Advances In Synthetic Biology Research Articles

Leveraging the Power of Enzymes in Engineered Dead and Living Materials

AbstractSignificant advances are being made in the incorporation of enzymes into functional materials, which leverage their inherent substrate specificity, efficient catalytic activity, and sustainable origin. These engineered “dead” materials, however, lack the incredible systems‐level control of enzyme activity that living organisms have evolved over millennia. This gap is now being bridged by the rapidly emerging field of engineered living materials (ELMs), which couples the tools of advanced synthetic biology with modern materials science. In this review, the impressive array of methodologies used to fabricate the extensive library of functional enzyme‐based dead materials is discussed, and the design strategies that facilitate their creation unpacked. The spectacular suite of natural and synthetic genetic and post‐translational control systems for enzymes in living organisms is then described. Finally, key recent examples of ELMs that utilize enzyme activity are reviewed, highlighting the central role of the living component in providing responsivity and adaptability to this new class of materials.

Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites.

Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.

Closed-loop synthetic gene circuits for cell-based therapies

Recent advances in synthetic biology have paved the way for new cellular therapies, using cells capable of autonomously treating chronic diseases. These cells integrate a set of genes functioning in a closed-loop synthetic circuit, delivering a therapeutic effector in response to a specific pathological signal. While promising in mice, these therapies face clinical challenges related to safety and feasibility of in vivo implementation. The latest generations of synthetic circuits aim to address these issues through advanced bioengineering strategies outlined in this article.

Toward the Exploitation of Sustainable Green Factory: Biotechnology Use of Nannochloropsis spp.

Securing food, energy, and raw materials for a growing population is one of the most significant challenges of our century. Algae play a central role as an alternative to plants. Wastewater and flue gas can secure nutrients and CO2 for carbon fixation. Unfortunately, algae domestication is necessary to enhance biomass production and reduce cultivation costs. Nannochloropsis spp. have increased in popularity among microalgae due to their ability to accumulate high amounts of lipids, including PUFAs. Recently, the interest in the use of Nannochloropsis spp. as a green bio-factory for producing high-value products increased proportionally to the advances of synthetic biology and genetic tools in these species. In this review, we summarized the state of the art of current nuclear genetic manipulation techniques and a few examples of their application. The industrial use of Nannochloropsis spp. has not been feasible yet, but genetic tools can finally lead to exploiting this full-of-potential microalga.

Mpox, smallpox and the increasing threat of orthopoxvirus epidemics

An epidemic of clade I mpox in the Democratic Republic of Congo, low population immunity to orthopoxviruses and advances in synthetic biology should be the triggers to raise our level of preparedness for resurgent orthopoxvirus epidemics.

Advancements in the Application of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs).

Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches.

A Numerical Bio-Geotechnical Model of Pressure-Responsive Microbially Induced Calcium Carbonate Precipitation

The employment of Microbially Induced Calcium Carbonate Precipitation (MICP) is of increasing interest as a technique for environmentally sustainable soil stabilisation. Recent advancements in synthetic biology have allowed for the conception of a pressure-responsive MICP process, wherein bacteria are engineered to sense environmental loads, thereby offering the potential to stabilise specific soil regions selectively. In this study, a 2D smart bio-geotechnical model is proposed based on a pressure-responsive MICP system. Experimentally obtained pressure-responsive genes and hypothetical genes with different pressure responses were applied in the model and two soil profiles were evaluated. The resulting model bridges scales from gene expression within bacteria cells to geotechnical simulations. The results show that both strata and gene expression–pressure relationships have a significant influence on the distribution pattern of calcium carbonate precipitation within the soil matrix. Among the evaluated experimental genes, Gene A demonstrates the best performance in both of the two soil profiles due to the effective stabilisation in the centre area beneath the load, while Genes B and C are more effective in reinforcing peripheral regions. Furthermore, when the hypothetical genes are utilised, there is an increasing stabilisation area with a decreased threshold value. The results show that the technique can be used for soil reinforcement in specific areas.

Siraitia grosvenorii As a Homologue of Food and Medicine: A Review of Biological Activity, Mechanisms of Action, Synthetic Biology, and Applications in Future Food.

