1
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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024; 124:11008-11062. [PMID: 39235427 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L Dunkelmann
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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2
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Niu W, Guo J. Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology. Chem Rev 2024; 124:10577-10617. [PMID: 39207844 DOI: 10.1021/acs.chemrev.3c00938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
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.
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Affiliation(s)
- Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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3
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Chen L, Xin X, Zhang Y, Li S, Zhao X, Li S, Xu Z. Advances in Biosynthesis of Non-Canonical Amino Acids (ncAAs) and the Methods of ncAAs Incorporation into Proteins. Molecules 2023; 28:6745. [PMID: 37764520 PMCID: PMC10534643 DOI: 10.3390/molecules28186745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The functional pool of canonical amino acids (cAAs) has been enriched through the emergence of non-canonical amino acids (ncAAs). NcAAs play a crucial role in the production of various pharmaceuticals. The biosynthesis of ncAAs has emerged as an alternative to traditional chemical synthesis due to its environmental friendliness and high efficiency. The breakthrough genetic code expansion (GCE) technique developed in recent years has allowed the incorporation of ncAAs into target proteins, giving them special functions and biological activities. The biosynthesis of ncAAs and their incorporation into target proteins within a single microbe has become an enticing application of such molecules. Based on that, in this study, we first review the biosynthesis methods for ncAAs and analyze the difficulties related to biosynthesis. We then summarize the GCE methods and analyze their advantages and disadvantages. Further, we review the application progress of ncAAs and anticipate the challenges and future development directions of ncAAs.
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Affiliation(s)
- Liang Chen
- College of Bioengineering, Beijing Polytechnic, Beijing 100176, China; (X.X.); (Y.Z.); (S.L.); (X.Z.); (S.L.); (Z.X.)
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4
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Gong X, Zhang H, Shen Y, Fu X. Update of the Pyrrolysyl-tRNA Synthetase/tRNA Pyl Pair and Derivatives for Genetic Code Expansion. J Bacteriol 2023; 205:e0038522. [PMID: 36695595 PMCID: PMC9945579 DOI: 10.1128/jb.00385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The cotranslational incorporation of pyrrolysine (Pyl), the 22nd proteinogenic amino acid, into proteins in response to the UAG stop codon represents an outstanding example of natural genetic code expansion. Genetic encoding of Pyl is conducted by the pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA, tRNAPyl. Owing to the high tolerance of PylRS toward diverse amino acid substrates and great orthogonality in various model organisms, the PylRS/tRNAPyl-derived pairs are ideal for genetic code expansion to insert noncanonical amino acids (ncAAs) into proteins of interest. Since the discovery of cellular components involved in the biosynthesis and genetic encoding of Pyl, synthetic biologists have been enthusiastic about engineering PylRS/tRNAPyl-derived pairs to rewrite the genetic code of living cells. Recently, considerable progress has been made in understanding the molecular phylogeny, biochemical properties, and structural features of the PylRS/tRNAPyl pair, guiding its further engineering and optimization. In this review, we cover the basic and updated knowledge of the PylRS/tRNAPyl pair's unique characteristics that make it an outstanding tool for reprogramming the genetic code. In addition, we summarize the recent efforts to create efficient and (mutually) orthogonal PylRS/tRNAPyl-derived pairs for incorporation of diverse ncAAs by genome mining, rational design, and advanced directed evolution methods.
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Affiliation(s)
- Xuemei Gong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research-Shenzhen, BGI, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Haolin Zhang
- BGI Research-Shenzhen, BGI, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Yue Shen
- BGI Research-Shenzhen, BGI, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
- BGI Research-Changzhou, BGI, Changzhou, China
| | - Xian Fu
- BGI Research-Shenzhen, BGI, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
- BGI Research-Changzhou, BGI, Changzhou, China
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5
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Sun J, Evans PN, Gagen EJ, Woodcroft BJ, Hedlund BP, Woyke T, Hugenholtz P, Rinke C. Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME COMMUNICATIONS 2021; 1:30. [PMID: 36739331 PMCID: PMC9723677 DOI: 10.1038/s43705-021-00032-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
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Affiliation(s)
- Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Emma J Gagen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Brian P Hedlund
- School of Life Sciences and Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
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6
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Ho JML, Miller CA, Smith KA, Mattia JR, Bennett MR. Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway. Nat Commun 2021; 12:3914. [PMID: 34168131 PMCID: PMC8225853 DOI: 10.1038/s41467-021-24183-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Pyrrolysine (Pyl, O) exists in nature as the 22nd proteinogenic amino acid. Despite being a fundamental building block of proteins, studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, we improve Pyl biosynthesis via rational engineering and directed evolution of the entire biosynthetic pathway. To accommodate toxicity of Pyl biosynthetic genes in Escherichia coli, we also develop Alternating Phage Assisted Non-Continuous Evolution (Alt-PANCE) that alternates mutagenic and selective phage growths. The evolved pathway provides 32-fold improved yield of Pyl-containing reporter protein compared to the rationally engineered ancestor. Evolved PylB mutants are present at up to 4.5-fold elevated levels inside cells, and show up to 2.2-fold increased protease resistance. This study demonstrates that Alt-PANCE provides a general approach for evolving proteins exhibiting toxic side effects, and further provides an improved pathway capable of producing substantially greater quantities of Pyl-proteins in E. coli. Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.
