1
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [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: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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Achatz S, Skerra A. Comparative genome analysis of three classical E. coli cloning strains designed for blue/white selection: JM83, JM109 and XL1-Blue. FEBS Open Bio 2024; 14:888-905. [PMID: 38726771 PMCID: PMC11148124 DOI: 10.1002/2211-5463.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 06/05/2024] Open
Abstract
The development of the Escherichia coli K-12 laboratory strains JM83, JM109 and XL1-Blue was instrumental in early gene technology. We report the comprehensive genome sequence analysis of JM83 and XL1-Blue using Illumina and Oxford Nanopore technologies and a comparison with both the wild-type sequence (MG1655) and the genome of JM109 deposited at GenBank. Our investigation provides insight into the way how the genomic background that allows blue/white colony selection-by complementing a functionally inactive ω-fragment of β-galactosidase (LacZ) with its α-peptide encoded on the cloning vector-has been implemented independently in these three strains using classical bacterial genetics. In fact, their comparative analysis reveals recurrent motifs: (i) inactivation of the native enzyme via large deletions of chromosomal regions encompassing the lac locus, or a chemically induced frameshift deletion at the beginning of the lacZ cistron, and (ii) utilization of a defective prophage (ϕ80), or an F'-plasmid, to provide the lacZ∆M15 allele encoding its ω-fragment. While the genetic manipulations of the E. coli strains involved repeated use of mobile genetic elements as well as harsh chemical or physical mutagenesis, the individual modified traits appear remarkably stable as they can be found even in distantly related laboratory strains, beyond those investigated here. Our detailed characterization at the genome sequence level not only offers clues about the mechanisms of classical gene transduction and transposition but should also guide the future fine-tuning of E. coli strains for gene cloning and protein expression, including phage display techniques, utilizing advanced tools for site-specific genome engineering.
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Affiliation(s)
- Stefan Achatz
- Lehrstuhl für Biologische ChemieTechnische Universität MünchenFreisingGermany
| | - Arne Skerra
- Lehrstuhl für Biologische ChemieTechnische Universität MünchenFreisingGermany
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3
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Romero Romero ML, Poehls J, Kirilenko A, Richter D, Jumel T, Shevchenko A, Toth-Petroczy A. Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough. Nat Commun 2024; 15:4446. [PMID: 38789441 PMCID: PMC11126739 DOI: 10.1038/s41467-024-48387-x] [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: 02/22/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Stop codon readthrough events give rise to longer proteins, which may alter the protein's function, thereby generating short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon readthrough events, we designed a library of reporters. We introduced premature stop codons into mScarlet, which enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon readthrough may occur at rates as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon readthrough events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon readthrough. The RNA polymerase was more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon readthrough by mass spectrometry revealed that temperature regulated the expression of cryptic sequences generated by stop codon readthrough in E. coli. Overall, our findings suggest that the environment affects the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Anastasiia Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Tobias Jumel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany.
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4
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Girardo B, Schopfer LM, Yue Y, Lockridge O, Larson MA. Polyaminated, acetylated and stop codon readthrough of recombinant Francisella tularensis universal stress protein in Escherichia coli. PLoS One 2024; 19:e0299701. [PMID: 38683788 PMCID: PMC11057771 DOI: 10.1371/journal.pone.0299701] [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] [Received: 11/09/2023] [Accepted: 02/14/2024] [Indexed: 05/02/2024] Open
Abstract
Recombinant Francisella tularensis universal stress protein with a C-terminal histidine-tag (rUsp/His6) was expressed in Escherichia coli. Endogenous F. tularensis Usp has a predicted molecular mass of 30 kDa, but rUsp/His6 had an apparent molecular weight of 33 kDa based on Western blot analyses. To determine the source of the higher molecular weight for rUsp/His6, post translational modifications were examined. Tryptic peptides of purified rUsp/His6 were subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS) and fragmentation spectra were searched for acetylated lysines and polyaminated glutamines. Of the 24 lysines in rUsp/His6, 10 were acetylated (K63, K68, K72, K129, K175, K201, K208, K212, K233, and K238) and three of the four glutamines had putrescine, spermidine and spermine adducts (Q55, Q60 and Q267). The level of post-translational modification was substoichiometric, eliminating the possibility that these modifications were the sole contributor to the 3 kDa extra mass of rUsp/His6. LC-MS/MS revealed that stop codon readthrough had occurred resulting in the unexpected addition of 20 extra amino acids at the C-terminus of rUsp/His6, after the histidine tag. Further, the finding of polyaminated glutamines in rUsp/His6 indicated that E. coli is capable of transglutaminase activity.
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Affiliation(s)
- Benjamin Girardo
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Lawrence M. Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Yinshi Yue
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Oksana Lockridge
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Marilynn A. Larson
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
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5
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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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6
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Bednar RM, Karplus PA, Mehl RA. Site-specific dual encoding and labeling of proteins via genetic code expansion. Cell Chem Biol 2023; 30:343-361. [PMID: 36977415 PMCID: PMC10764108 DOI: 10.1016/j.chembiol.2023.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.
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Affiliation(s)
- Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA.
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7
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Lyu Z, Wilson C, Ling J. Translational Fidelity during Bacterial Stresses and Host Interactions. Pathogens 2023; 12:383. [PMID: 36986305 PMCID: PMC10057733 DOI: 10.3390/pathogens12030383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Translational fidelity refers to accuracy during protein synthesis and is maintained in all three domains of life. Translational errors occur at base levels during normal conditions and may rise due to mutations or stress conditions. In this article, we review our current understanding of how translational fidelity is perturbed by various environmental stresses that bacterial pathogens encounter during host interactions. We discuss how oxidative stress, metabolic stresses, and antibiotics affect various types of translational errors and the resulting effects on stress adaption and fitness. We also discuss the roles of translational fidelity during pathogen-host interactions and the underlying mechanisms. Many of the studies covered in this review will be based on work with Salmonella enterica and Escherichia coli, but other bacterial pathogens will also be discussed.