Siraitia grosvenorii (SG), also known as Luo Han Guo or Monk fruit, boasts a significant history in food and medicine. This review delves into SG's historical role and varied applications in traditional Chinese culture, examining its phytochemical composition and the health benefits of its bioactive compounds. It further explores SG's biological activities, including antioxidant, anti-inflammatory, and antidiabetic properties and elucidates the mechanisms behind these effects. The review also highlights recent synthetic biology advances in enhancing the production of SG's bioactive compounds, presenting new opportunities for broadening their availability. Ultimately, this review emphasizes SG's value in food and medicine, showcasing its historical and cultural importance, phytochemistry, biological functions, action mechanisms, and the role of synthetic biology in its sustainable use.

Abstract IA005: Regional combating of immunosuppressive forces in the ovarian tumor microenvironment

Abstract IA005: Regional combating of immunosuppressive forces in the ovarian tumor microenvironment

Future advances of artificial biosensor technology in biomedical applications

Recent advancements in synthetic biology have facilitated the concept of a cell-based and cell-free biosensing platform, which enables the identification of molecular signals encompassing metal/chemical to disease biomarkers. The artificial sensing incorporates the concept of both whole-cell and cell-free biosensing strategies, which include highly regulated natural and synthetic components to exhibit genetically encoded molecular sensing properties. These sensors utilize protein expression to release signalling molecules as the result of received input to facilitate the detection of analytes. Intending to use modified living cells or artificial cells in biosensing, the proposed study highlights the importance of cell-based and cell-free sensors in biomedical and diagnostics. The article's first section will explain the biosensing types including cell-free, cell-based, vesicle-based, and paper-based sensing where sensing relies on cell, cellular components, and cell-free systems which mostly involve transcriptional or translational machinery. It highlights the advantages, disadvantages, and challenges of advancing approaches. The second section of the article elaborates on the principle of sensing and the strategies involved. Though very few studies have been reported on this topic, therefore, the current article focuses on the artificial sensors that have been designed for medical and diagnostic purposes. The review also marks the current and future advancements in the field including artificial intelligence, nanotechnology, stem cells, and omics. Sensing recently has a big impact on disease diagnosis as well as drug development and targeted therapies. While newly developed biology-based diagnostics technologies still have high costs, require highly trained personnel, suffer stability issues and reduce sensor performance. Therefore, this review brings readers’ attention to advances and challenges in the following field and promotes the resolution of medical and diagnostics issues in the future.

Preparing for the future of precision medicine: synthetic cell drug regulation.

Synthetic cells are a novel class of cell-like bioreactors, offering the potential for unique advancements in synthetic biology and biomedicine. To realize the potential of those technologies, synthetic cell-based drugs need to go through the drug approval pipeline. Here, we discussed several regulatory challenges, both unique to synthetic cells, as well as challenges typical for any new biomedical technology. Overcoming those difficulties could bring transformative therapies to the market and will create a path to the development and approval of cutting-edge synthetic biology therapies. Graphical Abstract.

Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis.

Advances in synthetic biology have enabled the incorporation of novel biochemical pathways for the production of high-value products into industrially important bacterial hosts. However, attempts to redirect metabolic fluxes towards desired products often lead to the buildup of toxic or undesirable intermediates or, more generally, unwanted metabolic cross-talk. The use of shells derived from self-assembling protein-based prokaryotic organelles, referred to as bacterial microcompartments (BMCs), as a scaffold for metabolic enzymes represents a sophisticated approach that can both insulate and integrate the incorporation of challenging metabolic pathways into industrially important bacterial hosts. Here we took a synthetic biology approach and introduced the model shell system derived from the myxobacterium Haliangium ochraceum (HO shell) into the industrially relevant organism Zymomonas mobilis with the aim of constructing a BMC-based spatial scaffolding platform. SDS-PAGE, transmission electron microscopy, and dynamic light scattering analyses collectively demonstrated the ability to express and purify empty capped and uncapped HO shells from Z. mobilis. As a proof of concept to internally load or externally decorate the shell surface with enzyme cargo, we have successfully targeted fluorophores to the surfaces of the BMC shells. Overall, our results provide the foundation for incorporating enzymes and constructing BMCs with synthetic biochemical pathways for the future production of high-value products in Z. mobilis.

Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities.

