Genetic Incorporation of Noncanonical Amino Acids Using Two Mutually Orthogonal Quadruplet Codons

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.

Quadruplet codon decoding-based versatile genetic biocontainment system

Biological resources, such as sequence information, genetic traits, materials and strains, pose risks when inadvertently released or deliberately misused. To address these concerns, we developed Quadruplet COdon DEcoding (QCODE), a versatile genetic biocontainment strategy that introduces a quadruplet codon (Q-codon) causing frameshifts, hindering proper gene expression. Strategically incorporating Q-codons in multiple genes prevents genetic trait escape, unallowed proliferation of microbial strains and unauthorized leakages of genetic materials. This multifaceted strategy, integrating Q-codons for genetic traits, materials and strains, ensures robust biocontainment across various levels. Notably, our system maintains sequence protection, safeguarding genetic sequence information against unauthorized access. The QCODE approach offers a versatile, efficient and compact solution to enhance biosecurity in diverse biological research settings.

Recent advances in the expanding genetic code

For over a billion years, the central dogma of biology has been limited largely to 20 canonical amino acids with relatively simple functionalities. The ability to rationally add new building blocks to the genetic code has enabled the site-specific incorporation of hundreds of noncanonical amino acids (ncAAs) with novel properties into proteins in living organisms. Recent technological advances have enabled high level mammalian expression of proteins containing ncAAs, the use of unique codons to direct ncAA incorporation, extension of this methodology to a range of eukaryotic organisms, and the ability to encode building blocks beyond α-amino acids. These ncAAs have been used to study and control proteins in their native cellular context and to engineer enzymes and biotherapeutics with improved or novel properties. Herein we discuss recent developments in the field and potential future research directions.

Reaching New Heights in Genetic Code Manipulation with High Throughput Screening

The chemical and physical properties of proteins are limited by the 20 canonical amino acids. Genetic code manipulation allows for the incorporation of noncanonical amino acids (ncAAs) that enhance or alter protein functionality. This review explores advances in the three main strategies for introducing ncAAs into biosynthesized proteins, focusing on the role of high throughput screening in these advancements. The first section discusses engineering aminoacyl-tRNA synthetases (aaRSs) and tRNAs, emphasizing how novel selection methods improve characteristics including ncAA incorporation efficiency and selectivity. The second section examines high-throughput techniques for improving protein translation machinery, enabling accommodation of alternative genetic codes. This includes opportunities to enhance ncAA incorporation through engineering cellular components unrelated to translation. The final section highlights various discovery platforms for high-throughput screening of ncAA-containing proteins, showcasing innovative binding ligands and enzymes that are challenging to create with only canonical amino acids. These advances have led to promising drug leads and biocatalysts. Overall, the ability to discover unexpected functionalities through high-throughput methods significantly influences ncAA incorporation and its applications. Future innovations in experimental techniques, along with advancements in computational protein design and machine learning, are poised to further elevate this field.

Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology

Over the past two decades, genetic code expansion (GCE)-enabled methods for incorporating noncanonical amino acids (ncAAs) into proteins have significantly advanced the field of synthetic biology while also reaping substantial benefits from it. On one hand, they provide synthetic biologists with a powerful toolkit to enhance and diversify biological designs beyond natural constraints. Conversely, synthetic biology has not only propelled the development of ncAA incorporation through sophisticated tools and innovative strategies but also broadened its potential applications across various fields. This Review delves into the methodological advancements and primary applications of site-specific cellular incorporation of ncAAs in synthetic biology. The topics encompass expanding the genetic code through noncanonical codon addition, creating semiautonomous and autonomous organisms, designing regulatory elements, and manipulating and extending peptide natural product biosynthetic pathways. The Review concludes by examining the ongoing challenges and future prospects of GCE-enabled ncAA incorporation in synthetic biology and highlighting opportunities for further advancements in this rapidly evolving field.

Tuning tRNAs for improved translation

Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.

Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers

Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.

Applications of genetic code expansion technology in eukaryotes

Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.