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Affiliation(s)
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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8
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Santos FB, Del-Bem LE. The Evolution of tRNA Copy Number and Repertoire in Cellular Life. Genes (Basel) 2022; 14:27. [PMID: 36672768 PMCID: PMC9858662 DOI: 10.3390/genes14010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
tRNAs are universal decoders that bridge the gap between transcriptome and proteome. They can also be processed into small RNA fragments with regulatory functions. In this work, we show that tRNA copy number is largely controlled by genome size in all cellular organisms, in contrast to what is observed for protein-coding genes that stop expanding between ~20,000 and ~35,000 loci per haploid genome in eukaryotes, regardless of genome size. Our analyses indicate that after the bacteria/archaea split, the tRNA gene pool experienced the evolution of increased anticodon diversity in the archaeal lineage, along with a tRNA gene size increase and mature tRNA size decrease. The evolution and diversification of eukaryotes from archaeal ancestors involved further expansion of the tRNA anticodon repertoire, additional increase in tRNA gene size and decrease in mature tRNA length, along with an explosion of the tRNA gene copy number that emerged coupled with accelerated genome size expansion. Our findings support the notion that macroscopic eukaryotes with a high diversity of cell types, such as land plants and vertebrates, independently evolved a high diversity of tRNA anticodons along with high gene redundancy caused by the expansion of the tRNA copy number. The results presented here suggest that the evolution of tRNA genes played important roles in the early split between bacteria and archaea, and in eukaryogenesis and the later emergence of complex eukaryotes, with potential implications in protein translation and gene regulation through tRNA-derived RNA fragments.
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Affiliation(s)
- Fenícia Brito Santos
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
| | - Luiz-Eduardo Del-Bem
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
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9
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DeBenedictis EA, Söll D, Esvelt KM. Measuring the tolerance of the genetic code to altered codon size. eLife 2022; 11:76941. [PMID: 35293861 PMCID: PMC9094753 DOI: 10.7554/elife.76941] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Translation using four-base codons occurs in both natural and synthetic systems. What constraints contributed to the universal adoption of a triplet codon, rather than quadruplet codon, genetic code? Here, we investigate the tolerance of the Escherichia coli genetic code to tRNA mutations that increase codon size. We found that tRNAs from all 20 canonical isoacceptor classes can be converted to functional quadruplet tRNAs (qtRNAs). Many of these selectively incorporate a single amino acid in response to a specified four-base codon, as confirmed with mass spectrometry. However, efficient quadruplet codon translation often requires multiple tRNA mutations. Moreover, while tRNAs were largely amenable to quadruplet conversion, only nine of the twenty aminoacyl tRNA synthetases tolerate quadruplet anticodons. These may constitute a functional and mutually orthogonal set, but one that sharply limits the chemical alphabet available to a nascent all-quadruplet code. Our results suggest that the triplet codon code was selected because it is simpler and sufficient, not because a quadruplet codon code is unachievable. These data provide a blueprint for synthetic biologists to deliberately engineer an all-quadruplet expanded genetic code.
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Affiliation(s)
- Erika Alden DeBenedictis
- Department of Biological Engineering, Massachusetts Institue of Technology, Cambridge, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Kevin M Esvelt
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, United States
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10
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Tanno H, Fujii T, Hirano K, Maeno S, Tonozuka T, Sakamoto M, Ohkuma M, Tochio T, Endo A. Characterization of fructooligosaccharide metabolism and fructooligosaccharide-degrading enzymes in human commensal butyrate producers. Gut Microbes 2022; 13:1-20. [PMID: 33439065 PMCID: PMC7833758 DOI: 10.1080/19490976.2020.1869503] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Butyrate produced by gut microbiota has multiple beneficial effects on host health, and oligosaccharides derived from host diets and glycans originating from host mucus are major sources of its production. A significant reduction of butyrate-producing bacteria has been reported in patients with inflammatory bowel diseases and colorectal cancers. Although gut butyrate levels are important for host health, oligosaccharide metabolic properties in butyrate producers are poorly characterized. We studied the metabolic properties of fructooligosaccharides (FOSs) and other prebiotic oligosaccharides (i.e. raffinose and xylooligosaccharides; XOSs) in gut butyrate producers. 1-Kestose (kestose) and nystose, FOSs with degrees of polymerization of 3 and 4, respectively, were also included. Fourteen species of butyrate producers were divided into four groups based on their oligosaccharide metabolic properties, which are group A (two species) metabolizing all oligosaccharides tested, group F (four species) metabolizing FOSs but not raffinose and XOSs, group XR (four species) metabolizing XOSs and/or raffinose but not FOSs, and group N (four species) metabolizing none of the oligosaccharides tested. Species assigned to groups A and XR are rich glycoside hydrolase (GH) holders, whereas those in groups F and N are the opposite. In total, 17 enzymes assigned to GH32 were observed in nine of the 14 butyrate producers tested, and species that metabolized FOSs had at least one active GH32 enzyme. The GH32 enzymes were divided into four clusters by phylogenetic analysis. Heterologous gene expression analysis revealed that the GH32 enzymes in each cluster had similar FOS degradation properties within clusters, which may be linked to the conservation/substitution of amino acids to bind with substrates in GH32 enzymes. This study provides important knowledge to understand the impact of FOS supplementation on the activation of gut butyrate producers. Abbreviations: SCFA, short chain fatty acid; FOS, fructooligosaccharide; XOS, xylooligosaccharide; CAZy, Carbohydrate Active Enzymes; CBM, carbohydrate-binding module; PUL, polysaccharide utilization locus; S6PH sucrose-6-phosphate hydrolase.
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Affiliation(s)
- Hiroki Tanno
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | | | | | - Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Ibaraki, Japan,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | | | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan,CONTACT Akihito Endo Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido099-2493, Japan
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11
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Bonilla E, Costa AR, van den Berg DF, van Rossum T, Hagedoorn S, Walinga H, Xiao M, Song W, Haas PJ, Nobrega FL, Brouns SJJ. Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae. DNA Res 2021; 28:6352498. [PMID: 34390569 PMCID: PMC8386662 DOI: 10.1093/dnares/dsab013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0–13%) identity to genomic phage sequences deposited in the GenBank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.
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Affiliation(s)
- Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Daan F van den Berg
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Teunke van Rossum
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Stefan Hagedoorn
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Hielke Walinga
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Franklin L Nobrega
- Fagenbank, Delft, The Netherlands.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
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12
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Albers S, Beckert B, Matthies MC, Mandava CS, Schuster R, Seuring C, Riedner M, Sanyal S, Torda AE, Wilson DN, Ignatova Z. Repurposing tRNAs for nonsense suppression. Nat Commun 2021; 12:3850. [PMID: 34158503 PMCID: PMC8219837 DOI: 10.1038/s41467-021-24076-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the TΨC-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 Å resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon.
