Expansion of the genetic code via expansion of the genetic alphabet

Dien, Vivian T.; Morris, Sydney E.; Karadeema, Rebekah J; Romesberg, Floyd E.

doi:10.1016/j.cbpa.2018.08.009

Cited by 51 publications

(38 citation statements)

References 44 publications

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“…In the course of these experiments, the E. coli cells take up the substrates of the tested NTTs, and thanks to the broad substrate spectrum of the P. tricornutum NTT2, this transport essay type of experiment has enabled a major breakthrough in synthetic biology: PtNTT2 accepts not only the natural nucleotide substrates as tested in [39], but also synthetic nucleobases, which can form unnatural base pairs [83]. Such unnatural base pairs can be used to expand the genetic code to include codons for non-canonical amino acids, which can provide additional chemical functions to proteins (reviewed in [84,85]). PtNTT2 allows the uptake of the artificial nucleosides dNaM and d5SICS in the form of triphosphates, which makes them accepted substrates for DNA polymerases and leads to their incorporation into DNA in vivo, when a template plasmid containing the unnatural base pair formed by d5SICS and dNaM has been added [83].…”

Section: Biotechnological Applications Of Diatom Nttsmentioning

confidence: 99%

“…For the use of an unnatural base pair in a new codon, however, more prerequisites have to be met. For transcription into RNA, nucleosides are needed in the form of ribotriphosphates, a new tRNA gene with the complementary anticodon has to be introduced, and it needs to be loaded with the cognate amino acid [84]. After optimization of the PtNTT2 gene sequence and expression system and a switch of the unnatural base pair to the better retained NaM-TPT3 [86], Zhang et al [87] succeeded in integrating unnatural base pairs and non-canonical amino acids into the full replication-transcription-translation chain of biological information storage and retrieval ( Figure 2).…”

Section: Biotechnological Applications Of Diatom Nttsmentioning

confidence: 99%

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Nucleotide Transport and Metabolism in Diatoms

Gruber

Haferkamp

2019

Biomolecules

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Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic tissues, or during the dark, depend on external supply of ATP. A dedicated antiporter that exchanges ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) takes over this function in most photosynthetic eukaryotes. Additional forms of such nucleotide transporters (NTTs), with deviating activities, are found in intracellular bacteria, and, surprisingly, also in diatoms, a group of algae that acquired their plastids from other eukaryotes via one (or even several) additional endosymbioses compared to algae with primary plastids and higher plants. In this review, we summarize what is known about the nucleotide synthesis and transport pathways in diatom cells, and discuss the evolutionary implications of the presence of the additional NTTs in diatoms, as well as their applications in biotechnology.Cyanobacteria store the photosynthesized carbohydrates in the bacterial cytoplasm in the form of glycogen and use these stores for the generation of energy via respiration, which allows them to tide over conditions in which photosynthesis is not possible, for instance in the absence of light [17]. In contrast, in the majority of photosynthetic eukaryotes, storage carbohydrates are located outside of the plastid stroma and hence outside of the former cyanobacterial cytosol. However, green algae and plants are a notable exception, because their starch metabolism has secondarily been re-allocated to the plastid [18,19]. Consequently, whenever photosynthesis is insufficient to meet the ATP demand, the plastid needs to be supplied with this energy currency from other sources. The corresponding ATP production can take place in mitochondria (through respiration), or in the cytosol (through substrate-level phosphorylation). In photosynthetic eukaryotes, plastidic ATP uptake is catalyzed by specific solute transport proteins called nucleotide transporters (NTTs) [20][21][22]. These NTTs are present in the inner envelope membrane, where they act as antiporters, exchanging ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) [20,23] (Figure 1a).

