPs as an inferred haplotype could successfully map known single gene traits and a cloned quantitative trait gene. Application of this method to high-density lipoprotein and gallstone phenotypes reproduced previously characterized quantitative trait loci (QTL). The inferred haplotype data also facilitates the refinement of QTL regions such that candidate genes can be more easily identified and characterized as shown for adenylate cyclase 7.

Adenylyl Cyclases

Clonotypic characterization defines B-cell drivers of clonal expansion and intratumor heterogeneity in IgM monoclonal gammopathies.

Waldenström macroglobulinemia (WM) and IgM monoclonal gammopathy of undetermined significance (MGUS) share the same cell of origin but differ in clonal size. Compared with other B-cell neoplasms, the lymphoplasmacytic clone in WM can be rather small, limiting our understanding of clonal expansion. We applied an integrative approach using single-cell RNA with B-cell receptor (BCR) sequencing, the assay for transposase-accessible chromatin, and whole-genome sequencing to characterize the tumor clone in patients with IgM MGUS, smoldering WM (SWM), and symptomatic WM (WM). IgM MGUS and low- or intermediate-risk SWM harbored multiple B-cell clones compared to WM. CD9, JCHAIN, RASSF6, and DUSP22 were the main markers of the dominant B-cell clone at gene expression and chromatin activity levels, with CD9 preferentially expressed in plasma cell-like tumor cells. POU2F2 had high activity in the tumor clone and was linked to CD9 regulatory regions. MYD88 and IGLL5 mutations, mainly associated with the mutational signature SBS5, were present in minor clones, whereas the MYD88 mutation was also detected in nonexpanded B-cells. The 6q deletion was present in tumor cells from high-risk patients, which harbored fitness advantage over copy-neutral tumor cells. Coding mutations clustered tumor and minor clones from oligoclonal patients and were associated with abnormal transcriptional programs. The B-cell clones also showed enriched predicted interactions with monocytes. Our integrative single-cell approach reveals the importance of clone size in IgM gammopathy and identifies key markers promoting clonal expansion.

Journal Article

Coexistence of carbapenemase and hypervirulence-associated genes among Klebsiella pneumoniae high-risk clones in Hungary.

INTRODUCTION: Strains of Klebsiella pneumoniae carrying hypervirulence and carbapenemase genes represent a rapidly emerging global public health threat. Our study aimed to comprehensively characterise the genomics of hypervirulence-associated and carbapenemase genes carrying K. pneumoniae (hv(a)CpKp) isolates in Hungary. MATERIALS AND METHODS: Between January 2022 and April 2024, 89 aerobactin (iucA-D/iutA)-positive non-duplicate carbapenemase-producing K. pneumoniae isolates from 15 Hungarian healthcare institutes underwent short-read (Illumina, MiSeq, NextSeq) whole-genome sequencing, followed by detailed plasmid analysis using long-read sequencing (Nanopore, MinION) in a representative subset of 32 strains. RESULTS: Most isolates (79/89) belonged to the high-risk clone ST147. Hypervirulence-associated (hva) genes-including rmpA/rmpA2, peg344, shiF, iucA-D, and iutA-were universally present, and 59 isolates possessed chromosomally integrated yersiniabactin loci. Most isolates (87/89) carried the bla NDM-1 carbapenemase gene. Hypervirulence-associated genes were most frequently (29/32) associated with IncHI1B/IncFIB(Mar) plasmids. Notably, we identified plasmids carrying both hva and carbapenemase genes-designated as hybrid plasmids-in 13 of 32 strains. The bla NDM-1 was linked to the IS26 transposase and was present in conserved, identical cassettes on all bla NDM-1-carrying plasmids. DISCUSSION/CONCLUSION: Our study identified hv(a)CpKp strains, particularly the ST147 clone, circulating in Hungary. Our findings highlight the need for routine virulence gene monitoring and continuous genomic and plasmid-based surveillance to mitigate the clinical and epidemiological impact of emerging hv(a)CpKp lineages.

Klebsiella pneumoniae

Conserved function of medaka pink-eyed dilution in melanin synthesis and its divergent transcriptional regulation in gonads among vertebrates.