Development of Multivalent Conjugates with a Single Non-Canonical Amino Acid

Proteins represent powerful biomacromolecules due to their unique functionality and broad utility both in the cell and in non-biological applications. The genetic encoding of non-canonical amino acids (ncAAs) facilitates functional diversification of these already powerful proteins. Specifically, ncAAs have been demonstrated to provide unique functional handles to bioorthogonally introduce novel functionality via conjugation reactions. Herein we examine the ability of a single ncAA to serve as a handle to generate multivalent bioconjugates to introduce two or more additional components to a protein, yielding a multivalent conjugate. To accomplish this aim, p-bromopropargyloxyphenyalanine (pBrPrF) was genetically encoded into both superfolder green fluorescent protein (sfGFP) and ubiquitin model proteins to serve as a conjugation handle. A sequential bioconjugation sequence involving a copper-assisted cycloaddition reaction coupled with a subsequent Sonogashira cross-coupling was then optimized. The linkage of two additional molecules to the model protein via these reactions yielded the desired multivalent bioconjugate. This domino approach using a single ncAA has a plethora of applications in both therapeutics and diagnostics as multiple unique moieties can be introduced into proteins in a highly controlled fashion.

Machine Learning-Guided Protein Engineering

Recent progress in engineering highly promising biocatalysts has increasingly involved machine learning methods. These methods leverage existing experimental and simulation data to aid in the discovery and annotation of promising enzymes, as well as in suggesting beneficial mutations for improving known targets. The field of machine learning for protein engineering is gathering steam, driven by recent success stories and notable progress in other areas. It already encompasses ambitious tasks such as understanding and predicting protein structure and function, catalytic efficiency, enantioselectivity, protein dynamics, stability, solubility, aggregation, and more. Nonetheless, the field is still evolving, with many challenges to overcome and questions to address. In this Perspective, we provide an overview of ongoing trends in this domain, highlight recent case studies, and examine the current limitations of machine learning-based methods. We emphasize the crucial importance of thorough experimental validation of emerging models before their use for rational protein design. We present our opinions on the fundamental problems and outline the potential directions for future research.

Site-specific dual encoding and labeling of proteins via genetic code expansion

The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.

Biocontainment Techniques and Applications for Yeast Biotechnology

Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.

Noncanonical amino acids as doubly bio-orthogonal handles for one-pot preparation of protein multiconjugates

Genetic encoding of noncanonical amino acid (ncAA) for site-specific protein modification has been widely applied for many biological and therapeutic applications. To efficiently prepare homogeneous protein multiconjugates, we design two encodable noncanonical amino acids (ncAAs), 4-(6-(3-azidopropyl)-s-tetrazin-3-yl) phenylalanine (pTAF) and 3-(6-(3-azidopropyl)-s-tetrazin-3-yl) phenylalanine (mTAF), containing mutually orthogonal and bioorthogonal azide and tetrazine reaction handles. Recombinant proteins and antibody fragments containing the TAFs can easily be functionalized in one-pot reactions with combinations of commercially available fluorophores, radioisotopes, PEGs, and drugs in a plug-and-play manner to afford protein dual conjugates to assess combinations of tumor diagnosis, image-guided surgery, and targeted therapy in mouse models. Furthermore, we demonstrate that simultaneously incorporating mTAF and a ketone-containing ncAA into one protein via two non-sense codons allows preparation of a site-specific protein triconjugate. Our results demonstrate that TAFs are doubly bio-orthogonal handles for efficient and scalable preparation of homogeneous protein multiconjugates.

Genetic Code Expansion in Mammalian Cells Through Quadruplet Codon Decoding

Genetic code expansion enables the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins both in vitro and in vivo. In addition to a widely applied nonsense suppression strategy, the use of quadruplet codons could further expand the genetic code. A general approach to genetically incorporate ncAAs in response to quadruplet codons is achieved by utilizing an engineered aminoacyl-tRNA synthetase (aaRS) together with a tRNA variant containing an expanded anticodon loop. Here we provide a protocol to decode quadruplet UAGA codon with a ncAA in mammalian cells. We also describe microscopy imaging and flow cytometry analysis of ncAA mutagenesis in response to quadruplet codons.

Genetic Code Expansion in Pseudomonas putida KT2440

Pseudomonas putida KT2440 is an emerging microbial chassis for biobased chemical production from renewable feedstocks and environmental bioremediation. However, tools for studying, engineering, and modulating protein complexes and biosynthetic enzymes in this organism are largely underdeveloped. Genetic code expansion for the incorporation of unnatural amino acids (unAAs) into proteins can advance such efforts and, furthermore, enable additional controls of biological processes of the strain. In this work, we established the orthogonality of two widely used archaeal tRNA synthetase and tRNA pairs in KT2440. Following the optimization of decoding systems, four unAAs were incorporated into proteins in response to a UAG stop codon at 34.6-78% efficiency. In addition, we demonstrated the utility of genetic code expansion through the incorporation of a photocross-linking amino acid, p-benzoyl-l-phenylalanine (pBpa), into glutathione S-transferase (GstA) and a chemosensory response regulator (CheY) for protein-protein interaction studies in KT2440. This work reported the successful genetic code expansion in KT2440 for the first time. Given the diverse structure and functions of unAAs that have been added to protein syntheses using the archaeal systems, our research lays down a solid foundation for future work to study and enhance the biological functions of KT2440.

Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography

Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (M^pro) and papain-like (PL^pro) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.

Expanding the chemical repertoire of protein-based polymers for drug-delivery applications

Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.

Rational incorporation of any unnatural amino acid into proteins by machine learning on existing experimental proofs

The unnatural amino acid (UAA) incorporation technique through genetic code expansion has been extensively used in protein engineering for the last two decades. Mutations into UAAs offer more dimensions to tune protein structures and functions. However, the huge library of optional UAAs and various circumstances of mutation sites on different proteins urge rational UAA incorporations guided by artificial intelligence. Here we collected existing experimental proofs of UAA-incorporated proteins in literature and established a database of known UAA substitution sites. By program designing and machine learning on the database, we showed that UAA incorporations into proteins are predictable by the observed evolutional, steric and physiochemical factors. Based on the predicted probability of successful UAA substitutions, we tested the model performance using literature-reported and freshly-designed experimental proofs, and demonstrated its potential in screening UAA-incorporated proteins. This work expands structure-based computational biology and virtual screening to UAA-incorporated proteins, and offers a useful tool to automate the rational design of proteins with any UAA.

Noncanonical amino acid mutagenesis in response to recoding signal-enhanced quadruplet codons

While amber suppression is the most common approach to introduce noncanonical amino acids into proteins in live cells, quadruplet codon decoding has potential to enable a greatly expanded genetic code with up to 256 new codons for protein biosynthesis. Since triplet codons are the predominant form of genetic code in nature, quadruplet codon decoding often displays limited efficiency. In this work, we exploited a new approach to significantly improve quadruplet UAGN and AGGN (N = A, U, G, C) codon decoding efficiency by using recoding signals imbedded in mRNA. With representative recoding signals, the expression level of mutant proteins containing UAGN and AGGN codons reached 48% and 98% of that of the wild-type protein, respectively. Furthermore, this strategy mitigates a common concern of reading-through endogenous stop codons with amber suppression-based system. Since synthetic recoding signals are rarely found near the endogenous UAGN and AGGN sequences, a low level of undesirable suppression is expected. Our strategy will greatly enhance the utility of noncanonical amino acid mutagenesis in live-cell studies.

Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms

The surging demand of value-added products has steered the transition of laboratory microbes to microbial cell factories (MCFs) for facilitating production of large quantities of important native and non-native biomolecules. This shift has been possible through rewiring and optimizing different biosynthetic pathways in microbes by exercising frameworks of metabolic engineering and synthetic biology principles. Advances in genome and metabolic engineering have provided a fillip to create novel biomolecules and produce non-natural molecules with multitude of applications. To this end, numerous MCFs have been developed and employed for production of non-natural nucleic acids, proteins and different metabolites to meet various therapeutic, biotechnological and industrial applications. The present review describes recent advances in production of non-natural amino acids, nucleic acids, biofuel candidates and platform chemicals.

Methods for the directed evolution of biomolecular interactions

Noncovalent interactions between biomolecules such as proteins and nucleic acids coordinate all cellular processes through changes in proximity. Tools that perturb these interactions are and will continue to be highly valuable for basic and translational scientific endeavors. By taking cues from natural systems, such as the adaptive immune system, we can design directed evolution platforms that can generate proteins that bind to biomolecules of interest. In recent years, the platforms used to direct the evolution of biomolecular binders have greatly expanded the range of types of interactions one can evolve. Herein, we review recent advances in methods to evolve protein-protein, protein-RNA, and protein-DNA interactions.

Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons

Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-canonical amino acid (ncAA) into the polypeptide chain. While this strategy is attractive for genome expansion in biotechnology and bioengineering endeavors, improving the yield is hampered by a lack of understanding of where the shift can occur in an elongation cycle of protein synthesis. Lacking a clear answer to this question, current efforts have focused on designing +1-frameshifting tRNAs with an extra nucleotide inserted to the anticodon loop for pairing with a quadruplet codon in the aminoacyl-tRNA binding (A) site of the ribosome. However, the designed and evolved +1-frameshifting tRNAs vary broadly in achieving successful genome expansion. Here we summarize recent work on +1-frameshifting tRNAs. We suggest that, rather than engineering the quadruplet anticodon-codon pairing scheme at the ribosome A site, efforts should be made to engineer the pairing scheme at steps after the A site, including the step of the subsequent translocation and the step that stabilizes the pairing scheme in the +1-frame in the peptidyl-tRNA binding (P) site.