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Affiliation(s)
- Joanne M L Ho
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Corwin A Miller
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Kathryn A Smith
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Jacob R Mattia
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA.
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7
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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8
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Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics. Appl Microbiol Biotechnol 2020; 104:4705-4716. [PMID: 32281023 DOI: 10.1007/s00253-020-10599-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023]
Abstract
Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.
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9
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Li H, Hua W, Wang Z, Liu A, Jiang J, Luo Y. Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine. J Phys Chem A 2020; 124:2215-2224. [PMID: 32091898 DOI: 10.1021/acs.jpca.9b10756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.
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Affiliation(s)
- Hongbao Li
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weijie Hua
- Department of Applied Physics, School of Science, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Zhiqiang Wang
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China
| | - Axue Liu
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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10
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Crnković A, Vargas-Rodriguez O, Söll D. Plasticity and Constraints of tRNA Aminoacylation Define Directed Evolution of Aminoacyl-tRNA Synthetases. Int J Mol Sci 2019; 20:ijms20092294. [PMID: 31075874 PMCID: PMC6540133 DOI: 10.3390/ijms20092294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic incorporation of noncanonical amino acids (ncAAs) has become a powerful tool to enhance existing functions or introduce new ones into proteins through expanded chemistry. This technology relies on the process of nonsense suppression, which is made possible by directing aminoacyl-tRNA synthetases (aaRSs) to attach an ncAA onto a cognate suppressor tRNA. However, different mechanisms govern aaRS specificity toward its natural amino acid (AA) substrate and hinder the engineering of aaRSs for applications beyond the incorporation of a single l-α-AA. Directed evolution of aaRSs therefore faces two interlinked challenges: the removal of the affinity for cognate AA and improvement of ncAA acylation. Here we review aspects of AA recognition that directly influence the feasibility and success of aaRS engineering toward d- and β-AAs incorporation into proteins in vivo. Emerging directed evolution methods are described and evaluated on the basis of aaRS active site plasticity and its inherent constraints.
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Affiliation(s)
- Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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11
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Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion. Emerg Top Life Sci 2018; 2:607-618. [PMID: 33525836 DOI: 10.1042/etls20180094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 11/17/2022]
Abstract
The 22nd amino acid discovered to be directly encoded, pyrrolysine, is specified by UAG. Until recently, pyrrolysine was only known to be present in archaea from a methanogenic lineage (Methanosarcinales), where it is important in enzymes catalysing anoxic methylamines metabolism, and a few anaerobic bacteria. Relatively new discoveries have revealed wider presence in archaea, deepened functional understanding, shown remarkable carbon source-dependent expression of expanded decoding and extended exploitation of the pyrrolysine machinery for synthetic code expansion. At the same time, other studies have shown the presence of pyrrolysine-containing archaea in the human gut and this has prompted health considerations. The article reviews our knowledge of this fascinating exception to the 'standard' genetic code.
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12
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Asayama S, Nagashima K, Negishi Y, Kawakami H. Byproduct-Free Intact Modification of Insulin by Cholesterol End-Modified Poly(ethylene glycol) for in Vivo Protein Delivery. Bioconjug Chem 2017; 29:67-73. [DOI: 10.1021/acs.bioconjchem.7b00593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shoichiro Asayama
- Department
of Applied Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Kana Nagashima
- Department
of Applied Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Yoichi Negishi
- School
of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Hiroyoshi Kawakami
- Department
of Applied Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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13
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Asayama S, Nagashima K, Kawakami H. Facile Method of Protein PEGylation by a Mono-Ion Complex. ACS OMEGA 2017; 2:2382-2386. [PMID: 31457587 PMCID: PMC6641148 DOI: 10.1021/acsomega.7b00462] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
Diethylaminoethyl end-modified poly(ethylene glycol) (DEAE-PEG) has been synthesized for the noncovalent PEGylation of proteins. The resulting DEAE-PEG and catalase formed an ion complex, that is, a protein mono-ion complex (MIC). The formation of the protein MIC was confirmed by native poly(acrylamide) gel electrophoresis and gel-filtration chromatography. The resulting catalase MIC preserved the catalase activity, confirmed by monitoring the O2 concentration with a Clark-type oxygen electrode, in spite of MIC formation. The catalase activity of the protein MIC was protected in the presence of a protease, trypsin, or 10% fetal bovine serum. Furthermore, less change in the circular dichroism measurements of the catalase MIC was observed as compared to those of a catalase-PEG conjugate (covalent PEGylation), suggesting less influence of the protein conformation. Consequently, the formation of the MIC is considered to be a facile method of protein PEGylation.
