The function of tcf3 in medaka embryos: efficient knockdown with pePNAs

Introduction of a phenylalanine sink in fast growing cyanobacterium Synechococcus elongatus PCC 11801 leads to improved PSII efficiency, linear electron transport, and carbon fixation

Cyanobacteria are investigated for fundamental photosynthesis research and sustainable production of valuable biochemicals. However, low product titer and biomass productivities are major bottlenecks to the economical scale-up. Recent studies have shown that the introduction of a metabolic sink, such as sucrose, 2,3-butanediol, and 2-phenyl ethanol, in cyanobacteria improves carbon fixation by relieving the "sink" limitation of photosynthesis. However, the impact of light intensity on the behavior of this sink-derived enhancement in carbon fixation is not well understood and is necessary for translation to outdoor cultivation. Here, using random mutagenesis, we engineered Synechococcus elongatus PCC 11801 to overproduce 1.24 g L-1 phenylalanine (Phe) in 3 days, identified L531W in the TolC protein as an important driver of Phe efflux, and investigated the effect of light intensity on total carbon fixation. We found that low light results in competition between biomass and Phe, whereas under excess light, a higher flux of fixed carbon is directed to the Phe sink. The introduction of the Phe sink improves the quantum yields of photosystem I and II with a concomitant increase in the total electron flow leading to nearly 70% increase in carbon fixation at high light in the mutant strain. Additionally, the cyclic electron flow decreased, which has implications for the ATP/NADPH production ratio. Our data highlight how light intensity affects the sink-derived enhancement in carbon fixation, the role of CEF to balance the source-sink demand for ATP and NADPH, and the enhancement of inorganic carbon fixation in cyanobacteria with an engineered sink.

Enhancement effect of urea toward electroporation-mediated plasmid transfection efficiency in the HEK-293 cell line

Background and purpose

Intracellular delivery is crucial in biological and medical studies. Although many molecular tools have been created for cell-based gene therapies, it remains challenging to introduce external molecules into cells. As one of the most popular non-viral transfection methods, electroporation induces transient pores in the cell membrane by applying an external electric field. Unsatisfactory transfection efficiency and low cell viability are the major drawbacks of electroporation. To overcome these issues, the current study investigated the effect of urea on electroporation-mediated transfection efficiency.

Experimental approach

Three voltages of electroporation, including 100, 120, and 140 V, and 3 concentrations of urea buffer, including 0.25%, 0.5%, and 1% W/V, were considered as variables in this study. The HEK-293 cell line was used for transfection, and green fluorescent protein (GFP) expression was evaluated using flow cytometry and fluorescence microscopy.

Findings/Results

The results showed that the combination of electroporation and urea increased electroporation efficacy, but the effect depended on voltage and urea concentration. When different concentrations of urea were added to HEK-293 cells at a voltage of 100 V, the number of cells transfected by pEGFP-N1 increased (from 12.3 ± 0.2% in untreated cells to 17.35 ± 0.55%, 23.3 ± 0.3%, and 14 ± 0.1% at urea concentrations of 0.25%, 0.5%, and 1% W/V, respectively). The electroporation buffer containing 0.5% W/V urea showed the highest EGFP expression (23.3 ± 0.3%) and high cell viability (over 90%).

Conclusion and implications

This research offers a new perspective for improving gene transfection efficiency once electroporation is utilized.

The Potential of Single-Chain Variable Fragment Antibody: Role in Future Therapeutic and Diagnostic Biologics

The advancement of genetic engineering has revolutionized the field of immunology by allowing the utilization of intrinsic antibody structures. One of the biologics that are being produced by recombinant antibody technology is single-chain fragments variable (scFv). Genes of variable regions, the heavy and light chains that are genetically linked into a single transcript by a short flexible linker peptide, are used to generate this fragment from cellular and synthetic libraries. The specificity and affinity of these molecules are comparable to those of parental antibodies. Fusion with marker proteins and other potent molecules improves their stability, circulation half-life, activity, and efficient purification. Besides, this review comprises construction protocols, therapeutics, and diagnostic applications of scFv, as well as related challenges. Nonetheless, there are still issues with efficacy, stability, safety, intracellular administration, and production costs that need to be addressed.

