Nature Protocols, Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 15, 2024
Language: Английский
Metabolic Engineering, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 1, 2025
Advanced genome engineering enables precise and customizable modifications of bacterial species, toolsets that exhibit broad-host compatibility are particularly valued owing to their portability. Tn5 transposon vectors have been widely used establish random integrations desired DNA sequences into genomes. However, the iteration procedure remains challenging because limited availability reusability selection markers. We addressed this challenge with CIFR, a mini-Tn5 integration system tailored for iterative engineering. The pCIFR incorporate attP attB sites flanking an antibiotic resistance marker select insertion. Subsequent removal determinants is facilitated by Bxb1 integrase paired user-friendly counter-selection marker, both encoded in auxiliary plasmids. CIFR delivers engineered strains harboring stable insertions free any cassette, allowing tool. was validated Pseudomonas putida, Escherichia coli, Cupriavidus necator, underscoring its portability across diverse industrially relevant hosts. toolbox calibrated through combinatorial chromoprotein genes P. generating displaying color palette. also introduced carotenoid biosynthesis pathway putida two-step process, showcasing potential tool balancing. broad utility expands toolkit metabolic engineering, construction complex phenotypes while opening new possibilities genetic manipulations.
Language: Английский
Citations
3
Microorganisms, Journal Year: 2025, Volume and Issue: 13(3), P. 599 - 599
Published: March 5, 2025
Microbial engineering has made a significant breakthrough in pharmaceutical biotechnology, greatly expanding the production of biologically active compounds, therapeutic proteins, and novel drug candidates. Recent advancements genetic engineering, synthetic biology, adaptive evolution have contributed to optimization microbial strains for applications, playing crucial role enhancing their productivity stability. The CRISPR-Cas system is widely utilized as precise genome modification tool, enabling enhancement metabolite biosynthesis activation biological pathways. Additionally, biology approaches allow targeted design microorganisms with improved metabolic efficiency potential, thereby accelerating development new products. integration artificial intelligence (AI) machine learning (ML) plays vital further advancing by predicting network interactions, optimizing bioprocesses, discovery process. However, challenges such efficient pathways, ensuring sustainable industrial-scale production, meeting international regulatory requirements remain critical barriers field. Furthermore, mitigate potential risks, it essential develop stringent biocontainment strategies implement appropriate oversight. This review comprehensively examines recent innovations analyzing key technological advancements, challenges, future perspectives.
Language: Английский
Citations
1
Tropical Medicine and Health, Journal Year: 2025, Volume and Issue: 53(1)
Published: April 2, 2025
Abstract Background Antimicrobial resistance (AMR) poses a global health threat, particularly in low- and middle-income countries (LMICs). Clustered regularly interspaced short palindromic repeats (CRISPR)–Cas system technology offers promising tool to combat AMR by targeting disabling genes WHO bacterial priority pathogens. Thus, we systematically reviewed the potential of CRISPR–Cas address AMR. Methods This systematic review adhered Preferred Reporting Items for Systematic Reviews Meta-Analyses (PRISMA) guidelines. A comprehensive literature search was conducted using Scopus PubMed databases, focusing on publications from 2014 June 2024. Keywords included “CRISPR/Cas,” “antimicrobial resistance,” “pathogen.” The eligibility criteria required original studies involving CRISPR/Cas systems that targeted Data were extracted eligible studies, qualitatively synthesized, assessed bias Joanna Briggs Institute (JBI)-standardized tool. Results 48 revealed diverse systems, including CRISPR–Cas9, CRISPR–Cas12a, CRISPR–Cas3, various genes, such as blaOXA-232, blaNDM, blaCTX-M, ermB, vanA, mecA , fosA3 blaKPC mcr-1, which are responsible carbapenem, cephalosporin, methicillin, macrolide, vancomycin, colistin, fosfomycin resistance. Some have explored role CRISPR virulence gene suppression, enterotoxin tsst1 iutA Staphylococcus aureus Klebsiella pneumoniae . Delivery mechanisms include bacteriophages, nanoparticles, electro-transformation, conjugative plasmids, demonstrate high efficiency vitro vivo. CRISPR-based diagnostic applications demonstrated sensitivity specificity, with detection limits low 2.7 × 10 2 CFU/mL, significantly outperforming conventional methods. Experimental reported significant reductions resistant populations complete suppression strains. Engineered phagemid particles plasmid-curing been shown eliminate IncF cured plasmids carrying vanA mcr-1 blaNDM 94% efficiency, restore antibiotic susceptibility. Gene re-sensitization strategies used susceptibility E. coli blaKPC-2-mediated carbapenem MDR bacteria. Whole-genome sequencing bioinformatics tools provided deeper insights into CRISPR-mediated defense mechanisms. Optimization enhanced gene-editing efficiencies, offering approach tackling high-priority Conclusions has across While promising, challenges optimizing vivo delivery, mitigating resistance, navigating ethical-regulatory barriers must be addressed facilitate clinical translation.