The development of microalgal biofuels is of significant importance in advancing the energy transition, alleviating food pressure, preserving the natural environment, and addressing climate change. Numerous countries and regions across the globe have conducted extensive research and strategic planning on microalgal bioenergy, investing significant funds and manpower into this field. However, the microalgae biofuel industry has faced a downturn due to the constraints of high costs. In the past decade, with the development of new strains, technologies, and equipment, the feasibility of large-scale production of microalgae biofuel should be re-evaluated. Here, we have gathered research results from the past decade regarding microalgae biofuel production, providing insights into the opportunities and challenges faced by this industry from the perspectives of microalgae selection, modification, and cultivation. In this review, we suggest that highly adaptable microalgae are the preferred choice for large-scale biofuel production, especially strains that can utilize high concentrations of inorganic carbon sources and possess stress resistance. The use of omics technologies and genetic editing has greatly enhanced lipid accumulation in microalgae. However, the associated risks have constrained the feasibility of large-scale outdoor cultivation. Therefore, the relatively controllable cultivation method of photobioreactors (PBRs) has made it the mainstream approach for microalgae biofuel production. Moreover, adjusting the performance and parameters of PBRs can also enhance lipid accumulation in microalgae. In the future, given the relentless escalation in demand for sustainable energy sources, microalgae biofuels should be deemed a pivotal constituent of national energy planning, particularly in the case of China. The advancement of synthetic biology helps reduce the risks associated with genetically modified (GM) microalgae and enhances the economic viability of their biofuel production.

Cloning and sequencing analysis of whole Spiroplasma genome in yeast.

Cloning and transfer of long-stranded DNA in the size of a bacterial whole genome has become possible by recent advancements in synthetic biology. For the whole genome cloning and whole genome transplantation, bacteria with small genomes have been mainly used, such as mycoplasmas and related species. The key benefits of whole genome cloning include the effective maintenance and preservation of an organism's complete genome within a yeast host, the capability to modify these genome sequences through yeast-based genetic engineering systems, and the subsequent use of these cloned genomes for further experiments. This approach provides a versatile platform for in-depth genomic studies and applications in synthetic biology. Here, we cloned an entire genome of an insect-associated bacterium, Spiroplasma chrysopicola, in yeast. The 1.12 Mbp whole genome was successfully cloned in yeast, and sequences of several clones were confirmed by Illumina sequencing. The cloning efficiency was high, and the clones contained only a few mutations, averaging 1.2 nucleotides per clone with a mutation rate of 4 × 10-6. The cloned genomes could be distributed and used for further research. This study serves as an initial step in the synthetic biology approach to Spiroplasma.

Extending a synthetic Notch morphogen circuit model to construct 2D cell structures

Morphogenesis, the process of cells forming a defined shape, is central during embryonic development. Among other cues it involves diffusible signaling molecules, known as morphogens, and concentration-dependent cellular responses to these molecules. Recent advances in synthetic biology have enabled the isolated design and study of cellular systems that mimic morphogenesis. Here, we build on a system from Toda et al. (2020) that uses a synthetic Notch morphogen circuit to trigger and modulate gene expression. Following our vision of a model-based design of different cellular shapes and patterns, we present extensions of this framework based on the current synthetic Notch signaling capabilities described in the literature. We show first results of implementing morphogen-dependent proliferation as a particular example. The proliferation triggered by the morphogen modulates the steepness of the morphogen gradient, which directly translates to the signal readout. Furthermore, our modeling framework allows us to consider and design patterns in 2D that can be modulated by varying the size and location of the morphogen source and those of the interacting molecules, such as morphogen inhibitors. This bottom-up engineering approach opens up opportunities to better understand the underlying principles of morphogenesis and to design complex tissues with desired functions.

Synthetic Proteins in Dental Applications

Biotechnology and artificial intelligence have sparked a revolution in dentistry, with a focus on restoring natural tissue functions. This transformation has given rise to bioactive materials, inspired by biomimetics, aimed at replicating the processes found in nature. As synthetic biology advances, there is a heightened focus on signaling systems crucial for bio-based diagnostics and therapeutics. Dentistry now harnesses synthetic proteins for tissue regeneration and dental material enhancement. A current research priority is bacterial biofilm inhibition, vital for dental health. Given the role of Streptococcus mutans in dental caries, the development of synthetic antimicrobial peptides targeting this bacterium is underway. The balance of dental enamel between demineralization and remineralization impacts caries formation. Factors such as the presence of hydroxyapatite and salivary peptides influence enamel health. Recent studies have spotlighted salivary protein-inspired peptides for enhanced remineralization. In the realm of bone regeneration, synthetic proteins like bone morphogenetic proteins (BMP) have been spotlighted, earning FDA approval. Research is currently delving into peptides such as cementum protein 1 peptide (CEMP-1-p1) and parathyroid hormone variants like PTH (1-34), underscoring their potential in advancing dental and bone health.

A Genetic Circuit Design for Targeted Viral RNA Degradation.