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14
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Mukai T, Crnković A, Umehara T, Ivanova NN, Kyrpides NC, Söll D. RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea. mBio 2017; 8:e00561-17. [PMID: 28487430 PMCID: PMC5424206 DOI: 10.1128/mbio.00561-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/17/2022] Open
Abstract
The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNACys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria ("Candidatus Parcubacteria" and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNACys species with cysteine in vitro Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.IMPORTANCE Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Takuya Umehara
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika-ku, Tokyo, Japan
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
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Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
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16
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Crnković A, Suzuki T, Söll D, Reynolds NM. Pyrrolysyl-tRNA synthetase, an aminoacyl-tRNA synthetase for genetic code expansion. CROAT CHEM ACTA 2016; 89:163-174. [PMID: 28239189 PMCID: PMC5321558 DOI: 10.5562/cca2825] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genetic code expansion (GCE) has become a central topic of synthetic biology. GCE relies on engineered aminoacyl-tRNA synthetases (aaRSs) and a cognate tRNA species to allow codon reassignment by co-translational insertion of non-canonical amino acids (ncAAs) into proteins. Introduction of such amino acids increases the chemical diversity of recombinant proteins endowing them with novel properties. Such proteins serve in sophisticated biochemical and biophysical studies both in vitro and in vivo, they may become unique biomaterials or therapeutic agents, and they afford metabolic dependence of genetically modified organisms for biocontainment purposes. In the Methanosarcinaceae the incorporation of the 22nd genetically encoded amino acid, pyrrolysine (Pyl), is facilitated by pyrrolysyl-tRNA synthetase (PylRS) and the cognate UAG-recognizing tRNAPyl. This unique aaRS•tRNA pair functions as an orthogonal translation system (OTS) in most model organisms. The facile directed evolution of the large PylRS active site to accommodate many ncAAs, and the enzyme's anticodon-blind specific recognition of the cognate tRNAPyl make this system highly amenable for GCE purposes. The remarkable polyspecificity of PylRS has been exploited to incorporate >100 different ncAAs into proteins. Here we review the Pyl-OT system and selected GCE applications to examine the properties of an effective OTS.
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Affiliation(s)
- Ana Crnković
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Tateki Suzuki
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Noah M. Reynolds
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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17
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Abstract
Antibody conjugates are important in many areas of medicine and biological research, and antibody-drug conjugates (ADCs) are becoming an important next generation class of therapeutics for cancer treatment. Early conjugation technologies relied upon random conjugation to multiple amino acid side chains, resulting in heterogeneous mixtures of labeled antibody. Recent studies, however, strongly support the notion that site-specific conjugation produces a homogeneous population of antibody conjugates with improved pharmacologic properties over randomly coupled molecules. Genetically incorporated unnatural amino acids (uAAs) allow unique orthogonal coupling strategies compared to those used for the 20 naturally occurring amino acids. Thus, uAAs provide a novel paradigm for creation of next generation ADCs. Additionally, uAA-based site-specific conjugation could also empower creation of additional multifunctional conjugates important as biopharmaceuticals, diagnostics, or reagents.
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Affiliation(s)
- Trevor J Hallam
- †Sutro Biopharma, 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Erik Wold
- ‡The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Wahl
- §Ambrx, Inc. 10975 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vaughn V Smider
- ‡The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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18
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Abstract
Antibody-drug conjugates are an important and emerging drug class for the treatment of cancer. Recent evidence strongly suggests that site-specific drug conjugation results in a homogenous population of molecules with more favorable activity and pharmacokinetic properties than randomly conjugated antibodies. Unnatural amino acids (uAAs) can be incorporated in recombinant proteins to enable unique orthogonal chemistries in comparison to the side chains of the natural 20 amino acids. Thus, uAAs present a novel platform for which to create next-generation antibody-drug conjugates. Furthermore, site-specific conjugation through uAAs can also enpower unique small molecule, bispecific, multispecific and other conjugates that could be important constructs for therapeutics, diagnostics and research reagents. Here, we review the progress in uAA incorporation and conjugate construction through both cell-based and -free approaches.
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19
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Ehrlich M, Gattner MJ, Viverge B, Bretzler J, Eisen D, Stadlmeier M, Vrabel M, Carell T. Orchestrating the Biosynthesis of an Unnatural Pyrrolysine Amino Acid for Its Direct Incorporation into Proteins Inside Living Cells. Chemistry 2015; 21:7701-4. [DOI: 10.1002/chem.201500971] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 12/31/2022]
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20
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Reducing the genetic code induces massive rearrangement of the proteome. Proc Natl Acad Sci U S A 2014; 111:17206-11. [PMID: 25404328 DOI: 10.1073/pnas.1420193111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Expanding the genetic code is an important aim of synthetic biology, but some organisms developed naturally expanded genetic codes long ago over the course of evolution. Less than 1% of all sequenced genomes encode an operon that reassigns the stop codon UAG to pyrrolysine (Pyl), a genetic code variant that results from the biosynthesis of Pyl-tRNA(Pyl). To understand the selective advantage of genetically encoding more than 20 amino acids, we constructed a markerless tRNA(Pyl) deletion strain of Methanosarcina acetivorans (ΔpylT) that cannot decode UAG as Pyl or grow on trimethylamine. Phenotypic defects in the ΔpylT strain were evident in minimal medium containing methanol. Proteomic analyses of wild type (WT) M. acetivorans and ΔpylT cells identified 841 proteins from >7,000 significant peptides detected by MS/MS. Protein production from UAG-containing mRNAs was verified for 19 proteins. Translation of UAG codons was verified by MS/MS for eight proteins, including identification of a Pyl residue in PylB, which catalyzes the first step of Pyl biosynthesis. Deletion of tRNA(Pyl) globally altered the proteome, leading to >300 differentially abundant proteins. Reduction of the genetic code from 21 to 20 amino acids led to significant down-regulation in translation initiation factors, amino acid metabolism, and methanogenesis from methanol, which was offset by a compensatory (100-fold) up-regulation in dimethyl sulfide metabolic enzymes. The data show how a natural proteome adapts to genetic code reduction and indicate that the selective value of an expanded genetic code is related to carbon source range and metabolic efficiency.