Language: Английский
Citations
1
Nature Reviews Bioengineering, Journal Year: 2024, Volume and Issue: 2(12), P. 1039 - 1055
Published: Aug. 22, 2024
Language: Английский
Citations
4
ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(9), P. 2693 - 2701
Published: Aug. 27, 2024
Deaminase-T7 RNA polymerase fusion (MutaT7) proteins are a growing class of synthetic biology tools used to diversify target genes during
Language: Английский
Citations
4
Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(5)
Published: Feb. 27, 2025
Abstract CRISPR-associated transposon (CAST) systems employ CRISPR–Cas as RNA-directed targeting modules for site-specific DNA insertion. Among them, type I CASTs rely on the coordinated action of guide RNA-bound Cascade complex and proteins TniQ, TnsC, TnsAB. The interaction between transposase TnsAB ATPase TnsC is crucial transposition activity, yet underlying molecular details have remained elusive. Here, we investigate I-B CAST system from Peltigera membranacea cyanobiont. Cryo-electron microscopic structures its with C-terminal region reveal that forms a heptameric ring recruits by interacting tail. In vitro binding assays indicate exclusively interacts heptamer without inducing disassembly, in contrast to V-K systems. Mutational analysis key structural features corroborates significance multimerization TnsB activity vivo. Altogether, these findings offer detailed functional insights into mechanism CAST, aim facilitating their development genome engineering tools.
Language: Английский
Citations
0
Oncology Reviews, Journal Year: 2025, Volume and Issue: 19
Published: April 14, 2025
The high incidence and mortality rates associated with gastrointestinal cancers represent a significant global health challenge. In recent years, CAR T cell therapy has emerged as promising immunotherapeutic approach, demonstrating favorable clinical outcomes. However, the application of traditional in faces numerous challenges, including suppressive tumor microenvironment limitations anti-tumor efficacy. engineered bacteria offers novel strategy to enhance by modulating boosting immune responses, potentially leading improved therapeutic This review synthesizes current research advancements related bacteria-assisted cancers, exploring its underlying mechanisms, applications, future developmental directions.
Language: Английский
Citations
0
Microorganisms, Journal Year: 2025, Volume and Issue: 13(5), P. 1062 - 1062
Published: May 2, 2025
Traditional food technologies, while essential, often face limitations in sensitivity, real-time detection, and adaptability to complex biological systems such as microbial biofilms. These constraints have created a growing demand for more advanced, precise, non-invasive tools ensure safety quality. In response these challenges, cross-disciplinary technological integration has opened new opportunities the industry public health, leveraging methods originally developed other scientific fields. Although their industrial-scale implementation is still evolving, application research pilot settings already significantly improved our ability detect control biofilms, thereby strengthening protocols. Advanced analytical techniques, identification of pathogenic species virulence markers, screening “natural” antimicrobial compounds can now be conceptualized interconnected elements within virtual framework centered on “food” “biofilm”. this short review, starting from basic concepts biofilm associated microorganisms, we highlight selection emerging approaches—from optical methods, microfluidics, Atomic Force Microscopy (AFM), biospeckle techniques molecular strategies like CRISPR, qPCR, NGS, use organoids. Initially conceived biomedical biotechnological applications, recently demonstrated value science by enhancing understanding behavior supporting discovery novel anti-biofilm strategies.
Language: Английский
Citations
0
Nature Reviews Bioengineering, Journal Year: 2025, Volume and Issue: unknown
Published: May 13, 2025
Language: Английский
Citations
0
Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown
Published: May 1, 2025
Language: Английский
Citations
0