Molecular strategies to enhance the keratinase gene expression and its potential implications in poultry feed industry

The tons of keratin waste are produced by the poultry and meat industry which is an insoluble and protein-rich material found in hair, feathers, wool, and some epidermal wastes. These waste products could be degraded and recycled to recover protein, which can save our environment. One of the potential strategy to achieve this target is use of microbial biotreatment which is more convenient, cost-effective, and environment-friendly by formulating hydrolysate complexes that could be administered as protein supplements, bioactive peptides, or animal feed ingredients. Keratin degradation shows great promise for long-term protein and amino acid recycling. According to the MEROPS database, known keratinolytic enzymes currently belong to at least 14 different protease families, including S1, S8, S9, S10, S16, M3, M4, M14, M16, M28, M32, M36, M38, and M55. In addition to exogenous attack (proteases from families S9, S10, M14, M28, M38, and M55), the various keratinolytic enzymes also function via endo-attack (proteases from families S1, S8, S16, M4, M16, and M36). Biotechnological methods have shown great promise for enhancing keratinase expression in different strains of microbes and different protein engineering techniques in genetically modified microbes such as bacteria and some fungi to enhance keratinase production and activity. Some microbes produce specific keratinolytic enzymes that can effectively degrade keratin substrates. Keratinases have been successfully used in the leather, textile, and pharmaceutical industries. However, the production and efficiency of existing enzymes need to be optimized before they can be used more widely in other processes, such as the cost-effective pretreatment of chicken waste. These can be improved more effectively by using various biotechnological applications which could serve as the best and novel approach for recycling and degrading biomass. This paper provides practical insights about molecular strategies to enhance keratinase expression to effectively utilize various poultry wastes like feathers and feed ingredients like soybean pulp. Furthermore, it describes the future implications of engineered keratinases for environment friendly utilization of wastes and crop byproducts for their better use in the poultry feed industry.

Expanding CAR-T cell immunotherapy horizons through microfluidics

Chimeric antigen receptor (CAR)-T cell therapies have revolutionized cancer treatment, particularly in hematological malignancies. However, their application to solid tumors is limited, and they face challenges in safety, scalability, and cost. To enhance current CAR-T cell therapies, the integration of microfluidic technologies, harnessing their inherent advantages, such as reduced sample consumption, simplicity in operation, cost-effectiveness, automation, and high scalability, has emerged as a powerful solution. This review provides a comprehensive overview of the step-by-step manufacturing process of CAR-T cells, identifies existing difficulties at each production stage, and discusses the successful implementation of microfluidics and related technologies in addressing these challenges. Furthermore, this review investigates the potential of microfluidics-based methodologies in advancing cell-based therapy across various applications, including solid tumors, next-generation CAR constructs, T-cell receptors, and the development of allogeneic "off-the-shelf" CAR products.

Natural and engineered cyclodipeptides: Biosynthesis, chemical diversity, and engineering strategies for diversification and high-yield bioproduction

Cyclodipeptides are diverse chemical scaffolds that show a broad range of bioactivities relevant for medicine, agriculture, chemical catalysis, and material sciences. Cyclodipeptides can be synthesized enzymatically through two unrelated enzyme families, non-ribosomal peptide synthetases (NRPS) and cyclodipeptide synthases (CDPSs). The chemical diversity of cyclodipeptides is derived from the two amino acid side chains and the modification of those side-chains by cyclodipeptide tailoring enzymes. While a large spectrum of chemical diversity is already known today, additional chemical space - and as such potential new bioactivities - could be accessed by exploring yet undiscovered NRPS and CDPS gene clusters as well as via engineering. Further, to exploit cyclodipeptides for applications, the low yield of natural biosynthesis needs to be overcome. In this review we summarize current knowledge on NRPS and CDPS-based cyclodipeptide biosynthesis, engineering approaches to further diversity the natural chemical diversity as well as strategies for high-yield production of cyclodipeptides, including a discussion of how advancements in synthetic biology and metabolic engineering can accelerate the translational potential of cyclodipeptides.

Engineering of global transcription factor FruR to redirect the carbon flow in Escherichia coli for enhancing L-phenylalanine biosynthesis

BACKGROUND

The catabolite repressor/activator protein (FruR) is a global regulatory protein known to control the expression of several genes concerned with carbon utilization and energy metabolism. This study aimed to illustrate effects of the FruR mutant on the _L-phenylalanine (_L-PHE) producing strain PHE01.

