Synthetic auxotrophy remains stable after continuous evolution and in coculture with mammalian cells

Advanced microbiome therapeutics for oral delivery of peptides and proteins: Advances, challenges, and opportunities

Peptide and protein medicines have changed the therapeutic landscape for many diseases, yet oral delivery remains a significant challenge due to enzymatic degradation, instability, and poor permeability in the gastrointestinal tract. Advanced Microbiome Therapeutics (AMTs) could overcome some of these barriers by producing and releasing therapeutic peptides directly in the gastrointestinal tract. AMTs can localize peptide production at the site of absorption, providing either sustained or controlled release while potentially reducing side effects associated with systemic administration. Here, this review assesses the status of AMTs for oral peptide delivery and discusses the potential integration of permeation enhancers, mucoadhesive systems, and receptor-mediated transport strategies to improve oral bioavailability further. Combining these approaches could pave the way for more widespread oral delivery strategies for peptide and protein medicines.

Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid

Microorganisms can be genetically engineered for intrinsic biological containment based on synthetic chemical provision. However, reliance on an exogenous chemical limits the contexts where a contained microorganism could survive. Here we design an orthogonal obligate commensalism in Escherichia coli that autonomously creates environments permissive for survival of a partner microbe. We engineer one E. coli strain (the producer) to biosynthesize a non-standard amino acid (nsAA) from simple carbon sources through heterologous expression. We engineer a second E. coli strain (the utilizer) to rely on the same nsAA for growth as a synthetic auxotroph, with a 14-day escape rate of 2.8 × 10-9 escapees per colony-forming unit. Co-culture experiments show utilizer dependence on the producer, with no escape detected during co-inoculation of ~107 colony-forming units of utilizer and a non-producer E. coli strain. Dependence is maintained within a simplified synthetic maize root-associated community. This work provides ecological insights and presents a potential biocontainment strategy independent of an exogenous chemical.

Genetic Code Expansion: Recent Developments and Emerging Applications

The concept of genetic code expansion (GCE) has revolutionized the field of chemical and synthetic biology, enabling the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins, thus opening new avenues in research and applications across biology and medicine. In this review, we cover the principles of GCE, including the optimization of the aminoacyl-tRNA synthetase (aaRS)/tRNA system and the advancements in translation system engineering. Notable developments include the refinement of aaRS/tRNA pairs, enhancements in screening methods, and the biosynthesis of noncanonical amino acids. The applications of GCE technology span from synthetic biology, where it facilitates gene expression regulation and protein engineering, to medicine, with promising approaches in drug development, vaccine production, and gene editing. The review concludes with a perspective on the future of GCE, underscoring its potential to further expand the toolkit of biology and medicine. Through this comprehensive review, we aim to provide a detailed overview of the current state of GCE technology, its challenges, opportunities, and the frontier it represents in the expansion of the genetic code for novel biological research and therapeutic applications.

A One-Pot Biocatalytic Cascade to Access Diverse L-Phenylalanine Derivatives from Aldehydes or Carboxylic Acids

Non-standard amino acids (nsAAs) that are L-phenylalanine derivatives with aryl ring functionalization have long been harnessed in natural product synthesis, therapeutic peptide synthesis, and diverse applications of genetic code expansion. Yet, to date these chiral molecules have often been the products of poorly enantioselective and environmentally harsh organic synthesis routes. Here, we reveal the broad specificity of multiple natural pyridoxal 5'-phosphate (PLP)-dependent enzymes, specifically an L-threonine transaldolase, a phenylserine dehydratase, and an aminotransferase, towards substrates that contain aryl side chains with diverse substitutions. We exploit this tolerance to construct a one-pot biocatalytic cascade that achieves high-yield synthesis of 18 diverse L-phenylalanine derivatives from aldehydes under mild aqueous reaction conditions. We demonstrate addition of a carboxylic acid reductase module to this cascade to enable the biosynthesis of L-phenylalanine derivatives from carboxylic acids that may be less expensive or less reactive than the corresponding aldehydes. Finally, we investigate the scalability of the cascade by developing a lysate-based route for preparative-scale synthesis of 4-formyl-L-phenylalanine, a nsAA with a bio-orthogonal handle that is not readily market-accessible. Overall, this work offers an efficient, versatile, and scalable route with the potential to lower manufacturing cost and democratize synthesis for many valuable nsAAs.