Advances in synthetic biology have led to the design of biological parts that can be assembled in different ways to perform specific functions. For example, genetic circuits can be designed to execute specific therapeutic functions, including gene therapy or targeted detection and the destruction of invading viruses. Viral infections are difficult to manage through drug treatment. Due to their high mutation rates and their ability to hijack the host's ribosomes to make viral proteins, very few therapeutic options are available. One approach to addressing this problem is to disrupt the process of converting viral RNA into proteins, thereby disrupting the mechanism for assembling new viral particles that could infect other cells. This can be done by ensuring precise control over the abundance of viral RNA (vRNA) inside host cells by designing biological circuits to target vRNA for degradation. RNA-binding proteins (RBPs) have become important biological devices in regulating RNA processing. Incorporating naturally upregulated RBPs into a gene circuit could be advantageous because such a circuit could mimic the natural pathway for RNA degradation. This review highlights the process of viral RNA degradation and different approaches to designing genetic circuits. We also provide a customizable template for designing genetic circuits that utilize RBPs as transcription activators for viral RNA degradation, with the overall goal of taking advantage of the natural functions of RBPs in host cells to activate targeted viral RNA degradation.

Genetic Engineering and Rebooting of Bacteriophages in L-Form Bacteria.

The rapid increase of circulating, antibiotic-resistant pathogens is a major ongoing global health crisis, and arguably, the end of the "golden age of antibiotics" is looming. This has led to a surge in research and development of alternative antimicrobials, including bacteriophages, to treat such infections (phage therapy). Isolating natural phage variants for the treatment of individual patients is an arduous and time-consuming task. Furthermore, the use of natural phages is frequently hampered by natural limitations, such as moderate in vivo activity, the rapid emergence of resistance, insufficient host range, or the presence of undesirable genetic elements within the phage genome. Targeted genetic editing of wild-type phages (phage engineering) has successfully been employed in the past to mitigate some of these pitfalls and to increase the therapeutic efficacy of the underlying phage variants. Clearly, there is a large potential for the development of novel, marker-less genome-editing methodologies to facilitate the engineering of therapeutic phages. Steady advances in synthetic biology have facilitated the in vitro assembly of modified phage genomes, which can be activated ("rebooted") upon transformation of a suitable host cell. However, this can prove challenging, especially in difficult-to-transform Gram-positive bacteria. In this chapter, we detail the production of cell wall-deficient L-form bacteria and their application to activate synthetic genomes of phages infecting Gram-positive host species.

Theoretical perspective on synthetic man‐made life: Learning from the origin of life

AbstractCreating a man‐made life in the laboratory is one of life science’s most intriguing yet challenging problems. Advances in synthetic biology and related theories, particularly those related to the origin of life, have laid the groundwork for further exploration and understanding in this field of artificial life or man‐made life. But there remains a wealth of quantitative mathematical models and tools that have yet to be applied to this area. In this paper, we review the two main approaches often employed in the field of man‐made life: the top‐down approach that reduces the complexity of extant and existing living systems and the bottom‐up approach that integrates well‐defined components, by introducing the theoretical basis, recent advances, and their limitations. We then argue for another possible approach, namely “bottom‐up from the origin of life”: Starting with the establishment of autocatalytic chemical reaction networks that employ physical boundaries as the initial compartments, then designing directed evolutionary systems, with the expectation that independent compartments will eventually emerge so that the system becomes free‐living. This approach is actually analogous to the process of how life originated. With this paper, we aim to stimulate the interest of synthetic biologists and experimentalists to consider a more theoretical perspective, and to promote the communication between the origin of life community and the synthetic man‐made life community.

Biomanufacturing of bioactive compounds: current situation, challenges, and future perspectives

Biomanufacturing uses biological systems, including cells, microorganisms, and enzymes, to produce natural or synthetic molecules with biological activities for use in various industries, such as pharmaceuticals, cosmetics, and agriculture. These bioactive compounds are expected to play important roles in improving the quality of life and prolonging its length. Fortunately, recent advances in synthetic biology and automation technologies have accelerated the development of biomanufacturing, enabling us to create new products and replace conventional methods in a more sustainable manner. As of now, the role of biomanufacturing in the growth and innovation of bioeconomy is steadily increasing, and this techbology becomes a prevalent technology in global markets. To gain a comprehensive understanding of this field, this article presents a retrospective review of Bloomage Biotechnology's Research and Development and briefly reviews the developments of biomanufacturing and offers insights into the futre prospects. In conclusion, biomanufacturing will continue to be an important, environmentally friendly, and sustainable production mode in the ongoing development of bioeconomy.