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Affiliation(s)
- Suki Albers
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marco C. Matthies
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Chandra Sekhar Mandava
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Raphael Schuster
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | | | - Maria Riedner
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | - Suparna Sanyal
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrew E. Torda
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Daniel N. Wilson
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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13
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Tharp JM, Vargas-Rodriguez O, Schepartz A, Söll D. Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons. ACS Chem Biol 2021; 16:766-774. [PMID: 33723984 DOI: 10.1021/acschembio.1c00120] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We recently described an orthogonal initiator tRNA (itRNATy2) that can initiate protein synthesis with noncanonical amino acids (ncAAs) in response to the UAG nonsense codon. Here, we report that a mutant of itRNATy2 (itRNATy2AUA) can efficiently initiate translation in response to the UAU tyrosine codon, giving rise to proteins with an ncAA at their N-terminus. We show that, in cells expressing itRNATy2AUA, UAU can function as a dual-use codon that selectively encodes ncAAs at the initiating position and predominantly tyrosine at elongating positions. Using itRNATy2AUA, in conjunction with its cognate tyrosyl-tRNA synthetase and two mutually orthogonal pyrrolysyl-tRNA synthetases, we demonstrate that UAU can be reassigned along with UAG or UAA to encode two distinct ncAAs in the same protein. Furthermore, by engineering the substrate specificity of one of the pyrrolysyl-tRNA synthetases, we developed a triply orthogonal system that enables simultaneous reassignment of UAU, UAG, and UAA to produce proteins containing three distinct ncAAs at precisely defined sites. To showcase the utility of this system, we produced proteins containing two or three ncAAs, with unique bioorthogonal functional groups, and demonstrate that these proteins can be separately modified with multiple fluorescent probes.
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14
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Hao R, Ma K, Ru Y, Li D, Song G, Lu B, Liu H, Li Y, Zhang J, Wu C, Zhang G, Hu H, Luo J, Zheng H. Amber codon is genetically unstable in generation of premature termination codon (PTC)-harbouring Foot-and-mouth disease virus (FMDV) via genetic code expansion. RNA Biol 2021; 18:2330-2341. [PMID: 33849391 DOI: 10.1080/15476286.2021.1907055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The foot-and-mouth disease virus (FMDV) is the causative agent of FMD, a highly infectious and devastating viral disease of domestic and wild cloven-hoofed animals. FMD affects livestock and animal products' national and international trade, causing severe economic losses and social consequences. Currently, inactivated vaccines play a vital role in FMD control, but they have several limitations. The genetic code expansion technology provides powerful strategies for generating premature termination codon (PTC)-harbouring virus as a live but replication-incompetent viral vaccine. However, this technology has not been explored for the design and development of new FMD vaccines. In this study, we first expanded the genetic code of the FMDV genome via a transgenic cell line containing an orthogonal translation machinery. We demonstrated that the transgenic cells stably integrated the orthogonal pyltRNA/pylRS pair into the genome and enabled efficient, homogeneous incorporation of unnatural amino acids into target proteins in mammalian cells. Next, we constructed 129 single-PTC FMDV mutants and four dual-PTC FMDV mutants after considering the tolerance, location, and potential functions of those mutated sites. Amber stop codons individually substituted the selected amino acid codons in four viral proteins (3D, L, VP1, and VP4) of FMDV. We successfully rescued PTC-FMDV mutants, but the amber codon unexpectedly showed a highly degree of mutation rate during PTC-FMDV packaging and replication. Our findings highlight that the genetic code expansion technology for the generation of PTC-FMD vaccines needs to be further improved and that the genetic stability of amber codons during the packaging and replication of FMDV is a concern.
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Affiliation(s)
- Rongzeng Hao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kun Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yi Ru
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Gaoyuan Song
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingzhou Lu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huanan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yajun Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jiaoyan Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunping Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guicai Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haitao Hu
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development and Institute for Human Infections and Immunity, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
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15
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Lakshmanan V, Sujith TN, Bansal D, Shivaprasad PV, Palakodeti D, Krishna S. Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs). RNA (NEW YORK, N.Y.) 2021; 27:477-495. [PMID: 33446492 PMCID: PMC7962491 DOI: 10.1261/rna.077701.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological processes such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration, suggesting a possible role for these small RNAs in the regulation of regeneration. In order to characterize planarian tRFs, we first annotated 457 tRNAs in S. mediterranea combining two tRNA prediction algorithms. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians-the shorter tRF-5s and itRFs, and the abundantly expressed 5'-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5'-tsRNA in planaria interact with all three SMEDWI proteins and an involvement of AGO1 in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalog of posttranscriptional regulatory systems in planaria, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.
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MESH Headings
- Algorithms
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Base Pairing
- Base Sequence
- Gene Expression Regulation
- Helminth Proteins/genetics
- Helminth Proteins/metabolism
- Molecular Sequence Annotation
- Nucleic Acid Conformation
- Planarians/genetics
- Planarians/metabolism
- RNA, Helminth/chemistry
- RNA, Helminth/classification
- RNA, Helminth/genetics
- RNA, Helminth/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/classification
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Regeneration/genetics
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Affiliation(s)
- Vairavan Lakshmanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
| | - T N Sujith
- National Centre for Biological Sciences (NCBS), 560065 Bangalore, India
| | - Dhiru Bansal
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | | | - Dasaradhi Palakodeti
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | - Srikar Krishna
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
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16
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Ho JML, Miller CA, Parks SE, Mattia JR, Bennett M. A suppressor tRNA-mediated feedforward loop eliminates leaky gene expression in bacteria. Nucleic Acids Res 2021; 49:e25. [PMID: 33290521 PMCID: PMC7969014 DOI: 10.1093/nar/gkaa1179] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Ligand-inducible genetic systems are the mainstay of synthetic biology, allowing gene expression to be controlled by the presence of a small molecule. However, 'leaky' gene expression in the absence of inducer remains a persistent problem. We developed a leak dampener tool that drastically reduces the leak of inducible genetic systems while retaining signal in Escherichia coli. Our system relies on a coherent feedforward loop featuring a suppressor tRNA that enables conditional readthrough of silent non-sense mutations in a regulated gene, and this approach can be applied to any ligand-inducible transcription factor. We demonstrate proof-of-principle of our system with the lactate biosensor LldR and the arabinose biosensor AraC, which displayed a 70-fold and 630-fold change in output after induction of a fluorescence reporter, respectively, without any background subtraction. Application of the tool to an arabinose-inducible mutagenesis plasmid led to a 540-fold change in its output after induction, with leak decreasing to the level of background mutagenesis. This study provides a modular tool for reducing leak and improving the fold-induction within genetic circuits, demonstrated here using two types of biosensors relevant to cancer detection and genetic engineering.