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21
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PEG — A versatile conjugating ligand for drugs and drug delivery systems. J Control Release 2014; 192:67-81. [DOI: 10.1016/j.jconrel.2014.06.046] [Citation(s) in RCA: 415] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 01/07/2023]
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22
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Meng L, Wang Z, Zhang J, Zhou M, Wu W. Low Energy Conformations and Gas-Phase Acidity and Basicity of Pyrrolysine. J Phys Chem A 2014; 118:7085-95. [DOI: 10.1021/jp503444h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lingbiao Meng
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Zhuo Wang
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Jicheng Zhang
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Minjie Zhou
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
| | - Weidong Wu
- Research Center of Laser
Fusion, China Academy of Engineering Physics, Mianyang 621900, China
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23
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Quitterer F, Beck P, Bacher A, Groll M. Pyrrolysin-Synthase (PylD) katalysiert die Bildung von Pyrrolin- und Tetrahydropyridinringen in Aminosäuren. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Quitterer F, Beck P, Bacher A, Groll M. The formation of pyrroline and tetrahydropyridine rings in amino acids catalyzed by pyrrolysine synthase (PylD). Angew Chem Int Ed Engl 2014; 53:8150-3. [PMID: 24916332 DOI: 10.1002/anie.201402595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Indexed: 11/11/2022]
Abstract
The dehydrogenase PylD catalyzes the ultimate step of the pyrrolysine pathway by converting the isopeptide L-lysine-Nε-3R-methyl-D-ornithine to the 22nd proteinogenic amino acid. In this study, we demonstrate how PylD can be harnessed to oxidize various isopeptides to novel amino acids by combining chemical synthesis with enzyme kinetics and X-ray crystallography. The data enable a detailed description of the PylD reaction trajectory for the biosynthesis of pyrroline and tetrahydropyridine rings as constituents of pyrrolysine analogues.
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Affiliation(s)
- Felix Quitterer
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching (Germany)
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25
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Wan W, Tharp JM, Liu WR. Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1059-70. [PMID: 24631543 DOI: 10.1016/j.bbapap.2014.03.002] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/01/2014] [Accepted: 03/05/2014] [Indexed: 11/16/2022]
Abstract
The genetic incorporation of the 22nd proteinogenic amino acid, pyrrolysine (Pyl) at amber codon is achieved by the action of pyrrolysyl-tRNA synthetase (PylRS) together with its cognate tRNA(Pyl). Unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate α-amine, and low selectivity toward the anticodon of tRNA(Pyl). These unique but ordinary features of PylRS as an aminoacyl-tRNA synthetase allow the Pyl incorporation machinery to be easily engineered for the genetic incorporation of more than 100 non-canonical amino acids (NCAAs) or α-hydroxy acids into proteins at amber codon and the reassignment of other codons such as ochre UAA, opal UGA, and four-base AGGA codons to code NCAAs.
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Affiliation(s)
- Wei Wan
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA.
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26
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Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:374146. [PMID: 24669202 PMCID: PMC3941956 DOI: 10.1155/2014/374146] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/19/2013] [Indexed: 02/06/2023]
Abstract
Pyrrolysine (Pyl), the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber tRNAPyl with an imperfect anticodon stem and a shortened tRNAPyl synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.
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27
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Krishnakumar R, Ling J. Experimental challenges of sense codon reassignment: an innovative approach to genetic code expansion. FEBS Lett 2013; 588:383-8. [PMID: 24333334 DOI: 10.1016/j.febslet.2013.11.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/19/2013] [Accepted: 11/27/2013] [Indexed: 10/25/2022]
Abstract
The addition of new and versatile chemical and biological properties to proteins pursued through incorporation of non-canonical amino acids is at present primarily achieved by stop codon suppression. However, it is critical to find new "blank" codons to increase the variety and efficiency of such insertions, thereby taking 'sense codon recoding' to center stage in the field of genetic code expansion. Current thought optimistically suggests the use of the pyrrolysine system coupled with re-synthesis of genomic information towards achieving sense codon reassignment. Upon review of the serious experimental challenges reported in recent studies, we propose that success in this area will depend on the re-synthesis of genomes, but also on 'rewiring' the mechanism of protein synthesis and of its quality control.
