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Results for “Synthetic promoters”

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At least 19 recordsLinked to original sources

PubMed2026

OsICL-associated metabolic reprogramming during dehydration in rice is regulated by ABA and modulated by ACC and its metabolites.

Drought coordinates hormonal, transcriptional, and metabolic reprogramming, but how abscisic acid (ABA) and 1-aminocyclopropane-1-carboxylic acid (ACC) jointly shape cereal dehydration responses remains unclear. We integrated hormone profiling, transcriptome and promoter analyses, synthetic promoter assays, and metabolite profiling in rice. ABA and ACC contents increased markedly in rice shoots under moderate soil water deficit. Combined ABA + ACC treatment showed larger absolute overlaps with dehydration-responsive genes than either ABA or ACC treatment alone in shoots; in roots, this pattern was observed for induced but not repressed genes. Promoters of dehydration- and ABA-inducible genes were enriched in ACGT-core motifs, including a CGTACG core preferentially embedded in ACGTACGT, designated the eXtended ACGT box (Xbox). Multimerised Xbox conferred transcriptional induction under soil water deficit and in response to ABA. OsICL was induced under soil water deficit and by ABA or ACC; in shoots, combined ABA + ACC treatment produced the highest mean transcript accumulation. OsICL overexpression and knockout lines showed altered organic-acid, sugar, and amino-acid profiles, particularly under soil water deficit, but several metabolites changed in the same direction in both line classes. These findings support an ABA-centred, ACC-modulated model of dehydration-responsive transcription and associate OsICL regulation with broader, condition-dependent changes in primary metabolism.

Oryza sativa↗

PubMed1976

Epidermal cell proliferation and promoting ability of phorbol esters.

Dose-response relationships on the abilities of several phorbol ester tumor promoters to promote skin tumors after 7,12-dimethylbenz[a]anthracene initiation and to bring about edema, inflammation, and epidermal hyperplasia were determined in female Charles River CD-1 mice. The promoting ability of the potent synthetic promoter, phorbol-12,13-dioctanoate (PdiC8), was determined over a dose range of 0.1-10 mug/application. Administration of PdiC8 two times weekly at dosages of 4, 6, 8, and 10 mug gave little variation in tumor response. A dose-dependent tumor response occurred at doses of 1-4 mug PdiC8. Only 1 papilloma was observed when PdiC8 was given twice weekly at a dose of 0.1 or 0.5 mug. A similar dose-response relation was observed for the ability of PdiC8 to stimulate epidermal hyperplasia. Investigations of other phorbol esters revealed an excellent correlation between their promoting ability and their ability to induce epidermal hyperplasia; however, that was not the case for compounds outside the phorbol ester series (i.e., acetic acid, cantharidin, and ethylphenylpropiolate).

9,10-Dimethyl-1,2-benzanthracene↗

PubMed2025

Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.

Core promoters are essential regulatory elements that control transcription initiation, but accurately predicting and designing their strength remains challenging due to complex sequence-function relationships and the limited generalizability of existing AI-based approaches. To address this, we developed a modular platform integrating rational library design, predictive modelling, and generative optimization into a closed-loop workflow for end-to-end core promoter engineering. Conserved and spacer region of core promoters exert distinct effects on transcriptional strength, with the former driving large-scale variation and the latter enabling finer gradation. Based on this insight, Mutation-Barcoding-Reverse Sequencing approach was used and constructed a synthetic promoter library comprising 112 955 variants with minimal redundancy and a 16 226-fold expression range. A Transformer-based model trained on this dataset achieved a Pearson correlation of 0.87 with experimentally measured promoter strengths. When combined with a conditional diffusion model, the system enabled de novo generation of promoter sequences with defined strengths, achieving a design-to-measurement correlation of 0.95 and maintaining high accuracy (R = 0.93) across varied sequence contexts. The designed promoters consistently preserved their intended strength gradients, demonstrating robust plug-and-play functionality. This work establishes a scalable and extensible platform (www.yudenglab.com) for deep learning-guided programmable design of Escherichia coli core promoters, enabling precise transcriptional control.

Promoter Regions, Genetic↗

PubMed2026

Glucose-responsive probiotics for glycaemic modulation in mice and monkeys.