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Affiliation(s)
- Joanne M L Ho
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
| | - Corwin A Miller
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
| | - Sydney E Parks
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
| | - Jacob R Mattia
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
- Department of Bioengineering, Rice University MS-140, 6100 Main St. Houston, TX 77005, USA
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17
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Abstract
A nonsense suppressor tRNA (sup-tRNA) allows a natural or non-natural amino acid to be assigned to a nonsense codon in mRNA. Sup-tRNAs were utilized initially for studying tRNA functions but lately are used more for protein engineering and gene regulation. In the latter application, a sup-tRNA that is aminoacylated with a natural amino acid by the corresponding aminoacyl-tRNA synthetase is used to express a full-length natural protein from its mutated gene with a nonsense codon in the middle. This type of sup-tRNA has recently been artificially evolved to develop biosensors. In these biosensors, an analyte induces the processing of an engineered premature sup-tRNA into a mature sup-tRNA, which suppresses the corresponding nonsense codon incorporated into a gene, encoding an easily detectable reporter protein. This review introduces sup-tRNA-based biosensors that the author's group has developed by utilizing bacterial and eukaryotic cell-free translation systems.
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18
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Belinky F, Ganguly I, Poliakov E, Yurchenko V, Rogozin IB. Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events. Int J Mol Sci 2021; 22:ijms22041876. [PMID: 33672790 PMCID: PMC7918605 DOI: 10.3390/ijms22041876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Nonsense mutations turn a coding (sense) codon into an in-frame stop codon that is assumed to result in a truncated protein product. Thus, nonsense substitutions are the hallmark of pseudogenes and are used to identify them. Here we show that in-frame stop codons within bacterial protein-coding genes are widespread. Their evolutionary conservation suggests that many of them are not pseudogenes, since they maintain dN/dS values (ratios of substitution rates at non-synonymous and synonymous sites) significantly lower than 1 (this is a signature of purifying selection in protein-coding regions). We also found that double substitutions in codons—where an intermediate step is a nonsense substitution—show a higher rate of evolution compared to null models, indicating that a stop codon was introduced and then changed back to sense via positive selection. This further supports the notion that nonsense substitutions in bacteria are relatively common and do not necessarily cause pseudogenization. In-frame stop codons may be an important mechanism of regulation: Such codons are likely to cause a substantial decrease of protein expression levels.
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Affiliation(s)
- Frida Belinky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (F.B.); (I.G.)
| | - Ishan Ganguly
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (F.B.); (I.G.)
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
- Correspondence: (V.Y.); (I.B.R.)
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (F.B.); (I.G.)
- Correspondence: (V.Y.); (I.B.R.)
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19
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Schwark DG, Schmitt MA, Fisk JD. Directed Evolution of the Methanosarcina barkeri Pyrrolysyl tRNA/aminoacyl tRNA Synthetase Pair for Rapid Evaluation of Sense Codon Reassignment Potential. Int J Mol Sci 2021; 22:E895. [PMID: 33477414 PMCID: PMC7830368 DOI: 10.3390/ijms22020895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic code expansion has largely focused on the reassignment of amber stop codons to insert single copies of non-canonical amino acids (ncAAs) into proteins. Increasing effort has been directed at employing the set of aminoacyl tRNA synthetase (aaRS) variants previously evolved for amber suppression to incorporate multiple copies of ncAAs in response to sense codons in Escherichia coli. Predicting which sense codons are most amenable to reassignment and which orthogonal translation machinery is best suited to each codon is challenging. This manuscript describes the directed evolution of a new, highly efficient variant of the Methanosarcina barkeri pyrrolysyl orthogonal tRNA/aaRS pair that activates and incorporates tyrosine. The evolved M. barkeri tRNA/aaRS pair reprograms the amber stop codon with 98.1 ± 3.6% efficiency in E. coli DH10B, rivaling the efficiency of the wild-type tyrosine-incorporating Methanocaldococcus jannaschii orthogonal pair. The new orthogonal pair is deployed for the rapid evaluation of sense codon reassignment potential using our previously developed fluorescence-based screen. Measurements of sense codon reassignment efficiencies with the evolved M. barkeri machinery are compared with related measurements employing the M. jannaschii orthogonal pair system. Importantly, we observe different patterns of sense codon reassignment efficiency for the M. jannaschii tyrosyl and M. barkeri pyrrolysyl systems, suggesting that particular codons will be better suited to reassignment by different orthogonal pairs. A broad evaluation of sense codon reassignment efficiencies to tyrosine with the M. barkeri system will highlight the most promising positions at which the M. barkeri orthogonal pair may infiltrate the E. coli genetic code.
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Affiliation(s)
| | | | - John D. Fisk
- Department of Chemistry, University of Colorado Denver, Campus Box 194, P.O. Box 173364, Denver, CO 80217-3364, USA; (D.G.S.); (M.A.S.)
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20
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Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. Proc Natl Acad Sci U S A 2020; 117:22167-22172. [PMID: 32839318 DOI: 10.1073/pnas.2013543117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate protein synthesis is a tightly controlled biological process with multiple quality control steps safeguarded by aminoacyl-transfer RNA (tRNA) synthetases and the ribosome. Reduced translational accuracy leads to various physiological changes in both prokaryotes and eukaryotes. Termination of translation is signaled by stop codons and catalyzed by release factors. Occasionally, stop codons can be suppressed by near-cognate aminoacyl-tRNAs, resulting in protein variants with extended C termini. We have recently shown that stop-codon readthrough is heterogeneous among single bacterial cells. However, little is known about how environmental factors affect the level and heterogeneity of stop-codon readthrough. In this study, we have combined dual-fluorescence reporters, mass spectrometry, mathematical modeling, and single-cell approaches to demonstrate that a metabolic stress caused by excess carbon substantially increases both the level and heterogeneity of stop-codon readthrough. Excess carbon leads to accumulation of acid metabolites, which lower the pH and the activity of release factors to promote readthrough. Furthermore, our time-lapse microscopy experiments show that single cells with high readthrough levels are more adapted to severe acid stress conditions and are more sensitive to an aminoglycoside antibiotic. Our work thus reveals a metabolic stress that promotes translational heterogeneity and phenotypic diversity.
