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Science China. Life Sciences Aug 2023Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss... (Review)
Review
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
Topics: Synthetic Biology; Artificial Intelligence; Biotechnology; Gene Editing; Genome
PubMed: 36753021
DOI: 10.1007/s11427-022-2214-2 -
Nature Aug 2023Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life. Here we report on how an... (Comparative Study)
Comparative Study
Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life. Here we report on how an engineered minimal cell contends with the forces of evolution compared with the Mycoplasma mycoides non-minimal cell from which it was synthetically derived. Mutation rates were the highest among all reported bacteria, but were not affected by genome minimization. Genome streamlining was costly, leading to a decrease in fitness of greater than 50%, but this deficit was regained during 2,000 generations of evolution. Despite selection acting on distinct genetic targets, increases in the maximum growth rate of the synthetic cells were comparable. Moreover, when performance was assessed by relative fitness, the minimal cell evolved 39% faster than the non-minimal cell. The only apparent constraint involved the evolution of cell size. The size of the non-minimal cell increased by 80%, whereas the minimal cell remained the same. This pattern reflected epistatic effects of mutations in ftsZ, which encodes a tubulin-homologue protein that regulates cell division and morphology. Our findings demonstrate that natural selection can rapidly increase the fitness of one of the simplest autonomously growing organisms. Understanding how species with small genomes overcome evolutionary challenges provides critical insights into the persistence of host-associated endosymbionts, the stability of streamlined chassis for biotechnology and the targeted refinement of synthetically engineered cells.
Topics: Biotechnology; Cell Division; Evolution, Molecular; Genome, Bacterial; Mutation; Mycoplasma mycoides; Genes, Essential; Synthetic Biology; Cell Size; Epistasis, Genetic; Selection, Genetic; Genetic Fitness; Symbiosis; Tubulin
PubMed: 37407813
DOI: 10.1038/s41586-023-06288-x -
Nature Communications Aug 2023Optical tweezers have profound importance across fields ranging from manufacturing to biotechnology. However, the requirement of refractive index contrast and high laser...
Optical tweezers have profound importance across fields ranging from manufacturing to biotechnology. However, the requirement of refractive index contrast and high laser power results in potential photon and thermal damage to the trapped objects, such as nanoparticles and biological cells. Optothermal tweezers have been developed to trap particles and biological cells via opto-thermophoresis with much lower laser powers. However, the intense laser heating and stringent requirement of the solution environment prevent their use for general biological applications. Here, we propose hypothermal opto-thermophoretic tweezers (HOTTs) to achieve low-power trapping of diverse colloids and biological cells in their native fluids. HOTTs exploit an environmental cooling strategy to simultaneously enhance the thermophoretic trapping force at sub-ambient temperatures and suppress the thermal damage to target objects. We further apply HOTTs to demonstrate the three-dimensional manipulation of functional plasmonic vesicles for controlled cargo delivery. With their noninvasiveness and versatile capabilities, HOTTs present a promising tool for fundamental studies and practical applications in materials science and biotechnology.
Topics: Biotechnology; CD40 Ligand; Cold Temperature; Commerce; Heating
PubMed: 37612299
DOI: 10.1038/s41467-023-40865-y -
Current Opinion in Microbiology Dec 2023Evolutionary observations have often served as an inspiration for biological design. Decoding of the central dogma of life at a molecular level and understanding of the... (Review)
Review
Evolutionary observations have often served as an inspiration for biological design. Decoding of the central dogma of life at a molecular level and understanding of the cellular biochemistry have been elegantly used to engineer various synthetic biology applications, including building genetic circuits in vitro and in cells, building synthetic translational systems, and metabolic engineering in cells to biosynthesize and even bioproduce complex high-value molecules. Here, we review three broad areas of synthetic biology that are inspired by evolutionary observations: (i) combinatorial approaches toward cell-based biomolecular evolution, (ii) engineering interdependencies to establish microbial consortia, and (iii) synthetic immunology. In each of the areas, we will highlight the evolutionary premise that was central toward designing these platforms. These are only a subset of the examples where evolution and natural phenomena directly or indirectly serve as a powerful source of inspiration in shaping synthetic biology and biotechnology.
Topics: Synthetic Biology; Biotechnology; Microbial Consortia; Gene Regulatory Networks; Metabolic Engineering
PubMed: 37801925
DOI: 10.1016/j.mib.2023.102394 -
Science (New York, N.Y.) Jan 2024The power and accuracy of computational protein design have been increasing rapidly with the incorporation of artificial intelligence (AI) approaches. This promises to...
The power and accuracy of computational protein design have been increasing rapidly with the incorporation of artificial intelligence (AI) approaches. This promises to transform biotechnology, enabling advances across sustainability and medicine. DNA synthesis plays a critical role in materializing designed proteins. However, as with all major revolutionary changes, this technology is vulnerable to misuse and the production of dangerous biological agents. To enable the full benefits of this revolution while mitigating risks that may emerge, all synthetic gene sequence and synthesis data should be collected and stored in repositories that are only queried in emergencies to ensure that protein design proceeds in a safe, secure, and trustworthy manner.