Sustained and controlled delivery of glucose-lowering agents using engineered designer cells is recognized as an effective strategy for diabetes therapy1. However, current technologies rely on external signal control or have been programmed into mammalian cells using synthetic gene networks, which pose safety concerns arising from transplantation2,3. Here we developed an engineered oral-deliverable glucose-sensing and functional response probiotic living drug for 'sense-and-respond'-based control of diabetic blood glucose. We created a glucose sensor based on a synthetic gene circuit that incorporates the glucose-responsive transcriptional regulator HexR, coupled with a synthetic promoter. Upon oral administration of the engineered probiotics carrying the sensor, the cells reside temporarily in the intestine and regulate the expression of therapeutic transgenes in response to glucose levels that exceed the normal threshold. We show efficacy from the engineered probiotics for glycaemic control in multiple diabetic mouse and non-human primate models, demonstrating that long-term oral administration drives clear improvements in lipid profiles, while also attenuating development of multiple diabetic complications. Our probiotics-based living drug enables therapeutic dosing in response to real-time blood glucose levels, providing a programmable, orally deliverable sense-and-respond platform for metabolic therapy without transplantation.

Animals↗

PubMed2025

Molecular mechanisms and breeding strategies for heat tolerance in vegetable crops under global warming.

Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops. This review synthesizes the multistage impacts of heat stress across critical developmental phases-from germination to reproduction-emphasizing morphological impairments (such as leaf wilting and floral abortion) and physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca2+-ROS signaling pathways; and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multistress tolerance by targeting conserved 'core response' pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with ''Climate-Responsive Carbon Optimization; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.

Journal Article↗

PubMed2025

Targeted, Genome-scale Overexpression in Proteobacteria.

Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, and basic research. Although CRISPRi knockdowns have been broadly applied in bacteria, options for genome-scale gene overexpression face key limitations. Here, we develop a facile approach for genome-scale overexpression in bacteria we call, "CRISPRtOE" (CRISPR transposition and OverExpression). We first create a platform for comprehensive gene targeting using CRISPR-associated transposons (CAST) and show that transposition occurs at a higher frequency in non-transcribed DNA. We then demonstrate that CRISPRtOE can upregulate gene expression in Proteobacteria with medical and industrial relevance by integrating synthetic promoters of varying strength upstream of target genes. Finally, we employ CRISPRtOE screening at the genome-scale in the model bacterium Escherichia coli and the non-model biofuel producer Zymomonas mobilis, recovering known and novel antibiotic and engineering targets. We envision that CRISPRtOE will be a valuable overexpression tool for antibiotic mode of action, industrial strain optimization, and gene function discovery in bacteria.

Journal Article↗

PubMed2026

Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae.

Synthetic biology and metabolic engineering increasingly demand predictable and interoperable gene expression across phylogenetically distant organisms, as the need for portable genetic systems and transferable metabolic pathways continues to grow. However, fundamental differences in promoter architecture and transcriptional logic across kingdoms remain a key bottleneck in developing universal expression platforms. Here, we designed a set of modular hybrid promoters that enable tunable and quantitatively consistent gene expression in both Escherichia coli and Saccharomyces cerevisiae. These promoters integrate bacterial -10/-35 motifs and Shine-Dalgarno sequences with minimal yeast TATA boxes and Kozak sequences to ensure transcriptional and translational compatibility. The promoter set supported weak, moderate, and strong expression with high relative consistency across species. Applied to the biosynthetic pathway for the valuable pigment prodeoxyviolacein, the hybrid promoters enabled coordinated production in both hosts. This work establishes a broadly compatible promoter architecture and provides a foundational toolkit for cross-kingdom, multi-host synthetic biology.

Promoter Regions, Genetic↗

PubMed2026

A stable and potent buffalo EF1α1 promoter for robust gene expression in mammalian systems.