RESULTS

Random mutagenesis libraries of fruR generated in vitro were first integrated into the chromosome of PHE01 by CRISPR/Cas9 technique, and then the best mutant PHE07 (FruR^E173K) was obtained. With this mutant, a final _L-PHE concentration of 70.50 ± 1.02 g/L was achieved, which was 23.34% higher than that of PHE01. To better understand the mechanism, both transcriptomes and metabolomes of PHE07 were carried out and compared to that of PHE01. Specifically, the transcript levels of genes involved in gluconeogenesis pathway, pentose phosphate pathway, Krebs cycle, and glyoxylate shunt were up-regulated in the FruR^E173K mutant, whereas genes aceEF, acnB, and icd were down-regulated. From the metabolite level, the FruR^E173K mutation led to an accumulation of pentose phosphate pathway and Krebs cycle products, whereas the products of pyruvate metabolism pathway: acetyl-CoA and cis-aconic acid, were down-regulated. As a result of the altered metabolic flows, the utilization of carbon sources was improved and the supply of precursors (phosphoenolpyruvate and erythrose 4-phosphate) for _L-PHE biosynthesis was increased, which together led to the enhanced production of _L-PHE.

CONCLUSION

A novel strategy for _L-PHE overproduction by modification of the global transcription factor FruR in E. coli was reported. Especially, these findings expand the scope of pathways affected by the fruR regulon and illustrate its importance as a global regulator in _L-PHE production.

CRISPR-Mediated Base Editing: From Precise Point Mutation to Genome-Wide Engineering in Nonmodel Microbes

Nonmodel microbes with unique and diverse metabolisms have become rising stars in synthetic biology; however, the lack of efficient gene engineering techniques still hinders their development. Recently, the use of base editors has emerged as a versatile method for gene engineering in a wide range of organisms including nonmodel microbes. This method is a fusion of impaired CRISPR/Cas9 nuclease and base deaminase, enabling the precise point mutation at the target without inducing homologous recombination. This review updates the latest advancement of base editors in microbes, including the conclusion of all microbes that have been researched by base editors, the introduction of newly developed base editors, and their applications. We provide a list that comprehensively concludes specific applications of BEs in nonmodel microbes, which play important roles in industrial, agricultural, and clinical fields. We also present some microbes in which BEs have not been fully established, in the hope that they are explored further and so that other microbial species can achieve arbitrary base conversions. The current obstacles facing BEs and solutions are put forward. Lastly, the highly efficient BEs and other developed versions for genome-wide reprogramming of cells are discussed, showing great potential for future engineering of nonmodel microbes.

T-Cell Factors as Transcriptional Inhibitors: Activities and Regulations in Vertebrate Head Development

Since its first discovery in the late 90s, Wnt canonical signaling has been demonstrated to affect a large variety of neural developmental processes, including, but not limited to, embryonic axis formation, neural proliferation, fate determination, and maintenance of neural stem cells. For decades, studies have focused on the mechanisms controlling the activity of β-catenin, the sole mediator of Wnt transcriptional response. More recently, the spotlight of research is directed towards the last cascade component, the T-cell factor (TCF)/Lymphoid-Enhancer binding Factor (LEF), and more specifically, the TCF/LEF-mediated switch from transcriptional activation to repression, which in both embryonic blastomeres and mouse embryonic stem cells pushes the balance from pluri/multipotency towards differentiation. It has been long known that Groucho/Transducin-Like Enhancer of split (Gro/TLE) is the main co-repressor partner of TCF/LEF. More recently, other TCF/LEF-interacting partners have been identified, including the pro-neural BarH-Like 2 (BARHL2), which belongs to the evolutionary highly conserved family of homeodomain-containing transcription factors. This review describes the activities and regulatory modes of TCF/LEF as transcriptional repressors, with a specific focus on the functions of Barhl2 in vertebrate brain development. Specific attention is given to the transcriptional events leading to formation of the Organizer, as well as the roles and regulations of Wnt/β-catenin pathway in growth of the caudal forebrain. We present TCF/LEF activities in both embryonic and neural stem cells and discuss how alterations of this pathway could lead to tumors.