Topics: Artificial Intelligence; Biosecurity; Biotechnology; Medicine; Protein Engineering; Genes, Synthetic
PubMed: 38271530
DOI: 10.1126/science.ado1671 -
The New Phytologist Jan 2024
Topics: Biotechnology; Microalgae; Biofuels
PubMed: 37855124
DOI: 10.1111/nph.19317 -
Nature Nov 2023Many bacteria use CRISPR-Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids. In turn, these invasive elements have evolved anti-CRISPR...
Many bacteria use CRISPR-Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids. In turn, these invasive elements have evolved anti-CRISPR proteins to block host immunity. Here we unveil a distinct type of CRISPR-Cas Inhibition strategy that is based on small non-coding RNA anti-CRISPRs (Racrs). Racrs mimic the repeats found in CRISPR arrays and are encoded in viral genomes as solitary repeat units. We show that a prophage-encoded Racr strongly inhibits the type I-F CRISPR-Cas system by interacting specifically with Cas6f and Cas7f, resulting in the formation of an aberrant Cas subcomplex. We identified Racr candidates for almost all CRISPR-Cas types encoded by a diverse range of viruses and plasmids, often in the genetic context of other anti-CRISPR genes. Functional testing of nine candidates spanning the two CRISPR-Cas classes confirmed their strong immune inhibitory function. Our results demonstrate that molecular mimicry of CRISPR repeats is a widespread anti-CRISPR strategy, which opens the door to potential biotechnological applications.
Topics: Bacteria; Bacteriophages; Biotechnology; CRISPR-Associated Proteins; CRISPR-Cas Systems; Molecular Mimicry; Plasmids; Prophages; RNA, Viral
PubMed: 37853129
DOI: 10.1038/s41586-023-06612-5 -
International Journal of Molecular... Aug 2023Stabilization and reusability of enzyme transglutaminase (TGM) are important goals for the enzymatic process since immobilizing TGM plays an important role in different... (Review)
Review
Stabilization and reusability of enzyme transglutaminase (TGM) are important goals for the enzymatic process since immobilizing TGM plays an important role in different technologies and industries. TGM can be used in many applications. In the food industry, it plays a role as a protein-modifying enzyme, while, in biotechnology and pharmaceutical applications, it is used in mediated bioconjugation due to its extraordinary crosslinking ability. TGMs (EC 2.3.2.13) are enzymes that catalyze the formation of a covalent bond between a free amino group of protein-bound or peptide-bound lysine, which acts as an acyl acceptor, and the γ-carboxamide group of protein-bound or peptide-bound glutamine, which acts as an acyl donor. This results in the modification of proteins through either intramolecular or intermolecular crosslinking, which improves the use of the respective proteins significantly.
Topics: Transglutaminases; Proteins; Biotechnology; Peptides; Glutamine
PubMed: 37569776
DOI: 10.3390/ijms241512402 -
Trends in Biotechnology Sep 2023Hydrovoltaic electricity generation (HEG) utilizes the latent environmental heat stored in water, and subsequently harvests the electrical energy. However, sustainable... (Review)
Review
Hydrovoltaic electricity generation (HEG) utilizes the latent environmental heat stored in water, and subsequently harvests the electrical energy. However, sustainable HEG has remained extremely challenging due either to complex fabrication and high cost, or to restricted environmental compatibility and renewability. Electroactive microorganisms are environmentally abundant and viable in performing directional electron transport to produce currents. These distinctive features have inspired microbial HEG systems that can convert environmental energy into hygroelectricity upon water circulation from raindrops, waves, and water moisture, and has recently succeeded as proof of concept for becoming a cutting-edge biotechnology. In this review, recent advances in microbial biofilm-based hydrovoltaic technology are highlighted to better understand a promising method of electricity generation from environmental energy with the aim of practical applications.
Topics: Bioelectric Energy Sources; Electricity; Biotechnology; Biofilms; Electrons; Electrodes
PubMed: 37085401
DOI: 10.1016/j.tibtech.2023.03.012 -
Nature Biotechnology Feb 2024Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New... (Review)
Review
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelerating the generation of proteins for applications in biotechnology and medicine. To make sense of the exploding diversity of machine learning approaches, we introduce a unifying framework that classifies models on the basis of their use of three core data modalities: sequences, structures and functional labels. We discuss the new capabilities and outstanding challenges for the practical design of enzymes, antibodies, vaccines, nanomachines and more. We then highlight trends shaping the future of this field, from large-scale assays to more robust benchmarks, multimodal foundation models, enhanced sampling strategies and laboratory automation.
Topics: Proteins; Machine Learning; Biotechnology; Amino Acid Sequence; Antibodies
PubMed: 38361074
DOI: 10.1038/s41587-024-02127-0