Medaka is emerging as a model organism for the study of vertebrate development and genetics, and its effectiveness in forward genetics should prove equal to that of zebrafish. Here, we identify by positional cloning a gene responsible for the medaka i-3 albino mutant. i-3 larvae have weakly tyrosinase-positive cells but lack strongly positive and dendritic cells, suggesting loss of fully differentiated melanophores. The region surrounding the i-3 locus is syntenic to human 19p13, but a BAC clone covering the i-3 locus contained orthologs located at 15q11-13, including OCA2 (P). Medaka P consists of 842 amino acids and shares approximately 65% identity with mammalian P proteins. The i-3 mutation is a four-base deletion in exon 13, which causes a frameshift and truncation of the protein. We detected medaka P transcripts in melanin-producing eyeballs and (putative) skin melanophores on embryos and an alternatively spliced form in the non-melanin-producing ovary or oocytes. The mouse p is similarly expressed in gonads, but not alternatively spliced. This is the first isolation of nonmammalian P, the functional mechanism of action of which has not yet been elucidated, even in mammals. Further investigation of the functions of P proteins and the regulation of their expression will provide new insight into body color determination and gene evolution.

Amino Acid Sequence

Infectious Clone Development of Zucchini Green Mottle Mosaic Virus Infecting Medicinal Plant Trichosanthes kirilowii and Establishment of a Serological Assay System.

Trichosanthes kirilowii has long been cultivated for application in traditional Chinese medicine. In this study, we identified two isolates of zucchini green mottle mosaic virus (ZGMMV; species Tobamovirus cucurbitae) from T. kirilowii plants. We determined the complete genome sequences of the ZGMMV isolates named ZGMMV-GL-1 and ZGMMV-GL-2. Each ZGMMV genome was 6,517 nucleotides in length, with only a single nucleotide variation detected between two sequences. Sequence analysis revealed that the ZGMMV isolates from this study shared 88.07 to 91.62% nucleotide identity with five other ZGMMV isolates deposited in GenBank. Phylogenetic analysis indicated that ZGMMV isolates can be clustered into two distinct groups; our two isolates shared the highest sequence similarity with the ZGMMV isolate from Nanning (GenBank accession number MF066176) and clustered within Group II. The coat protein (CP) gene was cloned from ZGMMV-infected T. kirilowii samples, and the CPZGMMV was expressed using the pET28(a) vector. Specific polyclonal antiserum CPZGMMV was generated by immunizing rabbits with the purified protein, and its sensitivity was determined to be satisfactory. Leveraging the high accuracy and sensitivity of the CPZGMMV antiserum, we developed a rapid, precise, and scalable diagnostic method for ZGMMV. We then constructed the full-length cDNA clones (ZGMMV-GL-1 and ZGMMV-GL-2). Additionally, the ZGMMV cDNA infectious clones from T. kirilowii were also able to infect Nicotiana benthamiana and Cucumis sativus systemically, inducing rough-textured and curled leaves in N. benthamiana and mosaic symptoms in C. sativus and T. kirilowii. In this study, we produced an antiserum against the ZGMMV CP and developed a sensitive, rapid, and reliable diagnostic assay, which lays a technical foundation for the detection and monitoring of ZGMMV. Therefore, the establishment of the ZGMMV infectious clone facilitates further research on viral protein functions, plant-pathogen interactions, and the formulation of effective ZGMMV management strategies.

Nicotiana benthamiana

Functional study of the AfRAP2 gene in Amorpha fruticosa L. tolerance to saline-alkali and drought stress.

BACKGROUND: Amorpha fruticosa L. is a leguminous shrub with high tolerance to drought, poor soil, and saline-alkali stress conditions. As a member of the family of transcription factors in higher plants, the ethylene response factor AP2/ERF plays a crucial role in both plant adaptation to abiotic stress and in growth and development. In this study, based on genes identified from the transcriptomic sequencing of Amorpha fruticosa L. under drought stress, the upregulated gene AfRAP2 was isolated from its seedlings, with the aim of elucidating its stress-response function using molecular biological techniques. RESULTS: In this study, the AfRAP2 gene was cloned from the leaves of Amorpha fruticosa L. using RT-PCR. Bioinformatics analysis revealed that AfRAP2 contains an AP2 domain and belongs to the DREB subfamily of the AP2/ERF transcription factor family, showing close phylogenetic relationships with LaEREBP from Lathyrus albus. Real-time quantitative PCR (RT-qPCR) results indicate that AfRAP2 is expressed in various tissues of Amorpha fruticosa L., with the highest expression in leaves and the lowest in stems, furthermore, its expression is significantly upregulated in roots and leaves upon induction by NaHCO3 and PEG6000. Subcellular localization experiments confirmed that the AfRAP2 protein is localized to the nucleus, and GUS histochemical staining assay revealed that its promoter drives GUS expression in anthers. Resistance analysis of overexpressing yeast strains showed that yeast transformed with the AfRAP2 gene exhibited significantly better growth under sorbitol, mannitol, and NaHCO3 stress conditions compared to the control, indicating that this gene enhances yeast tolerance to drought and saline-alkali stress. We screened transgenic tobacco and Populus davidiana × P. alba var. Pyramidalis. The results showed that under natural drought and saline-alkali stress treatments, the transgenic lines exhibited significantly improved growth and higher activities of the physiological indicators of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) compared with wild-type plants, indicating that the overexpression of the AfRAP2 gene plays a key role in the response to saline-alkali stress and drought stress. CONCLUSION: In summary, AfRAP2 contains an AP2 domain and belongs to the DREB subfamily of transcription factors, under abiotic stress induced by NaHCO₃ and mannitol, it can induce the expression of the AfRAP2 gene in tobacco and Populus davidiana×P. alba var. pyramidalis. AfRAP2 plays a vital role in the plant response to saline-alkali stress and drought stress and is a promising candidate gene for stress-tolerant breeding.