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Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD 20850, USA.
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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28
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Krzycki JA. The path of lysine to pyrrolysine. Curr Opin Chem Biol 2013; 17:619-25. [PMID: 23856058 DOI: 10.1016/j.cbpa.2013.06.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/12/2013] [Accepted: 06/17/2013] [Indexed: 01/05/2023]
Abstract
Pyrrolysine is the 22nd genetically encoded amino acid. For many years, its biosynthesis has been primarily a matter for conjecture. Recently, a pathway for the synthesis of pyrrolysine from two molecules of lysine was outlined in which a radical SAM enzyme acts as a lysine mutase to generate a methylated ornithine from lysine, which is then ligated to form an amide with the ɛ-amine of a second lysine. Oxidation of the isopeptide gives rise to pyrrolysine. Mechanisms have been proposed for both the mutase and the ligase, and structures now exist for each, setting the stage for a more detailed understanding of how pyrrolysine is synthesized and functions in bacteria and archaea.
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Affiliation(s)
- Joseph A Krzycki
- Department of Microbiology, 484 West 12th Avenue, Columbus, OH 43210, United States.
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29
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Han MY, Wang HZ, An WK, Jia JY, Ma BC, Zhang Y, Wang W. A concise synthesis of L-pyrrolysine. Chemistry 2013; 19:8078-81. [PMID: 23649505 DOI: 10.1002/chem.201300403] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Indexed: 11/05/2022]
Abstract
Organocatalysis: A concise synthesis of L-pyrrolysine has been accomplished in six steps from simple starting materials. The facile synthetic strategy relies on an organocatalytic Michael addition, an efficient amide coupling, and a challenging method for the imine-bond construction.
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Affiliation(s)
- Man-Yi Han
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, PR China
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30
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Wu IL, Patterson MA, Carpenter Desai HE, Mehl RA, Giorgi G, Conticello VP. Multiple Site-Selective Insertions of Noncanonical Amino Acids into Sequence-Repetitive Polypeptides. Chembiochem 2013; 14:968-78. [DOI: 10.1002/cbic.201300069] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 11/11/2022]
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31
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Abstract
Despite the fact that the genetic code is known to vary between organisms in rare cases, it is believed that in the lifetime of a single cell the code is stable. We found Acetohalobium arabaticum cells grown on pyruvate genetically encode 20 amino acids, but in the presence of trimethylamine (TMA), A. arabaticum dynamically expands its genetic code to 21 amino acids including pyrrolysine (Pyl). A. arabaticum is the only known organism that modulates the size of its genetic code in response to its environment and energy source. The gene cassette pylTSBCD, required to biosynthesize and genetically encode UAG codons as Pyl, is present in the genomes of 24 anaerobic archaea and bacteria. Unlike archaeal Pyl-decoding organisms that constitutively encode Pyl, we observed that A. arabaticum controls Pyl encoding by down-regulating transcription of the entire Pyl operon under growth conditions lacking TMA, to the point where no detectable Pyl-tRNA(Pyl) is made in vivo. Pyl-decoding archaea adapted to an expanded genetic code by minimizing TAG codon frequency to typically ~5% of ORFs, whereas Pyl-decoding bacteria (~20% of ORFs contain in-frame TAGs) regulate Pyl-tRNA(Pyl) formation and translation of UAG by transcriptional deactivation of genes in the Pyl operon. We further demonstrate that Pyl encoding occurs in a bacterium that naturally encodes the Pyl operon, and identified Pyl residues by mass spectrometry in A. arabaticum proteins including two methylamine methyltransferases.
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32
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O'Donoghue P, Prat L, Heinemann IU, Ling J, Odoi K, Liu WR, Söll D. Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion. FEBS Lett 2012; 586:3931-7. [PMID: 23036644 DOI: 10.1016/j.febslet.2012.09.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
Abstract
Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to 'statistical protein' that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNA(Pyl) orthogonal pair cannot completely outcompete contamination by natural amino acids.
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Affiliation(s)
- Patrick O'Donoghue
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States
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33
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Translational recoding in archaea. Extremophiles 2012; 16:793-803. [DOI: 10.1007/s00792-012-0482-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/09/2012] [Indexed: 12/31/2022]
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Quitterer F, List A, Beck P, Bacher A, Groll M. Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5Å resolution. J Mol Biol 2012; 424:270-82. [PMID: 22985965 DOI: 10.1016/j.jmb.2012.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/21/2012] [Accepted: 09/05/2012] [Indexed: 11/25/2022]
Abstract
The second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by PylC that forms the pseudopeptide L-lysine-N(ε)-3R-methyl-D-ornithine. Here, we present six crystal structures of the monomeric active ligase in complex with substrates, reaction intermediates, and products including ATP, the non-hydrolyzable ATP analogue 5'-adenylyl-β-γ-imidodiphosphate, ADP, D-ornithine (D-Orn), L-lysine (Lys), phosphorylated D-Orn, L-lysine-N(ε)-D-ornithine, inorganic phosphate, carbonate, and Mg(2+). The overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes; however, there exist unique structural and functional features for a topological control of successive substrate entry and product release. Furthermore, the presented high-resolution structures provide detailed insights into the reaction mechanism of isopeptide bond formation starting with phosphorylation of D-Orn by transfer of a phosphate moiety from activated ATP. The binding of Lys to the enzyme complex is then followed by an S(N)2 reaction resulting in L-lysine-N(ε)-D-ornithine and inorganic phosphate. Surprisingly, PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability as shown by mutagenesis.