Identification of a xylose-inducible promoter and its application for improving vitamin B12 production in Sinorhizobium meliloti

Sinorhizobium meliloti 320 is a vitamin B₁₂ (VB₁₂ ) high-producing strain that has been isolated and identified in our previous study. Because the regulatory toolbox for S. meliloti is limited, we searched for new genetic components and identified the two xylose-inducible promoters P_A and P_B based on a promoter-probe vector with a green fluorescent protein (GFP) as reporter. Compared with the P_araA promoter from S. meliloti, both promoters exhibited higher induced expression and lower basal expression. Subsequently, the influence of glucose or sucrose on the expression of GFP driven by these three promoters was assayed. Glucose repressed all three promoters, and the expression of P_araA was the lowest in the presence of glucose. Although sucrose repressed the expression of P_A by 35% and improved the expression of P_araA by 16%, the expression level of P_A was the highest and was 13% higher than that of P_araA . Lastly, we overexpressed the hemA gene in the C4 pathway using the P_A promoter in S. meliloti 320, and the VB₁₂ production of the engineered strain increased by 11%. The VB₁₂ production was further increased by 11% by adding 0.1% sodium succinate to the culture medium.

A simple and fast Agrobacterium-mediated transformation system for passion fruit KPF4 (Passiflora edulis f. edulis × Passiflora edulis f. flavicarpa)

BACKGROUND

Passion fruit (Passiflora edulis Sims) is an important horticultural crop in the tropics and subtropics, where it has great commercial potential due to high demand for fresh edible fruits and processed juice as well as source of raw materials in cosmetic industries. Genetic engineering shows great potential in passion fruit improvement and can compensate for the limitations of conventional breeding. Despite the success achieved in genetic modification of few passion fruit varieties, transgenic passion fruit production is still difficult for farmer-preferred cultivars. Therefore, it is important to establish a simple and fast Agrobacterium-mediated cell transformation of commercial hybrid passion fruit KPF4 (Passiflora edulis f. edulis × Passiflora edulis f. flavicarpa).

RESULTS

In the present study, we have developed a simple and fast Agrobacterium-mediated transformation system for hybrid passion fruit KPF4 using leaf disc explants. Factors affecting the rate of transient beta (β)-glucuronidase (gusA) expression and consequently transformation efficiency were optimized as follows: Agrobacterium cell density with an OD₆₀₀ of 0.5, 30 min infection time, 3 days of co-cultivation duration and the incorporation of 200 µM acetosyringone into Agrobacterium infection suspension medium. Using the optimized conditions, transgenic plants of KPF4 were produced within 2 months with an average transformation efficiency of 0.67%. The β-glucuronidase (GUS) histochemical staining confirmed the expression and integration of an intron-containing gusA gene into transformed leaf discs and transgenic plant lines of KPF4. The presence of gusA gene in the transgenic plants was confirmed by polymerase chain reaction (PCR). The results confirmed that the gusA gene was efficiently integrated into the passion fruit genome.

CONCLUSIONS

The developed transformation protocol is simple and rapid and could be useful for functional genomic studies and transferring agronomically important traits into passion fruit hybrid KPF4. This study developed a method that can be used to transfer traits such as resistance to viral diseases, low fruit quality and short storage life. To the best of our knowledge, this is the first report on genetic transformation system for commercial passion fruit hybrid KPF4.

A Dominant Negative Antisense Approach Targeting β-Catenin

There have been many attempts to unveil the therapeutic potential of antisense molecules during the last decade. Due to its specific role in canonical Wnt signalling, β-catenin is a potential target for an antisense-based antitumour therapy. In order to establish such a strategy with peptide nucleic acids, we developed a reporter assay for quantification of antisense effects. The luciferase-based assay detects splice blocking with high sensitivity. Using this assay, we show that the splice donor of exon 13 of β-catenin is particularly suitable for an antisense strategy, as it results in a truncated protein which lacks transactivating functions. Since the truncated proteins retain the interactions with Tcf/Lef proteins, they act in a dominant negative fashion competing with wild-type proteins and thus blocking the transcriptional activity of β-catenin. Furthermore, we show that the truncation does not interfere with binding of cadherin and α-catenin, both essential for its function in cell adhesion. Therefore, the antisense strategy blocks Wnt signalling with high efficiency but retains other important functions of β-catenin.