Towards the first synthetic eukaryotic cell

With the rapid advance in synthetic biology and the expanding field of synthetic genomics, the realization of a redesigned yeast genome has become an achievable milestone. Multiple eukaryotic chromosomes, meticulously designed and synthesized, are now being systematically integrated to create an entirely synthetic eukaryotic cell. This comprehensive review examines the fundamental design principles and construction strategies, highlighting critical technological breakthroughs in pursuing the first synthetic eukaryotic cell. Additionally, it underscores the critical contributions of the Sc2.0 project, which has provided essential tools and engineered cellular platforms that have significantly accelerated research and industrial progress. The ethical and legal implications arising from synthetic eukaryotic life are also explored, offering insights into future research directions for synthetic eukaryotic genomes. The remarkable advances in deoxyribonucleic acid synthesis hold immense potential, promising to unlock new opportunities across medicine, industry, agriculture, and research.

The biochemical mechanisms of plastic biodegradation

Since the invention of the first synthetic plastic, an estimated 12 billion metric tons of plastics have been manufactured, 70% of which was produced in the last 20 years. Plastic waste is placing new selective pressures on humans and the organisms we depend on, yet it also places new pressures on microorganisms as they compete to exploit this new and growing source of carbon. The limited efficacy of traditional recycling methods on plastic waste, which can leach into the environment at low purity and concentration, indicates the utility of this evolving metabolic activity. This review will categorize and discuss the probable metabolic routes for each industrially relevant plastic, rank the most effective biodegraders for each plastic by harmonizing and reinterpreting prior literature, and explain the experimental techniques most often used in plastic biodegradation research, thus providing a comprehensive resource for researchers investigating and engineering plastic biodegradation.

Advanced and Safe Synthetic Microbial Chassis with Orthogonal Translation System Integration

Through the use of CRISPR-assisted transposition, we have engineered a safe Escherichia coli chassis that integrates an orthogonal translation system (OTS) directly into the chromosome. This approach circumvents the limitations and genetic instability associated with conventional plasmid vectors. Precision in genome modification is crucial for the top-down creation of synthetic cells, especially in the orthogonalization of vital cellular processes, such as metabolism and protein translation. Here, we targeted multiple loci in the E. coli chromosome to integrate the OTS simultaneously, creating a synthetic auxotrophic chassis with an altered genetic code to establish a reliable, robust, and safe synthetic protein producer. Our OTS-integrated chassis enabled the site-specific incorporation of m-oNB-Dopa through in-frame amber stop codon readthrough. This allowed for the expression of advanced underwater bioglues containing Dopa-Lysine motifs, which are crucial for wound healing and tissue regeneration. Additionally, we have enhanced the expression process by incorporating scaffold-stabilizing fluoroprolines into bioglues, utilizing our chassis, which has been modified through metabolic engineering (i.e., by introducing proline auxotrophy). We also engineered a synthetic auxotroph reliant on caged Dopa, creating a genetic barrier (genetic firewall) between the synthetic cells and their surroundings, thereby boosting their stability and safety.

Engineering bacterial theranostics: from logic gates to in vivo applications

Over the past 2 decades, rapid advances in synthetic biology have enabled the design of increasingly intricate and biologically relevant systems with broad applications in healthcare. A growing area of interest is in designing bacteria that sense and respond to endogenous disease-associated signals, creating engineered theranostics that function as disease surveyors for human health. In particular, engineered cells hold potential in facilitating greatly enhanced temporal and spatial control over the release of a range of therapeutics. Such systems are particularly useful for targeting challenging, under-drugged disease targets in a more nuanced manner than is currently possible. This review provides an overview of the recent advances in the design, delivery, and dynamics of bacterial theranostics to enable safe, robust, and genetically tractable therapies to treat disease. It outlines the primary challenges in theranostic clinical translation, proposes strategies to overcome these issues, and explores promising future avenues for the field.

Roots of synthetic ecology: microbes that foster plant resilience in the changing climate

Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.