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Affiliation(s)
- Felix Quitterer
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
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35
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Jiang R, Krzycki JA. PylSn and the homologous N-terminal domain of pyrrolysyl-tRNA synthetase bind the tRNA that is essential for the genetic encoding of pyrrolysine. J Biol Chem 2012; 287:32738-46. [PMID: 22851181 DOI: 10.1074/jbc.m112.396754] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyrrolysine is represented by an amber codon in genes encoding proteins such as the methylamine methyltransferases present in some Archaea and Bacteria. Pyrrolysyl-tRNA synthetase (PylRS) attaches pyrrolysine to the amber-suppressing tRNA(Pyl). Archaeal PylRS, encoded by pylS, has a catalytic C-terminal domain but an N-terminal region of unknown function and structure. In Bacteria, homologs of the N- and C-terminal regions of archaeal PylRS are respectively encoded by pylSn and pylSc. We show here that wild type PylS from Methanosarcina barkeri and PylSn from Desulfitobacterium hafniense bind tRNA(Pyl) in EMSA with apparent K(d) values of 0.12 and 0.13 μM, respectively. Truncation of the N-terminal region of PylS eliminated detectable tRNA(Pyl) binding as measured by EMSA, but not catalytic activity. A chimeric protein with PylSn fused to the N terminus of truncated PylS regained EMSA-detectable tRNA(Pyl) binding. PylSn did not bind other D. hafniense tRNAs, nor did the competition by the Escherichia coli tRNA pool interfere with tRNA(Pyl) binding. Further indicating the specificity of PylSn interaction with tRNA(Pyl), substitutions of conserved residues in tRNA(Pyl) in the variable loop, D stem, and T stem and loop had significant impact in binding, whereas those having base changes in the acceptor stem or anticodon stem and loop still retained the ability to complex with PylSn. PylSn and the N terminus of PylS comprise the protein superfamily TIGR03129. The members of this family are not similar to any known RNA-binding protein, but our results suggest their common function involves specific binding of tRNA(Pyl).
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Affiliation(s)
- Ruisheng Jiang
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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Abstract
An efficient asymmetric synthesis of the 22nd amino acid L-pyrrolysine has been accomplished. The key stereogenic centers were installed by an asymmetric conjugate addition reaction. A Staudinger/aza-Wittig cyclization was used to form the acid-sensitive pyrroline ring. Pyrrolysine was synthesized in 13 steps in 20% overall yield.
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Affiliation(s)
- Margaret L. Wong
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706
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37
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Pasut G, Veronese FM. State of the art in PEGylation: the great versatility achieved after forty years of research. J Control Release 2011; 161:461-72. [PMID: 22094104 DOI: 10.1016/j.jconrel.2011.10.037] [Citation(s) in RCA: 544] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/27/2011] [Accepted: 10/31/2011] [Indexed: 12/15/2022]
Abstract
In the recent years, protein PEGylation has become an established and highly refined technology by moving forward from initial simple random coupling approaches based on conjugation at the level of lysine ε-amino group. Nevertheless, amino PEGylation is still yielding important conjugates, currently in clinical practice, where the degree of homogeneity was improved by optimizing the reaction conditions and implementing the purification processes. However, the current research is mainly focused on methods of site-selective PEGylation that allow the obtainment of a single isomer, thus highly increasing the degree of homogeneity and the preservation of bioactivity. Protein N-terminus and free cysteines were the first sites exploited for selective PEGylation but currently further positions can be addressed thanks to approaches like bridging PEGylation (disulphide bridges), enzymatic PEGylation (glutamines and C-terminus) and glycoPEGylation (sites of O- and N-glycosylation or the glycans of a glycoprotein). Furthermore, by combining the tools of genetic engineering with specific PEGylation approaches, the polymer can be basically coupled at any position on the protein surface, owing to the substitution of a properly chosen amino acid in the sequence with a natural or unnatural amino acid bearing an orthogonal reactive group. On the other hand, PEGylation has not achieved the same success in the delivery of small drugs, despite the large interest and several studies in this field. Targeted conjugates and PEGs for combination therapy might represent the promising answers for the so far unmet needs of PEG as carrier of small drugs. This review presents a thorough panorama of recent advances in the field of PEGylation.
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Affiliation(s)
- Gianfranco Pasut
- Department of Pharmaceutical Sciences, University of Padua, Via F. Marzolo 5, 35131 Padua, Italy.
