Publications The fruits of our labor
A Robust Growth-Based Selection Platform to Evolve an Enzyme via Dependency on Noncanonical Tyrosine Analogues
S.C. Jansen & C. Mayer*
JACS Au 2024 4:1583
Life-or-death selections evaluate the fitness of individual organisms on a population level. In enzyme engineering, such growth selections allow the rapid and straightforward identification of highly efficient biocatalysts from extensive libraries. However, selection-based improvement of (industrially-relevant) biocatalysts is challenging, as they require...
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Tethered Ribosomes: Toward the Synthesis of Nonproteinogenic Polymers in Bacteria
A. Staan & C. Mayer*
ChemBioChem 2023 24:e202200578
Joining ribosomal subunits with a small RNA linker has recently given rise to tethered ribosomes. Their ability to process orthogonal mRNAs (o-mRNA) independent of endogenous ribosomes allowed the identification of otherwise lethal, gain-of-function mutations. Thus, engineering tethered ribosomes promises to significantly expand the scope of building blocks...
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Selecting Better Biocatalysts by Complementing Recoded Bacteria
R. Rubini, S.C. Janssen, H. Beekhuis, H.J. Rozeboom & C. Mayer*
Angewandte Chemie International Edition 2023 62:e202213942
An in vivo selection strategy is presented, in which bacteria addicted to non-canonical amino acids (ncAAs) are complemented by enzymes that can yield these building blocks from synthetic precursors. As growth rates under selective conditions correlate with enzyme activities...
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Opportunities for interfacing organometallic catalysts with cellular metabolism
R. Rubini & C. Mayer*
in Comprehensive Organometallic Chemistry IV 2022
A concerted effort of synthetic chemistry and synthetic biology promises to expand biological function without the need for extensive genetic manipulation. In such scenarios, man-made catalysts perform new-to-nature transformations on molecules, which are either provided or further diversified by biocatalysts in designer microbes...
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A Strategy to Select Macrocyclic Peptides Featuring Asymmetric Molecular Scaffolds as Cyclization Units by Phage Display
T.R. Oppewal, I.D. Jansen, J. Hekelaar & C. Mayer*
J. Am. Chem. Soc. 2022 8:3644
Macrocyclic peptides (MPs) have positioned themselves as a privileged class of compounds for the discovery of therapeutics and development of chemical probes. Aided by the development of powerful selection strategies, high-affinity binders against biomolecular targets can readily...
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Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii
A. Marjanovic, H.J. Rozeboom, M.S. de Vries, C. Mayer, M. Otzen, H.J. Wijma, D.B. Janssen
Proteins 2021 89:1079
Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis, like 5-oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP-dependent acetone- and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli...
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Addicting Escherichia Coli to new-to-nature reactions
R. Rubini & C. Mayer*
in ACS Chemical Biology 2020 15:3093
Biocontainment is an essential feature when deploying genetically modified organisms (GMOs) in open system applications, as variants escaping their intended operating environments could negatively impact ecosystems and human health. To avoid breaches resulting from metabolic cross-feeding, horizontal gene transfer, and/or genetic mutations, synthetic auxotrophs....
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Gentic Code Expansion Strategies for Vaccine Development
J.A. Fok & C. Mayer*
in ChemBioChem 2020 21:3291
This article reviews the utility of genetic code expansion as an emerging tool for the development of vaccines. It highlights how the incorporation of immunogenic noncanonical amino acids (ncAA) can aid in eliciting immune responses against adverse self-proteins and highlights the potential of an expanded genetic code for the construction of live-attenuated virus vaccines...
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Chance emergence of catalytic activity and promiscuity in a self-replicator
J. Ottelé, A.S. Hussain, C. Mayer* & S. Otto*
in Nature Catalysis 2020 3:547
How life can emerge from inanimate matter is one of the grand questions in science. Self-replicating molecules are necessary for the transition from chemistry to biology, but they need to acquire additional functions for life to emerge. Catalysis is one of the most essential of such functionalities, but mechanisms through which self-replicators can acquire catalytic and, in extension, metabolic properties have remained elusive. ..
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Affinity-selected bicyclic peptide G-quadruplex ligands mimic a protein-like binding mechanism
K.C. Liu, K. Röder, C. Mayer, S. Adhikari, D.J. Wales* & S. Balasubramanian*
in J. Am. Chem. Soc. 2020 142:8367
The study of G-quadruplexes (G4s) in a cellular context has demonstrated links between these nucleic acid secondary structures, gene expression, and DNA replication. Ligands that bind to the G4 structure therefore present an excellent opportunity for influencing gene expression through the targeting of a nucleic acid structure rather than sequence...
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The importance of catalytic promiscuity for enzyme design and evolution
R.B. Leveson-Gower, C. Mayer* & G. Roelfes*
in Nat. Rev. Chem. 2019 3:687
The ability of one enzyme to catalyse multiple, mechanistically distinct transformations likely played a crucial role in organisms’ abilities to adapt to changing external stimuli in the past and can still be observed in extant enzymes. Given the importance of catalytic promiscuity in nature, enzyme designers have recently begun to create catalytically promiscuous enzymes in order to expand the canon of transformations...
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A screening platform to identify and tailor biocompatible small-molecule catalysts
R. Rubini, I. Ivanov & C. Mayer*
in Chem. Eur. J. 2019 25:16017
A multi-well screen that rapidly reports the catalytic activity of transition-metal catalysts in presence of live cells is reported. The activity of a catalyst to yield a non-canonical amino acid (ncAA) from an appropriate precursor is coupled to the incorporation of the nonstandard building block into GFP (quantifiable readout; see scheme)...