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Section: Biotechnological Applications Of Diatom Nttsmentioning

confidence: 99%

Section: Biotechnological Applications Of Diatom Nttsmentioning

confidence: 99%

Nucleotide Transport and Metabolism in Diatoms

Gruber

Haferkamp

2019

Biomolecules

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“…This approach does not interfere with the natural system because it does not involve the canonical codons, while the new ones are free of any natural role. Such experiments with at least three pairs of the fifth and the sixth nucleotide were already carried out and appeared promising [Ishikawa et al, 2000, Ohtsuki et al, 2001, Yang et al, 2007, Kimoto et al, 2009, Malyshev et al, 2009, Dien et al, 2018, Hamashima et al, 2018]. Protein synthesis using this approach occurred successfully in semi-synthetic bacteria [Zhang et al, 2017].…”

Section: Introductionmentioning

confidence: 99%

Basic principles of the genetic code extension

Błażej

Wnętrzak

Mackiewicz

et al. 2019

Preprint

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Compounds including non-canonical amino acids or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the non-canonical amino acids can be constantly delivered in a stable way by organisms with the customized genetic code. Among several methods of engineering the code, using non-canonical base pairs is especially promising, because it enables generating many new codons, which can be used to encode any new amino acid. Since even one pair of new bases can extend the SGC up to 216 codons generated by six-letter nucleotide alphabet, the extension of the SGC can be achieved in many ways. Here, we proposed a stepwise procedure of the SGC extension with one pair of non-canonical bases to minimize the consequences of point mutations. We reported relationships between codons in the framework of graph theory. All 216 codons were represented as nodes of the graph, whereas its edges were induced by all possible single nucleotide mutations occurring between codons. Therefore, every set of canonical and newly added codons induces a specific subgraph. We characterized the properties of the induced subgraphs generated by selected sets of codons. Thanks to that, we were able to describe a procedure for incremental addition of the set of meaningful codons up to the full coding system consisting of three pairs of bases. The procedure of gradual extension of the SGC makes the whole system robust to changing genetic information due to mutations and is compatible with the views assuming that codons and amino acids were added successively to the primordial SGC, which evolved to minimize harmful consequences of mutations or mistranslations of encoded proteins.

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“…This approach does not interfere with the natural system because it does not involve the canonical codons, while the new ones are free of any natural role. Such experiments with at least three pairs of the fifth and the sixth nucleotide were already carried out and appeared promising [16][17][18][19][20][21][22]. Protein synthesis using this approach occurred successfully in semi-synthetic bacteria [23].…”

mentioning

confidence: 99%

Basic principles of the genetic code extension

et al. 2020

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Compounds including non-canonical amino acids (ncAAs) or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the ncAAs can be constantly delivered in a stable way by organisms with the customized genetic code. Among several methods of engineering the code, using non-canonical base pairs is especially promising, because it enables generating many new codons, which can be used to encode any new amino acid. Since even one pair of new bases can extend the SGC up to 216 codons generated by a six-letter nucleotide alphabet, the extension of the SGC can be achieved in many ways. Here, we proposed a stepwise procedure of the SGC extension with one pair of non-canonical bases to minimize the consequences of point mutations. We reported relationships between codons in the framework of graph theory. All 216 codons were represented as nodes of the graph, whereas its edges were induced by all possible single nucleotide mutations occurring between codons. Therefore, every set of canonical and newly added codons induces a specific subgraph. We characterized the properties of the induced subgraphs generated by selected sets of codons. Thanks to that, we were able to describe a procedure for incremental addition of the set of meaningful codons up to the full coding system consisting of three pairs of bases. The procedure of gradual extension of the SGC makes the whole system robust to changing genetic information due to mutations and is compatible with the views assuming that codons and amino acids were added successively to the primordial SGC, which evolved minimizing harmful consequences of mutations or mistranslations of encoded proteins.

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Expansion of the genetic code via expansion of the genetic alphabet

Cited by 51 publications

References 44 publications

Nucleotide Transport and Metabolism in Diatoms

Nucleotide Transport and Metabolism in Diatoms

Basic principles of the genetic code extension

Basic principles of the genetic code extension

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