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38
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Antonczak AK, Morris J, Tippmann EM. Advances in the mechanism and understanding of site-selective noncanonical amino acid incorporation. Curr Opin Struct Biol 2011; 21:481-7. [DOI: 10.1016/j.sbi.2011.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 04/28/2011] [Indexed: 01/01/2023]
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39
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Hertweck C. Biosynthese und Einbau von Pyrrolysin, der 22. genetisch codierten Aminosäure. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103769] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Hertweck C. Biosynthesis and Charging of Pyrrolysine, the 22nd Genetically Encoded Amino Acid. Angew Chem Int Ed Engl 2011; 50:9540-1. [DOI: 10.1002/anie.201103769] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Indexed: 11/08/2022]
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41
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Fekner T, Chan MK. Hidden in Plain Sight: The Biosynthetic Source of Pyrrolysine Revealed. Chembiochem 2011; 12:2117-9. [DOI: 10.1002/cbic.201100374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Indexed: 11/12/2022]
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42
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Beta-glucuronidase as a sensitive and versatile reporter in actinomycetes. Appl Environ Microbiol 2011; 77:5370-83. [PMID: 21685164 DOI: 10.1128/aem.00434-11] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we describe a versatile and sensitive reporter system for actinomycetes that is based on gusA, which encodes the β-glucuronidase enzyme. A series of gusA-containing transcriptional and translational fusion vectors were constructed and utilized to study the regulatory cascade of the phenalinolactone biosynthetic gene cluster. Furthermore, these vectors were used to study the efficiency of translation initiation at the ATG, GTG, TTG, and CTG start codons. Surprisingly, constructs using a TTG start codon showed the best activity, whereas those using ATG or GTG were approximately one-half or one-third as active, respectively. The CTG fusion showed only 5% of the activity of the TTG fusion. A suicide vector, pKGLP2, carrying gusA in its backbone was used to visually detect merodiploid formation and resolution, making gene targeting in actinomycetes much faster and easier. Three regulatory genes, plaR1, plaR2, and plaR3, involved in phenalinolactone biosynthesis were efficiently replaced with an apramycin resistance marker using this system. Finally, we expanded the genetic code of actinomycetes by introducing the nonproteinogenic amino acid N-epsilon-cyclopentyloxycarbonyl-l-lysine with the GusA protein as a reporter.
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Chen Y, Apolinario E, Brachova L, Kelman Z, Li Z, Nikolau BJ, Showman L, Sowers K, Orban J. A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans. BMC Genomics 2011; 12 Suppl 1:S7. [PMID: 21810209 PMCID: PMC3223730 DOI: 10.1186/1471-2164-12-s1-s7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Correct annotation of function is essential if one is to take full advantage of the vast amounts of genomic sequence data. The accuracy of sequence-based functional annotations is often variable, particularly if the sequence homology to a known function is low. Indeed recent work has shown that even proteins with very high sequence identity can have different folds and functions, and therefore caution is needed in assigning functions by sequence homology in the absence of experimental validation. Experimental methods are therefore needed to efficiently evaluate annotations in a way that complements current high throughput technologies. Here, we describe the use of nuclear magnetic resonance (NMR)-based ligand screening as a tool for testing functional assignments of putative enzymes that may be of variable reliability. Results The target genes for this study are putative enzymes from the methanogenic archaeon Methanosarcina acetivorans (MA) that have been selected after manual genome re-annotation and demonstrate detectable in vivo expression at the level of the transcriptome. The experimental approach begins with heterologous E. coli expression and purification of individual MA gene products. An NMR-based ligand screen of the purified protein then identifies possible substrates or products from a library of candidate compounds chosen from the putative pathway and other related pathways. These data are used to determine if the current sequence-based annotation is likely to be correct. For a number of case studies, additional experiments (such as in vivo genetic complementation) were performed to determine function so that the reliability of the NMR screen could be independently assessed. Conclusions In all examples studied, the NMR screen was indicative of whether the functional annotation was correct. Thus, the case studies described demonstrate that NMR-based ligand screening is an effective and rapid tool for confirming or negating the annotated gene function of putative enzymes. In particular, no protein-specific assay needs to be developed, which makes the approach broadly applicable for validating putative functions using an automated pipeline strategy.
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Affiliation(s)
- Yihong Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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Site-specific protein modifications through pyrroline-carboxy-lysine residues. Proc Natl Acad Sci U S A 2011; 108:10437-42. [PMID: 21670250 DOI: 10.1073/pnas.1105197108] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pyrroline-carboxy-lysine (Pcl) is a demethylated form of pyrrolysine that is generated by the pyrrolysine biosynthetic enzymes when the growth media is supplemented with D-ornithine. Pcl is readily incorporated by the unmodified pyrrolysyl-tRNA/tRNA synthetase pair into proteins expressed in Escherichia coli and in mammalian cells. Here, we describe a broadly applicable conjugation chemistry that is specific for Pcl and orthogonal to all other reactive groups on proteins. The reaction of Pcl with 2-amino-benzaldehyde or 2-amino-acetophenone reagents proceeds to near completion at neutral pH with high efficiency. We illustrate the versatility of the chemistry by conjugating Pcl proteins with poly(ethylene glycol)s, peptides, oligosaccharides, oligonucleotides, fluorescence, and biotin labels and other small molecules. Because Pcl is genetically encoded by TAG codons, this conjugation chemistry enables enhancements of the pharmacology and functionality of proteins through site-specific conjugation.