Genetic Code Expansion Through Quadruplet Codon Decoding

Noncanonical amino acid mutagenesis has emerged as a powerful tool for the study of protein structure and function. While triplet nonsense codons, especially the amber codon, have been widely employed, quadruplet codons have attracted attention for the potential of creating additional blank codons for noncanonical amino acids mutagenesis. In this review, we discuss methodologies and applications of quadruplet codon decoding in genetic code expansion both in vitro and in vivo.

Multiplex suppression of four quadruplet codons via tRNA directed evolution

Genetic code expansion technologies supplement the natural codon repertoire with assignable variants in vivo, but are often limited by heterologous translational components and low suppression efficiencies. Here, we explore engineered Escherichia coli tRNAs supporting quadruplet codon translation by first developing a library-cross-library selection to nominate quadruplet codon-anticodon pairs. We extend our findings using a phage-assisted continuous evolution strategy for quadruplet-decoding tRNA evolution (qtRNA-PACE) that improved quadruplet codon translation efficiencies up to 80-fold. Evolved qtRNAs appear to maintain codon-anticodon base pairing, are typically aminoacylated by their cognate tRNA synthetases, and enable processive translation of adjacent quadruplet codons. Using these components, we showcase the multiplexed decoding of up to four unique quadruplet codons by their corresponding qtRNAs in a single reporter. Cumulatively, our findings highlight how E. coli tRNAs can be engineered, evolved, and combined to decode quadruplet codons, portending future developments towards an exclusively quadruplet codon translation system.

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis, here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.

Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons

We recently described an orthogonal initiator tRNA (itRNA^Ty2) that can initiate protein synthesis with noncanonical amino acids (ncAAs) in response to the UAG nonsense codon. Here, we report that a mutant of itRNA^Ty2 (itRNA^Ty2_AUA) can efficiently initiate translation in response to the UAU tyrosine codon, giving rise to proteins with an ncAA at their N-terminus. We show that, in cells expressing itRNA^Ty2_AUA, UAU can function as a dual-use codon that selectively encodes ncAAs at the initiating position and predominantly tyrosine at elongating positions. Using itRNA^Ty2_AUA, in conjunction with its cognate tyrosyl-tRNA synthetase and two mutually orthogonal pyrrolysyl-tRNA synthetases, we demonstrate that UAU can be reassigned along with UAG or UAA to encode two distinct ncAAs in the same protein. Furthermore, by engineering the substrate specificity of one of the pyrrolysyl-tRNA synthetases, we developed a triply orthogonal system that enables simultaneous reassignment of UAU, UAG, and UAA to produce proteins containing three distinct ncAAs at precisely defined sites. To showcase the utility of this system, we produced proteins containing two or three ncAAs, with unique bioorthogonal functional groups, and demonstrate that these proteins can be separately modified with multiple fluorescent probes.

Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer?

Synthetic biology has promised and delivered on an impressive array of applications based on genetically modified microorganisms. While novel biotechnology undoubtedly offers benefits, like all new technology, precautions should be considered during implementation to reduce the risk of both known and unknown adverse effects. To achieve containment of transgenic microorganisms, confidence to a near-scientific certainty that they cannot transfer their transgenic genes to other organisms, and that they cannot survive to propagate in unintended environments, is a priority. Here, we present an in-depth summary of biological containment systems for micro-organisms published to date, including the production of a genetic firewall through genome recoding and physical containment of microbes using auxotrophies, regulation of essential genes, and expression of toxic genes. The level of containment required to consider a transgenic organism suitable for deployment is discussed, as well as standards of practice for developing new containment systems.

Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life

The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.

The role of antibody delivery formation in cancer therapy

Cancer has become one of the major threats to human survival. Because of antibodies specificity and low toxicity, it is the primary choice to diagnose and treat cancer. It is easy to be cleared from the blood circulation or distributing throughout the body and causes unnecessary side effects. It is necessary to delivery antibodies to the tumour region in a stable, safe and effective manner. In this review, we discuss the latest studies that aimed to delivery antibodies to tumour sites via several vector forms, such as liposomes, carbon nanomaterials, and gold nanomaterials. How to deliver antibodies to the target site is a difficulty for antibody therapy. This review summarises the antibody's therapeutic forms and carrier materials in recent years, and to explore how antibodies can be safely and stably delivered to the target site.