This study reports the first isolation and characterization of the buffalo EF1α1 promoter, demonstrating its strong gene expression activity both in vitro across diverse cultured cell types and in vivo across multiple mouse organs. Although viral promoters, such as cytomegalovirus (CMV) and simian virus (SV40), are widely used for their strong expression in various cell lines in mammalian expression systems and in animal tissues, they are prone to methylation-induced transcriptional silencing and subsequent loss of exogenous gene expression. The most effective alternative to viral promoters is the synthetic hybrid CAG promoter (cytomegalovirus major immediate-early enhancer combined with the chicken beta-actin promoter) or mammalian cellular promoter such as human elongation factor 1 alpha (hEF1α), which drives strong gene expression but lacks consistency and is limited in their in vivo expression potential due to their vulnerability to epigenetic silencing. To overcome these challenges, the bbEF1α1 promoter was cloned and evaluated both in vitro and in vivo. It consistently drives higher levels of exogenous gene expression than CMV in diverse cell lines. Importantly, transgene expression was achieved in various organs of transgenic mice and in muscle tissue following in vivo electroporation. These findings establish the bbEF1α1 promoter as a powerful ubiquitous driver of gene expression, offering high stability with broad applications in gene therapy, biopharmaceutical production, and functional genomics.

Animals↗

PubMed1979

A synthetic tyrosine suppressor tRNA gene with an altered promoter sequence. Its cloning and relative expression in vivo.

The total synthesis of a tyrosine suppressor tRNA gene with a modified promoter is described. The alteration involves the replacement of the four G:C base pairs immediately preceding the start point of transcription by A:T base pairs. The new sequence contains the recognition sequence for the HindIII restriction endonuclease at the transcriptional start point, thus permitting fusion of the structural gene with promoters containing independent sequence modifications. The construction, cloning, and biological activity of several recombinant DNAs containing the tRNA gene with the modified promoter are described. The expression of this gene in vivo is compared with that of both the unmodified synthetic suppressor gene and a naturally occurring tyr su3+ gene cloned onto a multicopy plasmid.

Base Sequence↗

PubMed1979

Total synthesis of a tyrosine suppressor transfer RNA gene. XVII. Transcription, in vitro, of the synthetic gene and processing of the primary transcript to transfer RNA.

Primer- and promoter-dependent transcription of the synthesis gene had been studied. Primer-dependent transcription gave, as a major product, an end-to-end transcript which was strand-specific. The transcript was characterized rigorously by two-dimensional separation and analysis of the oligonucleotides formed on digestion with T1-RNase and pancreatic RNase and by nearest neighbor analyses of the oligonucleotides obtained when different alpha-32P-labeled ribonucleoside triphosphates were used as substrates. Minor products accompanying the major transcript were characterized similarly. The major transcript, when treated with an Escherichia coli S-100 extract, was processed to the tRNATyr with correct 5'- and 3'-ends. The nucleolytic cleavages occurring at the 3'-end were characterized. In promoter-dependent transcription, transcription of a restriction fragment containing phi80psu+III gene and the synthetic gene with and without the promoter were compared. Transcription of the synthetic gene was promoter-dependent and strand-specific, the initiation of transcription occurring at the same point as previously found in vivo. Although the synthetic gene contains only 16 base pairs corresponding to the natural sequence following the C-C-A end, processing of the transcript at the 3'-end occurred normally, the endonucleolytic cleavage being followed by exonucleolytic cleavages. The products of promoter-dependent transcription were completely characterized. An examination of the base modifications of the primary transcript during treatment of the latter with E. coli S-100 extract showed couplete modification of uridine to pseudouridine and partial methylation of uridine to ribosylthymine in TpsiCG sequence and partial formation of pseudouridine in the anticodon loop. However, hardly any formation of 2'-O-methylguanosine or of 2-methylthio-6-isopentenyl adenosine could be detected.

Base Sequence↗

PubMed2026

Synthetic transcriptional repression systems in plants.

Transcriptional repression is a fundamental regulatory mechanism that enables precise control of gene expression in response to developmental signals and environmental stimuli. Synthetic biology can leverage this process within plants to engineer programmable transgene repression systems. This review examines strategies for harnessing prokaryotic repressors in eukaryotic systems to develop synthetic repression systems in plants. These systems utilize modular promoter and repressor architectures that can be tuned through operator placement and repression-domain fusion, respectively, to adjust transcriptional regulation. Chemically dependent inducibility can also be introduced either through use of native derepression mechanisms of the prokaryotic repressors or the incorporation of ligand-binding domains. Finally, this review explores key challenges in designing synthetic repression systems, including kinetics constraints, balancing ON and OFF states, and differences between transient and transgenic expression contexts. Overall, this review highlights modular design frameworks for tunable transgene expression in plants.