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The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 2011; 471:647-50. [PMID: 21455182 PMCID: PMC3070376 DOI: 10.1038/nature09918] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 02/09/2011] [Indexed: 11/24/2022]
Abstract
Pyrrolysine, the 22nd amino acid to be found in the natural genetic code1–4, is necessary for all known pathways of methane formation from methylamines5,6. The residue is comprised of a methylated pyrroline carboxylate in amide linkage to the ε-amino group of L-lysine2,7,8. The three different methyltransferases that initiate methanogenesis from different methylamines9–11 have genes with an in-frame amber codon12,13 translated as pyrrolysine2,7,8. E. coli transformed with pylTSBCD from methanogenic Archaea can incorporate endogenously biosynthesized pyrrolysine into protein14. The decoding of UAG as pyrrolysine requires pylT1,6 which produces tRNAPyl (also called tRNACUA), and pylS1 encoding a pyrrolysyl-tRNA synthetase4,15,16. The pylBCD genes1 are each required for tRNA-independent pyrrolysine synthesis14. Pyrrolysine has been the last remaining genetically encoded amino acid with an unknown biosynthetic pathway. Here, we provide genetic and mass spectroscopic evidence for a pylBCD-dependent pathway in which pyrrolysine arises from two lysines. We show that a new UAG encoded residue, desmethylpyrrolysine, is made from lysine and exogenous D-ornithine in a pylC, then a pylD, dependent process, but is not further converted to pyrrolysine. These results indicate that the radical S-adenosyl-methionine (SAM) protein PylB mediates a lysine mutase reaction producing 3-methylornithine, which is then ligated to a second molecule of lysine by PylC before oxidation by PylD results in pyrrolysine. The discovery of lysine as sole precursor to pyrrolysine will further inform discussions of the evolution the genetic code and amino acid biosynthetic pathways, while intermediates of the pathway may provide new avenues by which the pyl system may be exploited for production of recombinant proteins with useful modified residues.
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47
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Gaston MA, Jiang R, Krzycki JA. Functional context, biosynthesis, and genetic encoding of pyrrolysine. Curr Opin Microbiol 2011; 14:342-9. [PMID: 21550296 DOI: 10.1016/j.mib.2011.04.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 04/01/2011] [Accepted: 04/06/2011] [Indexed: 01/14/2023]
Abstract
In Methanosarcina spp., amber codons in methylamine methyltransferase genes are translated as the 22nd amino acid, pyrrolysine. The responsible pyl genes plus amber-codon containing methyltransferase genes have been identified in four archaeal and five bacterial genera, including one human pathogen. In Escherichia coli, the recombinant pylBCD gene products biosynthesize pyrrolysine from two molecules of lysine and the pylTS gene products direct pyrrolysine incorporation into protein. In the proposed biosynthetic pathway, PylB forms methylornithine from lysine, which is joined to another lysine by PylC, and oxidized to pyrrolysine by PylD. Structures of the catalytic domain of pyrrolysyl-tRNA synthetase (archaeal PylS or bacterial PylSc) revealed binding sites for tRNAPyl and pyrrolysine. PylS and tRNAPyl are now being exploited as an orthogonal pair in recombinant systems for introduction of useful modified amino acids into proteins.
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Affiliation(s)
- Marsha A Gaston
- Department of Microbiology, 484 West 12th Avenue, The Ohio State University, Columbus, OH 43210, United States
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Cellitti SE, Ou W, Chiu HP, Grünewald J, Jones DH, Hao X, Fan Q, Quinn LL, Ng K, Anfora AT, Lesley SA, Uno T, Brock A, Geierstanger BH. D-Ornithine coopts pyrrolysine biosynthesis to make and insert pyrroline-carboxy-lysine. Nat Chem Biol 2011; 7:528-30. [DOI: 10.1038/nchembio.586] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 04/19/2011] [Indexed: 11/09/2022]
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The pyrrolysine translational machinery as a genetic-code expansion tool. Curr Opin Chem Biol 2011; 15:387-91. [PMID: 21507706 DOI: 10.1016/j.cbpa.2011.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 03/14/2011] [Accepted: 03/15/2011] [Indexed: 11/20/2022]
Abstract
The discovery of pyrrolysine not only expanded the set of the known proteinogenic amino acids but also revealed unusual features of its encoding mechanism. The engagement of a canonical stop codon and a unique aminoacyl-tRNA synthetase-tRNA pair that can be used to accommodate a broad range of unnatural amino acids while maintaining strict orthogonality in a variety of prokaryotic and eukaryotic expression systems has proven an invaluable combination. Within a few years since its properties were elucidated, the pyrrolysine translational machinery has become a popular choice for the synthesis of recombinant proteins bearing a wide variety of otherwise hard-to-introduce functional groups. It is also central to the development of new synthetic strategies that rely on stop-codon suppression.
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Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010. [PMID: 20847933 PMCID: PMC2933860 DOI: 10.1155/2010/453642] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/13/2010] [Indexed: 01/21/2023]
Abstract
Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism.
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