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21
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Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase. J Mol Biol 2020; 432:4690-4704. [PMID: 32569745 DOI: 10.1016/j.jmb.2020.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/15/2022]
Abstract
Genetic code expansion (GCE) technologies incorporate non-canonical amino acids (ncAAs) into proteins at amber stop codons. To avoid unwanted truncated protein and improve ncAA-protein yields, genomically recoded strains of Escherichia coli lacking Release Factor 1 (RF1) are becoming increasingly popular expression hosts for GCE applications. In the absence of RF1, however, endogenous near-cognate amber suppressing tRNAs can lead to contaminating protein forms with natural amino acids in place of the ncAA. Here, we show that a second-generation amino-acyl tRNA synthetase (aaRS)/tRNACUA pair for site-specific incorporation of 3-nitro-tyrosine could not outcompete near-cognate suppression in an RF1-deficient expression host and therefore could not produce homogenously nitrated protein. To resolve this, we used Rosetta to target positions in the nitroTyr aaRS active site for improved substrate binding, and then constructed of a small library of variants to subject to standard selection protocols. The top selected variant had an ~2-fold greater efficiency, and remarkably, this relatively small improvement enabled homogeneous incorporation of nitroTyr in an RF1-deficient expression host and thus eliminates truncation issues associated with typical RF1-containing expression hosts. Structural and biochemical data suggest the aaRS efficiency improvement is based on higher affinity substrate binding. Taken together, the modest improvement in aaRS efficiency provides a large practical impact and expands our ability to study the role protein nitration plays in disease development through producing homogenous, truncation-free nitroTyr-containing protein. This work establishes Rosetta-guided design and incremental aaRS improvement as a viable and accessible path to improve GCE systems challenged by truncation and/or near-cognate suppression issues.
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22
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Tharp JM, Hampton JT, Reed CA, Ehnbom A, Chen PHC, Morse JS, Kurra Y, Pérez LM, Xu S, Liu WR. An amber obligate active site-directed ligand evolution technique for phage display. Nat Commun 2020; 11:1392. [PMID: 32170178 PMCID: PMC7070036 DOI: 10.1038/s41467-020-15057-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/14/2020] [Indexed: 01/19/2023] Open
Abstract
Although noncanonical amino acids (ncAAs) were first incorporated into phage libraries through amber suppression nearly two decades ago, their application for use in drug discovery has been limited due to inherent library bias towards sense-containing phages. Here, we report a technique based on superinfection immunity of phages to enrich amber-containing clones, thus avoiding the observed bias that has hindered incorporation of ncAAs into phage libraries. We then take advantage of this technique for development of active site-directed ligand evolution of peptides, where the ncAA serves as an anchor to direct the binding of its peptides to the target’s active site. To demonstrate this, phage-displayed peptide libraries are developed that contain a genetically encoded butyryl lysine and are subsequently used to select for ligands that bind SIRT2. These ligands are then modified to develop low nanomolar inhibitors of SIRT2. Most epigenetic regulator inhibitors target tunnels of active sites, rather than the peptide binding groove, leading to concerns with low selectivity. Here the authors use an amber obligate phage library to rapidly identify isoform-selective inhibitors of SIRT2.
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Affiliation(s)
- Jeffery M Tharp
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - J Trae Hampton
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Catrina A Reed
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Andreas Ehnbom
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Peng-Hsun Chase Chen
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jared S Morse
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagirri Kurra
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lisa M Pérez
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA. .,Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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23
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Fan Y, Thompson L, Lyu Z, Cameron TA, De Lay NR, Krachler AM, Ling J. Optimal translational fidelity is critical for Salmonella virulence and host interactions. Nucleic Acids Res 2019; 47:5356-5367. [PMID: 30941426 PMCID: PMC6547416 DOI: 10.1093/nar/gkz229] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 01/09/2023] Open
Abstract
Translational fidelity is required for accurate flow of genetic information, but is frequently altered by genetic changes and environmental stresses. To date, little is known about how translational fidelity affects the virulence and host interactions of bacterial pathogens. Here we show that surprisingly, either decreasing or increasing translational fidelity impairs the interactions of the enteric pathogen Salmonella Typhimurium with host cells and its fitness in zebrafish. Host interactions are mediated by Salmonella pathogenicity island 1 (SPI-1). Our RNA sequencing and quantitative RT-PCR results demonstrate that SPI-1 genes are among the most down-regulated when translational fidelity is either increased or decreased. Further, this down-regulation of SPI-1 genes depends on the master regulator HilD, and altering translational fidelity destabilizes HilD protein via enhanced degradation by Lon protease. Our work thus reveals that optimal translational fidelity is pivotal for adaptation of Salmonella to the host environment, and provides important mechanistic insights into this process.
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Affiliation(s)
- Yongqiang Fan
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, People's Republic of China
| | - Laurel Thompson
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Nicholas R De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Anne Marie Krachler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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24
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Kato Y. Translational Control using an Expanded Genetic Code. Int J Mol Sci 2019; 20:ijms20040887. [PMID: 30781713 PMCID: PMC6412442 DOI: 10.3390/ijms20040887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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25
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Sant'Anna CL, Gama WA, Rigonato J, Correa G, Mesquita MC, Marinho MM. Phylogenetic connection among close genera of Aphanizomenonaceae (Cyanobacteria): Amphiheterocytum gen. nov., Cylindrospermopsis and Sphaerospermopsis. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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26
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Fu X, Crnković A, Sevostyanova A, Söll D. Designing seryl-tRNA synthetase for improved serylation of selenocysteine tRNAs. FEBS Lett 2018; 592:3759-3768. [PMID: 30317559 PMCID: PMC6263840 DOI: 10.1002/1873-3468.13271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 12/28/2022]
Abstract
Selenocysteine (Sec) lacks a cognate aminoacyl-tRNA synthetase. Instead, seryl-tRNA synthetase (SerRS) produces Ser-tRNASec , which is subsequently converted by selenocysteine synthase to Sec-tRNASec . Escherichia coli SerRS serylates tRNASec poorly; this may hinder efficient production of designer selenoproteins in vivo. Guided by structural modelling and selection for chloramphenicol acetyltransferase activity, we evolved three SerRS variants capable of improved Ser-tRNASec synthesis. They display 10-, 8-, and 4-fold increased kcat /KM values compared to wild-type SerRS using synthetic tRNASec species as substrates. The enzyme variants also facilitate in vivo read-through of a UAG codon in the position of the critical serine146 of chloramphenicol acetyltransferase. These results indicate that the naturally evolved SerRS is capable of further evolution for increased recognition of a specific tRNA isoacceptor.