Plant Proteins

Transcriptional Mapping of the Human Cannabinoid Receptor 1 (CNR1) Gene Promoter.

The transcriptional regulation of the cannabinoid receptor 1 (CB1R) by promoter/enhancer elements and transcription factors is an area of cannabinoid research that has historically been understudied. To map the promoter region of the human CNR1 gene (the gene encoding CB1R), a 997-base-pair fragment from the sequence upstream of the CNR1 gene was cloned into a secreted luciferase reporter vector, and a series of deletion fragments were constructed. The transcriptional activity of these constructs was tested in human cell lines from three tissues: neuronal tissue (SHSY5Y), kidney tissue (HEK293T), and colonic epithelium (HCT116). Through this mapping, we have identified two key regulatory regions within the promoter. Increased levels of cAMP suppressed reporter expression from the full-length promoter fragment in all three cell lines, and in silico modeling predicts potential cAMP response elements (CRE) within one of the key regulatory sequences. Additionally, the minimal promoter region for CNR1 also appears to be in the second regulatory region identified, and in silico modeling predicts BRE and INR elements within this sequence. These findings begin to unravel the mechanisms by which CNR1 is transcriptionally regulated.

Humans

Heterologous expression and optimization of the antimicrobial peptide acidocin 4356 in Komagataella phaffii to target Pseudomonas aeruginosa.

Multidrug-resistant (MDR) pathogens, particularly Pseudomonas aeruginosa, pose a serious global health threat due to their increasing prevalence and limited therapeutic options. Antimicrobial peptides (AMPs) offer promising alternatives to traditional antibiotics, yet their large-scale application remains constrained by high production costs and technical challenges. This research sought to develop a yeast-based system for the cost-efficient synthesis of acidocin 4356 (ACD), an antimicrobial peptide proven effective against P. aeruginosa. A codon-optimized ACD gene was cloned into the pPICZα-A expression vector and integrated into the Komagataella phaffii (formerly Pichia pastoris) GS115 genome. Colony PCR confirmed successful integration, and specific transformants demonstrated expression of the 6 × His-ECS-rACD fusion protein, as verified by SDS-PAGE and dot blot analysis. After Ni-NTA chromatography and enterokinase digestion, rACD was found at ~ 20 kDa instead of 8.3 kDa, suggesting oligomerization or post-translational modifications. Response surface methodology determined the optimal temperature, pH, and methanol concentration for peptide synthesis. Under optimal circumstances (21 °C, pH 6.24, and 1.089% methanol), rACD synthesis increased by 34.12% over baseline conditions (30 °C, pH 6, 1% methanol). AlphaFold structural modeling identified three α-helices in high-confidence regions, implicated in bacterial membrane disruption. Antimicrobial assays demonstrated potent rACD activity against P. aeruginosa, yielding a 58.29% reduction in growth at 150 µg/mL and MIC50 and MIC90 values of 143.04 and 320.64 µg/mL, respectively. These findings underscore K. phaffii as a robust platform for AMP production and highlight rACD's therapeutic potential as an effective agent against MDR P. aeruginosa, warranting further investigation into its clinical and industrial applications. KEY POINTS: • Developing a novel K. phaffii strain for heterologous expression supports efficient rACD peptide production. • Optimized conditions boosted expression yield by 34.12% above the reference fermentation settings. • Recombinant acidocin suppressed Pseudomonas aeruginosa growth by 58%, indicating anti-MDR activity.

Pseudomonas aeruginosa