Gene Expression Regulation, Plant↗

PubMed1977

Enhancement of the DNA synthetic response of antigen-primed lymph node cells by splenic promoter cells: characterization of the splenic promoter cells.

Rabbits were immunized in the footpad with diphtheria toxoid in complete Freund's adjuvant. At various times after immunization, cells harvested from the spleen, the draining (immune) and the opposing (control) lymph nodes (LN) were assayed for their proliferative response to incorporate tritiated thymidine upon exposure to the priming antigen. Although the immune LN cells responded by a substantial incorporation of thymidine, cells from the control LN and the spleen either did not respond or responded feebly. An enhancement in the response of the immune LN cells was observed when they were cultured in the presence of nonresponsive spleen cells. Pretreatment of spleen cells with mitomycin C did not abolish the enhancement. This suggests that the target cells which respond to the antigen are derived from the immune LN whereas the promoter cells which enhance the response are present in the spleen. The removal of adhering cells by glass wool columns and of Ig-bearing cells by anti-Ig immunoabsorbent columns from the spleen did not reduce the enhancing capacity of the nonadhering cells. Conversely, the killing of splenic T cells by specific heterologous antiserum directed against rabbit thymus lymphocyte antigen abolished the enhancement. Thus, the promoter cell which facilitates the enhancement has been characterized as a nonadherent, splenic T cell.

Animals↗

PubMed2026

Decoding microbial metabolic complementarity from individual traits to community structuring.

A fundamental challenge in microbiome research lies in elucidating the functional capacity of microbial communities through community membership and genomic data. As community structuring and emergent functional traits are determined by bacterial community metabolic networks, it is important to gain insights into the principles that govern bacteria-bacteria interactions. Here, we applied an integrative framework linking individual strain-level traits to community structuring in a simplified synthetic bacterial community (SSC8) that promotes the growth of ungrafted watermelon. By combining mono- and coculture assays with genome-scale metabolic modeling and metabolomic profiling of spent media, we characterized directional interactions and resource dependencies among community members. Our findings show that positive interactions dominated the community network, accounting for 55% of all pairwise combinations, indicating a high prevalence of growth-promoting effects among strains. Genome-scale metabolic modeling showed that functional divergence among strains enhanced the potential for metabolic complementarity as phylogenetic distance increased. Integrating metabolic modeling with metabolomics further suggested that Pseudomonas azotifigens Q6 not only benefited from all other community members, but also exhibited mutualistic interactions with the other three strains, with metabolite exchange involving compounds such as L-lysine and L-cysteine. Pseudomonas azotifigens Q6 acted as an important driver of community composition by affecting the abundance of several other consortium members in vitro. These findings highlight the role of metabolic complementarity in driving community structuring by promoting selective persistence of specific strains. Our work provides mechanistic insights into microbial interaction networks in vitro and offers a conceptual foundation for the rational design of functionally robust and plant-beneficial microbiomes.

Bacteria↗

PubMed1977

The translocation of Ca2+ across phospholipid bilayers induced by a synthetic neutral Ca2+ -ionophore.

The effect of a neutral synthetic Ca2+ -ligand, which induces selective Ca2+ transport in electrodialysis experiments in bulk membranes, on the Ca2+ permeability of phospholipid bilayers has been investigated. The ligand is able to promote the transport of Ca2+ across synthetic phospholipid bilayers and can therefore be classified as a Ca2+ -ionophore. Its activity is enhanced by the uncoupler carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP). The efficiency of the neutral carrier-mediated Ca2+ transport is rather low as compared with that of the charged Ca2+ -ionophore X537A. The Ca2+ selectivity of the nuetral ionophore is decreased by its incorporation in the low dielectric ambient of the phospholipid bilayer.

Biological Transport, Active↗

PubMed1976

Mechanism of D-amphetamine inhibition of protein synthesis.