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MESH Headings
- Base Sequence
- Codon, Terminator/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Kinetics
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Protein Domains
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Selenoproteins/genetics
- Selenoproteins/metabolism
- Serine/genetics
- Serine/metabolism
- Serine-tRNA Ligase/chemistry
- Serine-tRNA Ligase/genetics
- Serine-tRNA Ligase/metabolism
- Substrate Specificity
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Affiliation(s)
- Xian Fu
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Ana Crnković
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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27
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Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. [A facile method for producing selenocysteine-containing proteins]. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 130:7333-7337. [PMID: 30002564 PMCID: PMC6039127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ein einfacher Ansatz nutzt einen erweiterten genetischen Code von Escherichia coli zur Biosynthese von Selenoproteinen mit zahlreichen Sec-Resten. Kürzlich wurden so genannte allo-tRNAs entdeckt. Diese verfügen über eine ungewöhnliche Struktur, sind genauso effiziente Serinakzeptoren wie die normale tRNASer aus E. coli und werden von der Aeromonas-salmonicida-Selenocysteinsynthase (SelA) von Ser-allo-tRNA zu Sec-allo-tRNA umgesetzt. Anschließend ermöglicht es Sec-allo-tRNA, fünf UAG-Stop-Codons auf der fdhF-mRNA für E.-coli-Formatdehydrogenase H als Sec zu translatieren und katalytisch aktive E.-coli-Formatdehydrogenase mit fünf Sec-Resten in E. coli zu produzieren. Weiterhin konnte gezeigt werden, dass sich in E. coli durch Kombination genetischer Varianten von allo-tRNA und SelA mit einem modifizierten Selenstoffwechsel das humane Selenoenzym GPx1 mit über 80% Sec-Einbaurate rekombinant produzieren lässt. Beide Beispiele belegen den Wert von allo-tRNAUTu als molekulare Plattform zur Entwicklung neuartiger Selenoproteine.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
| | - Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
| | - Xian Fu
- 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)
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28
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Ryvkin A, Ashkenazy H, Weiss-Ottolenghi Y, Piller C, Pupko T, Gershoni JM. Phage display peptide libraries: deviations from randomness and correctives. Nucleic Acids Res 2018; 46:e52. [PMID: 29420788 PMCID: PMC5961013 DOI: 10.1093/nar/gky077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/25/2017] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.
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Affiliation(s)
- Arie Ryvkin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yael Weiss-Ottolenghi
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Piller
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan M Gershoni
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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29
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Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. A Facile Method for Producing Selenocysteine-Containing Proteins. Angew Chem Int Ed Engl 2018; 57:7215-7219. [PMID: 29631320 DOI: 10.1002/anie.201713215] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/20/2018] [Indexed: 01/14/2023]
Abstract
Selenocysteine (Sec, U) confers new chemical properties on proteins. Improved tools are thus required that enable Sec insertion into any desired position of a protein. We report a facile method for synthesizing selenoproteins with multiple Sec residues by expanding the genetic code of Escherichia coli. We recently discovered allo-tRNAs, tRNA species with unusual structure, that are as efficient serine acceptors as E. coli tRNASer . Ser-allo-tRNA was converted into Sec-allo-tRNA by Aeromonas salmonicida selenocysteine synthase (SelA). Sec-allo-tRNA variants were able to read through five UAG codons in the fdhF mRNA coding for E. coli formate dehydrogenase H, and produced active FDHH with five Sec residues in E. coli. Engineering of the E. coli selenium metabolism along with mutational changes in allo-tRNA and SelA improved the yield and purity of recombinant human glutathione peroxidase 1 (to over 80 %). Thus, our allo-tRNAUTu system offers a new selenoprotein engineering platform.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xian Fu
- 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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30
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Fan Y, Evans CR, Barber KW, Banerjee K, Weiss KJ, Margolin W, Igoshin OA, Rinehart J, Ling J. Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness. Mol Cell 2017; 67:826-836.e5. [PMID: 28781237 PMCID: PMC5591071 DOI: 10.1016/j.molcel.2017.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/22/2017] [Accepted: 07/07/2017] [Indexed: 12/30/2022]
Abstract
Gene expression noise (heterogeneity) leads to phenotypic diversity among isogenic individual cells. Our current understanding of gene expression noise is mostly limited to transcription, as separating translational noise from transcriptional noise has been challenging. It also remains unclear how translational heterogeneity originates. Using a transcription-normalized reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, and individual cells with higher UGA readthrough grow faster from stationary phase. Our work also revealed that individual cells with lower protein synthesis levels exhibited higher UGA readthrough, which was confirmed with ribosome-targeting antibiotics (e.g., chloramphenicol). Further experiments and mathematical modeling suggest that varied competition between ternary complexes and release factors perturbs the UGA readthrough level. Our results indicate that fluctuations in the concentrations of translational components lead to UGA readthrough heterogeneity among single cells, which enhances phenotypic diversity of the genetically identical population and facilitates its adaptation to changing environments.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Codon, Terminator
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/genetics
- Gene Expression Regulation, Bacterial
- Genes, Reporter
- Genetic Fitness
- Genotype
- Kinetics
- Luminescent Proteins/biosynthesis
- Luminescent Proteins/genetics
- Microscopy, Fluorescence
- Models, Genetic
- One-Carbon Group Transferases
- Phenotype
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Transcription, Genetic
- Red Fluorescent Protein
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Karl W Barber
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kinshuk Banerjee
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Kalyn J Weiss
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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31
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Xuan W, Schultz PG. A Strategy for Creating Organisms Dependent on Noncanonical Amino Acids. Angew Chem Int Ed Engl 2017; 56:9170-9173. [PMID: 28593724 PMCID: PMC5580492 DOI: 10.1002/anie.201703553] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 11/11/2022]
Abstract