Phage lysins for intestinal microbiome modulation: current challenges and enabling techniques

The importance of the microbiota in the intestinal tract for human health has been increasingly recognized. In this perspective, microbiome modulation, a targeted alteration of the microbial composition, has gained interest. Phage lysins, peptidoglycan-degrading enzymes encoded by bacteriophages, are a promising new class of antibiotics currently under clinical development for treating bacterial infections. Due to their high specificity, lysins are considered microbiome-friendly. This review explores the opportunities and challenges of using lysins as microbiome modulators. First, the high specificity of endolysins, which can be further modulated using protein engineering or targeted delivery methods, is discussed. Next, obstacles and possible solutions to assess the microbiome-friendliness of lysins are considered. Finally, lysin delivery to the intestinal tract is discussed, including possible delivery methods such as particle-based and probiotic vehicles. Mapping the hurdles to developing lysins as microbiome modulators and identifying possible ways to overcome these hurdles can help in their development. In this way, the application of these innovative antimicrobial agents can be expanded, thereby taking full advantage of their characteristics.

A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid

Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid (unAA) provides a powerful strategy to restrict unwanted propagation of genetically modified organisms (GMOs) in open environments and potentially prevent industrial espionage. Here, we describe a generic approach for robust biocontainment of budding yeast dependent on unAA. By understanding escape mechanisms, we specifically optimize our strategies by introducing designed "immunity" to the generation of amber-suppressor tRNAs and developing the transcriptional- and translational-based biocontainment switch. We further develop a fitness-oriented screening method to easily obtain multiplex safeguard strains that exhibit robust growth and undetectable escape frequency (<~10-9) on solid media for 14 days. Finally, we show that employing our multiplex safeguard system could restrict the proliferation of strains of interest in a real fermentation scenario, highlighting the great potential of our yeast biocontainment strategy to protect the industrial proprietary strains.

Coordinated microbial lysis bursts into the drug delivery scene

To address limitations in dosing and releasing cargo from engineered microbes, Din et al. harnessed a previously designed oscillatory genetic circuit to achieve the synchronized release of cancer-killing protein payloads. Here, we briefly recap this study published in 2016 and its transformative impact on the field.

A swapped genetic code prevents viral infections and gene transfer

Engineering the genetic code of an organism has been proposed to provide a firewall from natural ecosystems by preventing viral infections and gene transfer1-6. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus7-9, potentially rendering a genetic-code-based firewall ineffective. Here we show that such mobile transfer RNAs (tRNAs) enable gene transfer and allow viral replication in Escherichia coli despite the genome-wide removal of 3 of the 64 codons and the previously essential cognate tRNA and release factor genes. We then establish a genetic firewall by discovering viral tRNAs that provide exceptionally efficient codon reassignment allowing us to develop cells bearing an amino acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino acid-swapped genetic code renders cells resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to biocontain this virus-resistant host through dependence on an amino acid not found in nature10. Our results may provide the basis for a general strategy to make any organism safely resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.

Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment

Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.

Genetically stable CRISPR-based kill switches for engineered microbes

Microbial biocontainment is an essential goal for engineering safe, next-generation living therapeutics. However, the genetic stability of biocontainment circuits, including kill switches, is a challenge that must be addressed. Kill switches are among the most difficult circuits to maintain due to the strong selection pressure they impart, leading to high potential for evolution of escape mutant populations. Here we engineer two CRISPR-based kill switches in the probiotic Escherichia coli Nissle 1917, a single-input chemical-responsive switch and a 2-input chemical- and temperature-responsive switch. We employ parallel strategies to address kill switch stability, including functional redundancy within the circuit, modulation of the SOS response, antibiotic-independent plasmid maintenance, and provision of intra-niche competition by a closely related strain. We demonstrate that strains harboring either kill switch can be selectively and efficiently killed inside the murine gut, while strains harboring the 2-input switch are additionally killed upon excretion. Leveraging redundant strategies, we demonstrate robust biocontainment of our kill switch strains and provide a template for future kill switch development.

In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology

Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.

Advances in engineering microbial biosynthesis of aromatic compounds and related compounds

Aromatic compounds have broad applications and have been the target of biosynthetic processes for several decades. New biomolecular engineering strategies have been applied to improve production of aromatic compounds in recent years, some of which are expected to set the stage for the next wave of innovations. Here, we will briefly complement existing reviews on microbial production of aromatic compounds by focusing on a few recent trends where considerable work has been performed in the last 5 years. The trends we highlight are pathway modularization and compartmentalization, microbial co-culturing, non-traditional host engineering, aromatic polymer feedstock utilization, engineered ring cleavage, aldehyde stabilization, and biosynthesis of non-standard amino acids. Throughout this review article, we will also touch on unmet opportunities that future research could address.