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Selection, addiction & catalysis: emerging trends for the incorporation of non-canonical amino acids into peptides and proteins in vivo
C. Mayer*
in ChemBioChem 2019 20:1357
This article highlights recent advances in applying genetic code expansion strategies for: 1) the incorporation of non-standard amino acids (ncAAs) in the biosynthesis and selection of macrocyclic peptides, 2) synthetic biocontainment strategies based on the addiction....
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Directed evolution of a designer enzyme featuring an unnatural catalytic amino acid
C. Mayer*, C. Dulson, E. Reddem, A-M. W.H. Thunnissen & G. Roelfes*
in Angew. Chem. 2019 131:2105
The directed evolution of a designer enzyme featuring a uniquely reactive aniline side chain as catalytic residue (in red) is reported. Multiple beneficial mutations were identified (blue), which when combined increase the turnover frequency (kcat) of the designer enzyme by more...
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Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts
B. Herdy, C. Mayer, D. Varshney, G. Marsico, P. Murat, C. Taylor, C. D'Santos, D. Tannahill & S. Balasubramanian*
in Nuc. Ac. Res. 2018 46:11592
RNA G-quadruplexes (rG4s) are secondary structures in mRNAs known to influence RNA post-transcriptional mechanisms thereby impacting neurodegenerative disease and cancer. A detailed knowledge of rG4–protein interactions is vital to understand rG4 function...
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A designer enzyme for hydrazone and oxime formation featuring an unnatural catalytic aniline residue
I. Drienovská, C. Mayer, C. Dulson & J.G. Roelfes*
in Nat. Chem. 2018 10:946
Creating designer enzymes with the ability to catalyse abiological transformations is a formidable challenge. Efforts toward this goal typically consider only canonical amino acids in the initial design process. However, incorporating unnatural amino acids that feature uniquely reactive side chains could significantly expand the catalytic repertoire of designer enzymes. To explore the potential...
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G-quadruplex structures within the 3’-UTR of LINE-1 elements stimulate retrotransposition
A.B. Sahakyan, P. Murat, C. Mayer & S. Balasubramanian*
in Nat. Struct. Mol. Biol. 2017 24:243
Long interspersed nuclear elements (LINEs) are ubiquitous transposable elements in higher eukaryotes that have a significant role in shaping genomes, owing to their abundance. Here we report that guanine-rich sequences in the 3′ untranslated regions (UTRs) of hominoid-specific LINE-1 elements are coupled...
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An epigenetics-inspired DNA-based data storage system
C. Mayer, G.R. McInroy, P. Murat, P. van Delft & S. Balasubramanian*
in Angew. Chem. 2016 128:11310
Inspired by the epigenetic regulation of genomic information in cells, it is shown how digital data can undergo controlled changes when encoded in synthetic DNA strands. Chemical transformations were used to alter naturally occurring cytosine derivatives, which enabled the reversible recovery of multiple data layers from a single DNA template...
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Building proficient enzymes with foldamer prostheses
C. Mayer, M.M. Müller, S.H. Gellman, & D. Hilvert*
in Angew. Chem. 2014 126:7098
Foldamers are non-natural oligomers that adopt stable conformations reminiscent of those found in proteins. To evaluate the potential of foldameric subunits for catalysis, semisynthetic enzymes containing foldamer fragments constructed from α- and β-amino acid....
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Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase
N. Preiswerk, T. Beck, J.D. Schulz, P. Milovnik, C. Mayer, J.B. Siegel, D. Baker & D. Hilvert*
in Proc. Nat. Acad. Sci. U.S.A. 2014 111:8013
Creating artificial enzymes that catalyze arbitrary chemical reactions is challenging. Although computational approaches to this problem hold great promise, starting designs typically exhibit low efficiency and require extensive optimization through directed evolution. In this study, we chronicle the evolution of a modestly active, computationally designed Diels-Alderase...
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A genetically encodable ligand for transfer hydrogenation
C. Mayer & D. Hilvert*
in Eur. J. Org. Chem. 2013 17:3427
Simple tripeptides are shown to be effective ligands for iridium-catalyzed transfer hydrogenations. Peptide–iridium complexes efficiently reduce ketones, aldehydes, imines, and NAD+ under mild conditions in aqueous buffer. As genetically encodable foldamers, peptides are attractive ligands for the construction of artificial metalloenzymes for diverse biotechnological applications...
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An artificial metalloenzyme for olefin metathesis
C. Mayer D.G. Gillingham, T.R. Ward & D. Hilvert*
in Chem. Comm. 2011 47:12068
A Grubbs–Hoveyda type olefin metathesis catalyst, equipped with an electrophilic bromoacetamide group, was used to modify a cysteine-containing variant of a small heat shock protein from Methanocaldococcus jannaschii. The resulting artificial metalloenzyme was found to be active under acidic conditions in a benchmark ring closing metathesis reaction...
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Synthesis of gamma-halogenated and long-chain ß-hydroxy-a-amino acids and 2-amino-1,3-diols using threonine aldolases
J. Steinreiber, K. Fresko, C. Mayer, C. Reisinger, M. Schürmann & H. Griengl*
in Tetrahedron 2007 63:8088
The L- and D-threonine aldolase catalyzed formation of γ-halogenated and long-chain l- and d-3-alkylserine-derivatives 1–12, respectively, was shown starting from glycine and halogenated C2– or C4–C12 aldehydes...
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