The use of noncanonical amino acids (ncAAs) to control the viability of an organism provides a strategy for the development of conditional "kill switches" for live vaccines or engineered human cells. We report an approach inspired by the posttranslational acetylation/deacetylation of lysine residues, in which a protein encoded by a gene with an in-frame nonsense codon at an essential lysine can be expressed in its native state only upon genetic incorporation of N-ϵ-acetyl-l-Lys (AcK), and subsequent enzymatic deacetylation in the host cell. We applied this strategy to two essential E. coli enzymes: the branched-chain aminotransferase BCAT and the DNA replication initiator protein DnaA. We also devised a barnase-based conditional suicide switch to further lower the escape frequency of the host cells. This strategy offers a number of attractive features for controlling host viability, including a single small-molecule-based kill switch, low escape frequency, and unaffected protein function.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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32
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Chemla Y, Friedman M, Heltberg M, Bakhrat A, Nagar E, Schwarz R, Jensen MH, Alfonta L. Expanding the Genetic Code of a Photoautotrophic Organism. Biochemistry 2017; 56:2161-2165. [PMID: 28394580 DOI: 10.1021/acs.biochem.7b00131] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photoautotrophic freshwater cyanobacterium Synechococcus elongatus is widely used as a chassis for biotechnological applications as well as a photosynthetic bacterial model. In this study, a method for expanding the genetic code of this cyanobacterium has been established, thereby allowing the incorporation of unnatural amino acids into proteins. This was achieved through UAG stop codon suppression, using an archaeal pyrrolysyl orthogonal translation system. We demonstrate incorporation of unnatural amino acids into green fluorescent protein with 20 ± 3.5% suppression efficiency. The introduced components were shown to be orthogonal to the host translational machinery. In addition, we observed that no significant growth impairment resulted from the integration of the system. To interpret the observations, we modeled and investigated the competition over the UAG codon between release factor 1 and pyl-tRNACUA. On the basis of the model results, and the fact that 39.6% of the stop codons in the S. elongatus genome are UAG stop codons, the suppression efficiency in S. elongatus is unexpectedly high. The reason for this unexpected suppression efficiency has yet to be determined.
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Affiliation(s)
- Yonatan Chemla
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Mor Friedman
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Mathias Heltberg
- Niels Bohr Institute, University of Copenhagen , Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Anna Bakhrat
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | - Mogens Høgh Jensen
- Niels Bohr Institute, University of Copenhagen , Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
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33
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A Nonsense Mutation in Mycobacterium marinum That Is Suppressible by a Novel Mechanism. Infect Immun 2017; 85:IAI.00653-16. [PMID: 27789543 DOI: 10.1128/iai.00653-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/17/2016] [Indexed: 11/20/2022] Open
Abstract
Mycobacterial pathogens use the ESAT-6 system 1 (Esx-1) exporter to promote virulence. Previously, we used gene disruption and complementation to conclude that the MMAR_0039 gene in Mycobacterium marinum is required to promote Esx-1 export. Here we applied molecular genetics, proteomics, and whole-genome sequencing to demonstrate that the MMAR_0039 gene is not required for Esx-1 secretion or virulence. These findings suggest that we initially observed an indirect mechanism of genetic complementation. We identified a spontaneous nonsense mutation in a known Esx-1-associated gene which causes a loss of Esx-1 activity. We show that the Esx-1 function was restored by nonsense suppression. Moreover, we identified a polar mutation in the ppsC gene which reduced cellular impermeability but did not impact cytotoxicity in macrophages. Our studies reveal insight into Esx-1 export, nonsense suppression, and cell envelope lipid biogenesis.
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34
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van der Gulik PTS, Hoff WD. Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code. PLoS One 2016; 11:e0158342. [PMID: 27454314 PMCID: PMC4959769 DOI: 10.1371/journal.pone.0158342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/14/2016] [Indexed: 11/19/2022] Open
Abstract
Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA.
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Affiliation(s)
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
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35
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Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements. Cell Syst 2016; 3:199-207. [PMID: 27426981 DOI: 10.1016/j.cels.2016.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 05/06/2016] [Accepted: 06/17/2016] [Indexed: 11/21/2022]
Abstract
Horizontally transferred genetic elements such as viruses and conjugative plasmids move DNA between organisms, increasing genetic diversity but destabilizing engineered biological systems. Here, we used a genomically recoded Escherichia coli strain lacking UAG stop codons and the recognition protein release factor 1 to study how an alternative genetic code influences horizontally transferred genetic element propagation. The alternative genetic code conferred resistance to multiple viruses (λ, M13, P1, MS2) at titers up to 10(11) PFU/ml and impaired conjugative plasmids (F and RK2) up to 10(5)-fold. By recoding UAG codons to UAA in viruses and plasmids, we restored viral infectivity and conjugative function. Propagating viruses on a mixed community of cells with standard and alternative genetic codes reduced viral titer, and over time viruses adapted to the alternative genetic code. This work demonstrates that altering the genetic code broadly obstructs the propagation of horizontally transferred genetic elements and supports the use of genomic recoding as a strategy to stabilize engineered biological systems.
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36
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Lajoie MJ, Söll D, Church GM. Overcoming Challenges in Engineering the Genetic Code. J Mol Biol 2016; 428:1004-21. [PMID: 26348789 PMCID: PMC4779434 DOI: 10.1016/j.jmb.2015.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/19/2015] [Accepted: 09/01/2015] [Indexed: 11/24/2022]
Abstract
Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code.
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Affiliation(s)
- M J Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - D Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - G M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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37
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Abstract
The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.
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38
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Ling J, O'Donoghue P, Söll D. Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology. Nat Rev Microbiol 2015; 13:707-721. [PMID: 26411296 DOI: 10.1038/nrmicro3568] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The genetic code, initially thought to be universal and immutable, is now known to contain many variations, including biased codon usage, codon reassignment, ambiguous decoding and recoding. As a result of recent advances in the areas of genome sequencing, biochemistry, bioinformatics and structural biology, our understanding of genetic code flexibility has advanced substantially in the past decade. In this Review, we highlight the prevalence, evolution and mechanistic basis of genetic code variations in microorganisms, and we discuss how this flexibility of the genetic code affects microbial physiology.
