Update of the Pyrrolysyl-tRNA Synthetase/tRNAPyl Pair and Derivatives for Genetic Code Expansion

Removing redundancy of the NCN codons in vitro for maximal sense codon reassignment

Expanding the genetic code affords exciting opportunities for synthetic biology, studies of protein function, and creation of diverse peptide libraries by mRNA display. Maximal expansion with the standard 64 codon code requires breaking the degeneracy of the 61 sense codons which encode for only 20 amino acids. In E. coli these 61 codons are decoded by 46 different tRNAs. Moreover, many codons are decoded by multiple tRNAs, further complicating efforts to break this redundancy. The overlapping decoding patterns of the 11 tRNAs in E. coli which read the 16 codons that encode serine, proline, threonine, and alanine codons exemplify this difficulty. Here we tackle this challenge by first outlining a general process to evaluate codons for their potential for reassignment. We then use this knowledge to assign these 16 codons to 10 different amino acids, more than doubling their encoding potential. Our work highlights the expanded potential of sense codon reassignment and points the way to a dramatically expanded code containing more than 30 monomers.

Streamlining tRNA-Synthetase Evolution for Genetic Code Expansion and Deep Sequencing Analyses of Its Evolved Variants

Proteins are typically composed of 20 amino acids encoded by 61 codons. However, some bacteria and archaea have evolved to incorporate additional amino acids by repurposing stop codons, a phenomenon that led to the development of genetic code expansion (GCE) in the early 21st century. This approach introduces orthogonal tRNA and aminoacyl-tRNA-synthetase (aaRS) pairs into target organisms, enabling the incorporation of noncanonical amino acids (ncAAs) with distinct side chains into proteins. GCE has broad applications, including site-specific cross-linking, fluorescence labeling, and electron-transfer functionalities. Despite its versatility, improving the efficiency of ncAA incorporation remains a challenge. Directed evolution provides a powerful solution by introducing mutations into the aaRS sequence and applying selection to identify variants with enhanced activity. Here, we present a simplified directed evolution system designed to improve the activity of pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei. Our approach is accessible, requiring only basic laboratory equipment, making it suitable and facile to implement by graduate students. We evolved PylRS variants toward three distinct substrates, each pathway yielding unique, substrate-specific mutations. We characterized the impact of these mutations on both PylRS activity and expression levels, demonstrating that tandem codon randomization can be an effective strategy for improving PylRS function through additive effects of the mutations. Additionally, deep sequencing validated our approach, confirming its efficiency, revealing conserved and mutationally flexible sites and reinforcing the advantage of tandem mutations in PylRS evolution. Collectively, these findings streamline the process of evolving PylRS and provide insights into strategies for enhancing ncAA incorporation in synthetic biology and protein engineering.

Optogenetics with Atomic Precision─A Comprehensive Review of Optical Control of Protein Function through Genetic Code Expansion

Conditional control of protein activity is important in order to elucidate the particular functions and interactions of proteins, their regulators, and their substrates, as well as their impact on the behavior of a cell or organism. Optical control provides a perhaps optimal means of introducing spatiotemporal control over protein function as it allows for tunable, rapid, and noninvasive activation of protein activity in its native environment. One method of introducing optical control over protein activity is through the introduction of photocaged and photoswitchable noncanonical amino acids (ncAAs) through genetic code expansion in cells and animals. Genetic incorporation of photoactive ncAAs at key residues in a protein provides a tool for optical activation, or sometimes deactivation, of protein activity. Importantly, the incorporation site can typically be rationally selected based on structural, mechanistic, or computational information. In this review, we comprehensively summarize the applications of photocaged lysine, tyrosine, cysteine, serine, histidine, glutamate, and aspartate derivatives, as well as photoswitchable phenylalanine analogues. The extensive and diverse list of proteins that have been placed under optical control demonstrates the broad applicability of this methodology.

Genetic Code Expansion of the Silkworm Bombyx mori Using a Pyrrolysyl-tRNA Synthetase/tRNAPyl Pair

The domesticated silkworm Bombyx mori, an essential industrial animal for silk production, has attracted attention as a host for protein production due to its remarkable protein synthesis capability. Here, we applied genetic code expansion (GCE) using a versatile pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pair from Methanosarcina mazei to B. mori; GCE enables synthetic amino acid incorporation into proteins to give them non-natural functions. Transgenic B. mori lines expressing M. mazei PylRS and its cognate tRNAPyl were generated and cross-mated to obtain their F1 hybrid. Orally administering a click-compatible synthetic amino acid, trans-cyclooctene-lysine (TCO-Lys), to the F1 hybrid has led to the production of silk fiber incorporated with TCO-Lys. TCO-Lys incorporation in silk fiber was verified by selective labeling of the TCO group by click chemistry. The developed system is available for large-scale protein production with a wide variety of synthetic amino acids.

Pyrrolysine Aminoacyl-tRNA Synthetase as a Tool for Expanding the Genetic Code

In addition to the 20 canonical amino acids encoded in the genetic code, there are two non-canonical ones: selenocysteine and pyrrolysine. The discovery of pyrrolysine synthetases (PylRSs) was a key event in the field of genetic code expansion research. The importance of this discovery is mainly due to the fact that the translation systems involving PylRS, pyrrolysine tRNA (tRNAPyl) and pyrrolysine are orthogonal to the endogenous translation systems of organisms that do not use this amino acid in protein synthesis. In addition, pyrrolysine synthetases belonging to different groups are also mutually orthogonal. This orthogonality is based on the structural features of PylRS and tRNAPyl, which include identical elements, such as a condensed core, certain base pairs and the structural motifs of tRNAPyl. This suggests that targeted structural changes in these molecules enable changes in their specificity for the amino acid and the codon. Such modifications were successfully used to obtain different aaRS/tRNA pairs that allow the incorporation of unnatural amino acids into peptides. This review presents the results of recent studies related to the correlation between the structure and activity of PylRS and tRNAPyl and the use of pyrrolysine synthetases to extend the genetic code.