At 1 h after intraperitoneal administration of D-amphetamine sulphate (15 mg/kg), rat brain polyribosomes show disaggregation accompanied by reduced capacity for in vitro peptide chain elongation. The direct action of amphetamine on cell-fine protein-synthesizing systems was therefore explored. When brain or liver polyribosomes from untreated rats were incubated with pH 5 enzyme, peptide chain elongation was not inhibited by the addition 4 mM amphetamine to the medium. On the other hand, an initiation-dependent system consisting of rat liver of brain mRNA and wheat germ S-30 fraction showed inhibition of [3H]leucine incorporation by 50% when 4 mM amphetamine were added. The metabolites of amphetamine, p-hydroxyamphetamine and p-hydroxynorephedrine, had no inhibitory action in either system, but the potent neurotoxin p-chloroamphetamine was a more powerful inhibitor of initiation than amphetamine. By using [3H]amphetamine, it was shown that amphetamine binds to the 80-S ribosomes of the wheat germ system. This binding depended on the presence in the system of natural liver or brain mRNA or several synthetic mRNAs, but was not promoted by polyuridylic acid as the messenger. Significantly, polyuridylic acid-dependent polyphenylalanine synthesis by the wheat germ system was not inhibited by amphetamine or p-chloroamphetamine. Therefore, it was concluded that amphetamine inhibits protein synthesis by interfering with initiation through a step related to formation of the mRNA ribosome complex.

Animals↗

PubMed2014

Genome-wide computational analysis reveals cardiomyocyte-specific transcriptional Cis-regulatory motifs that enable efficient cardiac gene therapy.

Gene therapy is a promising emerging therapeutic modality for the treatment of cardiovascular diseases and hereditary diseases that afflict the heart. Hence, there is a need to develop robust cardiac-specific expression modules that allow for stable expression of the gene of interest in cardiomyocytes. We therefore explored a new approach based on a genome-wide bioinformatics strategy that revealed novel cardiac-specific cis-acting regulatory modules (CS-CRMs). These transcriptional modules contained evolutionary-conserved clusters of putative transcription factor binding sites that correspond to a "molecular signature" associated with robust gene expression in the heart. We then validated these CS-CRMs in vivo using an adeno-associated viral vector serotype 9 that drives a reporter gene from a quintessential cardiac-specific α-myosin heavy chain promoter. Most de novo designed CS-CRMs resulted in a >10-fold increase in cardiac gene expression. The most robust CRMs enhanced cardiac-specific transcription 70- to 100-fold. Expression was sustained and restricted to cardiomyocytes. We then combined the most potent CS-CRM4 with a synthetic heart and muscle-specific promoter (SPc5-12) and obtained a significant 20-fold increase in cardiac gene expression compared to the cytomegalovirus promoter. This study underscores the potential of rational vector design to improve the robustness of cardiac gene therapy.

Animals↗

PubMed1979

Semisynthesis of human somatotropin analogs.

Complementation of the natural NH2-terminal 134-amino acid fragment of the reduced, carbamoylmethylated human somatotropin with synthetic analogs of COOH-terminal fragments of 57, 42, or 38 amino acids of reduced, carbamoyl-methylated human somatotropin has been investigated. It was found that synthetic fragments of 57 and 42 amino acids gave recombinants with full growth-promoting activity, whereas attempts to obtain a recombinant with the synthetic 38-amino acid fragment were unsuccessful. The synthesis of two analogs of the COOH-terminal fragment of human somatotropin, human [N]e170, Ala165,182,189] somatotropin-(150-191) and human [Nle170, Ala165,182,189] somatotropin-(154-191), is herein described.

Amino Acid Sequence↗

PubMed1979

Evidence that endotoxin is the cyclic 3':5'-GMP--promoting factor in erythropoietin preparations.

Since Ep preparations are contaminated with endotoxin, the possibility that the latter might be the factor in crude Ep which increases cGMP levels in rat fetal liver cells was examined. Endotoxin produced a striking elevation of cGMP in rat fetal liver cells without affecting cAMP levels or heme synthesis. Absorption with Limulus lysate of more than 99% of the endotoxin in a crude Ep preparation caused a parallel decrease in the cGMP-promoting activity without reduction of heme synthetic potency. It is concluded that endotoxin is the component of crude Ep which increases cGMP levels in rat fetal liver. The precise role of elevated cGMP in the action of endotoxin on cells and the universality of this effect remain to be determined.

Animals↗