Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides

Cui, Zhenling; Johnston, Wayne A.; Alexandrov, Kirill

doi:10.3389/fbioe.2020.01031

Cited by 36 publications

(25 citation statements)

References 221 publications

(329 reference statements)

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“…Use of non-canonical amino acids (ncAAs) through codon reassignment has been applied in analysis of protein structure and interaction, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates and novel enzymes [115]. The scope of applications of codon usage analysis is thus immense.…”

Section: Applications Of Codon Usage Studiesmentioning

confidence: 99%

Codon usage bias

2021

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Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.

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Section: Applications Of Codon Usage Studiesmentioning

confidence: 99%

Codon usage bias

2021

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“…Well over 100 noncanonical amino acids (ncAAs) with a wide variety of side chains have been incorporated into proteins by genetic encoding. − Among these, some are capable of binding metal ions. For example, bipyridylalanine ( BpyAla , Figure ) has successfully been used to endow proteins with new hydrolytic function or greater stability enabled by its capacity to bind divalent metal ions. , Paramagnetic transition metal ions, such as Co(II), which prefer nitrogen ligands and require fewer coordination sites than Ln(III) ions, can be coordinated by BpyAla .…”

Section: General Overview Of Natural and Chemically Generated Paramag...mentioning

confidence: 99%

Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

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“…For recombinant protein production, CFE systems offer a distinct advantage for the synthesis of specialty proteins, peptides or small molecules that are difficult to make in a cell (Zimmerman et al, 2014;Dudley et al, 2020;Meyer et al, 2021;Tian et al, 2022). For example, non-canonical AAs or posttranslation modifications (Cui et al, 2020;Charna et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

A ubiquitous amino acid source for prokaryotic and eukaryotic cell-free transcription-translation systems

Nagappa

Sato

Alam

et al. 2022

Front. Bioeng. Biotechnol.

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Cell-free gene expression (CFE) systems are an attractive tool for engineering within synthetic biology and for industrial production of high-value recombinant proteins. CFE reactions require a cell extract, energy system, amino acids, and DNA, to catalyse mRNA transcription and protein synthesis. To provide an amino acid source, CFE systems typically use a commercial standard, which is often proprietary. Herein we show that a range of common microbiology rich media (i.e., tryptone, peptone, yeast extract and casamino acids) unexpectedly provide an effective and low-cost amino acid source. We show that this approach is generalisable, by comparing batch variability and protein production in the following range of CFE systems: Escherichia coli (Rosetta™ 2 (DE3), BL21(DE3)), Streptomyces venezuelae and Pichia pastoris. In all CFE systems, we show equivalent or increased protein synthesis capacity upon replacement of the commercial amino acid source. In conclusion, we suggest rich microbiology media provides a new amino acid source for CFE systems with potential broad use in synthetic biology and industrial biotechnology applications.

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Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides

Cited by 36 publications

References 221 publications

Codon usage bias

Codon usage bias

Paramagnetic Chemical Probes for Studying Biological Macromolecules

A ubiquitous amino acid source for prokaryotic and eukaryotic cell-free transcription-translation systems

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