Genetic Code Expansion History and Modern Innovations

The genetic code is the foundation for all life. With few exceptions, the translation of nucleic acid messages into proteins follows conserved rules, which are defined by codons that specify each of the 20 proteinogenic amino acids. For decades, leading research groups have developed a catalogue of innovative approaches to extend nature's amino acid repertoire to include one or more noncanonical building blocks in a single protein. In this review, we summarize advances in the history of in vitro and in vivo genetic code expansion, and highlight recent innovations that increase the scope of biochemically accessible monomers and codons. We further summarize state-of-the-art knowledge in engineered cellular translation, as well as alterations to regulatory mechanisms that improve overall genetic code expansion. Finally, we distill existing limitations of these technologies into must-have improvements for the next generation of technologies, and speculate on future strategies that may be capable of overcoming current gaps in knowledge.

Directed Evolution of Candidatus Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase for the Genetic Incorporation of Two Different Noncanonical Amino Acids in One Protein

The genetic code expansion technique is a powerful chemical biology tool to install noncanonical amino acids (ncAAs) in proteins. As a key enzyme for this technique, pyrrolysyl-tRNA synthetase (PylRS), coupled with its cognate amber suppressor tRNAPyl, has been engineered for the genetic incorporation of more than 200 ncAAs. Using PylRS clones from different archaeal origins, two ncAAs have also been genetically encoded in one protein. In this work, we show that the C41AU mutant of tRNAPyl from Candidatus Methanomethylophilus alvus (CmatRNAPyl) is catalytically inert toward PylRS from Methanosarcina mazei (MmPylRS) but has weak activity toward PylRS from Ca. M. alvus (CmaPylRS). To improve the catalytic efficiency of CmaPylRS toward CmatRNAPyl-C41AU, we conducted a directed evolution of CMaPylRS by randomizing its coding sequence, followed by the screening of active mutant clones. After three rounds of randomization and screening, we identified 4 mutations, Y16F/N57D/E161G/N182I, that improve the catalytic efficiency of CMaPylRS toward CMatRNAPyl-C41AU. This new clone, named R3-14, coupling with CmatRNAPyl-C41AU to recognize an amber codon, has been successfully used together with an evolved MmPylRS clone, coupling with a mutant M. mazei tRNAPyl to recognize an ochre codon, to genetically incorporate two different ncAAs, N ε-(t-butoxycarbonyl)-lysine and N ε-acetyl-lysine, into one model protein.

Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis

Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.

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.

Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids

Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.

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.

Site-specific protein labeling strategies for super-resolution microscopy

Super-resolution microscopy (SRM) has transformed our understanding of proteins' subcellular organization and revealed cellular details down to nanometers, far beyond conventional microscopy. While localization precision is independent of the number of fluorophores attached to a biomolecule, labeling density is a decisive factor for resolving complex biological structures. The average distance between adjacent fluorophores should be less than half the desired spatial resolution for optimal clarity. While this was not a major limitation in recent decades, the success of modern microscopy approaching molecular resolution down to the single-digit nanometer range will depend heavily on advancements in fluorescence labeling. This review highlights recent advances and challenges in labeling strategies for SRM, focusing on site-specific labeling technologies. These advancements are crucial for improving SRM precision and expanding our understanding of molecular interactions.

Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification

Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.

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.

Amber-codon suppression for spatial localization and in vivo photoaffinity capture of the interactome of the Pseudomonas aeruginosa rare lipoprotein A lytic transglycosylase

The 11 lytic transglycosylases of Pseudomonas aeruginosa have overlapping activities in the turnover of the cell-wall peptidoglycan. Rare lipoprotein A (RlpA) is distinct among the 11 by its use of only peptidoglycan lacking peptide stems. The spatial localization of RlpA and its interactome within P. aeruginosa are unknown. We employed suppression of introduced amber codons at sites in the rlpA gene for the introduction of the unnatural-amino-acids Νζ -[(2-azidoethoxy)carbonyl]-l-lysine (compound 1) and Nζ -[[[3-(3-methyl-3H-diazirin-3-yl)propyl]amino]carbonyl]-l-lysine (compound 2). In live P. aeruginosa, full-length RlpA incorporating compound 1 into its sequence was fluorescently tagged using strained-promoted alkyne-azide cycloaddition and examined by fluorescence microscopy. RlpA is present at low levels along the sidewall length of the bacterium, and at higher levels at the nascent septa of replicating bacteria. In intact P. aeruginosa, UV photolysis of full-length RlpA having compound 2 within its sequence generated a transient reactive carbene, which engaged in photoaffinity capture of neighboring proteins. Thirteen proteins were identified. Three of these proteins-PBP1a, PBP5, and MreB-are members of the bacterial divisome. The use of the complementary methodologies of non-canonical amino-acid incorporation, photoaffinity proximity analysis, and fluorescent microscopy confirm a dominant septal location for the RlpA enzyme of P. aeruginosa, as a divisome-associated activity. This accomplishment adds to the emerging recognition of the value of these methodologies for identification of the intracellular localization of bacterial proteins.