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Affiliation(s)
- Jiqiang Ling
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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39
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A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation. Nat Commun 2015; 6:8130. [PMID: 26350500 PMCID: PMC4566969 DOI: 10.1038/ncomms9130] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/22/2015] [Indexed: 11/23/2022] Open
Abstract
Biochemical investigation of protein phosphorylation events is limited by inefficient production of the phosphorylated and non-phosphorylated forms of full-length proteins. Here using a genomically recoded strain of E. coli with a flexible UAG codon we produce site-specific serine- or phosphoserine-containing proteins, with purities approaching 90%, from a single recombinant DNA. Specifically, we synthesize human MEK1 kinase with two serines or two phosphoserines, from one DNA template, and demonstrate programmable kinase activity. Programmable protein phosphorylation is poised to help reveal the structural and functional information encoded in the phosphoproteome. The effects of protein phosphorylation, a common post-translational modification, are difficult to study using recombinant proteins. Here the authors use genomically engineered E. coli to enhance translation systems that express phosphor-serine containing proteins, and use these systems to produce phosphorylated MEK1 kinase.
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40
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Abstract
Bacterial strains carrying nonsense suppressor tRNA genes played a crucial role in early work on bacterial and bacterial viral genetics. In eukaryotes as well, suppressor tRNAs have played important roles in the genetic analysis of yeast and worms. Surprisingly, little is known about genetic suppression in archaea, and there has been no characterization of suppressor tRNAs or identification of nonsense mutations in any of the archaeal genes. Here, we show, using the β-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the serine and tyrosine tRNAs of the archaeon Haloferax volcanii are active in suppression of their corresponding stop codons. Using a promoter for tRNA expression regulated by tryptophan, we also show inducible and regulatable suppression of all three stop codons in H. volcanii. Additionally, transformation of a ΔpyrE2 H. volcanii strain with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on agar plates lacking uracil. Thus, an auxotrophic amber mutation in the pyrE2 gene can be complemented by expression of the amber suppressor tRNA. These results pave the way for generating archaeal strains carrying inducible suppressor tRNA genes on the chromosome and their use in archaeal and archaeviral genetics. We also provide possible explanations for why suppressor tRNAs have not been identified in archaea.
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41
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Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ. Recoded organisms engineered to depend on synthetic amino acids. Nature 2015; 518:89-93. [PMID: 25607356 PMCID: PMC4590768 DOI: 10.1038/nature14095] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 11/17/2014] [Indexed: 01/21/2023]
Abstract
Genetically modified organisms (GMOs) are increasingly used in research and industrial systems to produce high-value pharmaceuticals, fuels, and chemicals1. Genetic isolation and intrinsic biocontainment would provide essential biosafety measures to secure these closed systems and enable safe applications of GMOs in open systems2,3, which include bioremediation4 and probiotics5. Although safeguards have been designed to control cell growth by essential gene regulation6, inducible toxin switches7, and engineered auxotrophies8, these approaches are compromised by cross-feeding of essential metabolites, leaked expression of essential genes, or genetic mutations9,10. Here, we describe the construction of a series of genomically recoded organisms (GROs)11 whose growth is restricted by the expression of multiple essential genes that depend on exogenously supplied synthetic amino acids (sAAs). We introduced a Methanocaldococcus jannaschii tRNA:aminoacyl-tRNA synthetase (aaRS) pair into the chromosome of a GRO that lacks all TAG codons and release factor 1, endowing this organism with the orthogonal translational components to convert TAG into a dedicated sense codon for sAAs. Using multiplex automated genome engineering (MAGE)12, we introduced in-frame TAG codons into 22 essential genes, linking their expression to the incorporation of synthetic phenylalanine-derived amino acids. Of the 60 sAA-dependent variants isolated, a notable strain harboring 3 TAG codons in conserved functional residues13 of MurG, DnaA and SerS and containing targeted tRNA deletions maintained robust growth and exhibited undetectable escape frequencies upon culturing ∼1011 cells on solid media for seven days or in liquid media for 20 days. This is a significant improvement over existing biocontainment approaches2,3,6-10. We constructed synthetic auxotrophs dependent on sAAs that were not rescued by cross-feeding in environmental growth assays. These auxotrophic GROs possess alternate genetic codes that impart genetic isolation by impeding horizontal gene transfer11 and now depend on the use of synthetic biochemical building blocks, advancing orthogonal barriers between engineered organisms and the environment.
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Affiliation(s)
- Alexis J Rovner
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Adrian D Haimovich
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Spencer R Katz
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Zhe Li
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Michael W Grome
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Brandon M Gassaway
- 1] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA [2] Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520, USA
| | - Miriam Amiram
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jaymin R Patel
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Ryan R Gallagher
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jesse Rinehart
- 1] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA [2] Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520, USA
| | - Farren J Isaacs
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
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42
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Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, Gregg CJ, Stoddard BL, Church GM. Biocontainment of genetically modified organisms by synthetic protein design. Nature 2015; 518:55-60. [PMID: 25607366 DOI: 10.1038/nature14121] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
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Affiliation(s)
- Daniel J Mandell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marc J Lajoie
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Program in Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Michael T Mee
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Ryo Takeuchi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Gleb Kuznetsov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Julie E Norville
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher J Gregg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - George M Church
- 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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43
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Fan C, Ho JML, Chirathivat N, Söll D, Wang YS. Exploring the substrate range of wild-type aminoacyl-tRNA synthetases. Chembiochem 2014; 15:1805-1809. [PMID: 24890918 DOI: 10.1002/cbic.201402083] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Indexed: 01/02/2023]
Abstract
We tested the substrate range of four wild-type E. coli aminoacyl-tRNA synthetases (AARSs) with a library of nonstandard amino acids (nsAAs). Although these AARSs could discriminate efficiently against the other canonical amino acids, they were able to use many nsAAs as substrates. Our results also show that E. coli tryptophanyl-tRNA synthetase (TrpRS) and tyrosyl-tRNA synthetase have overlapping substrate ranges. In addition, we found that the nature of the anticodon sequence of tRNA(Trp) altered the nsAA substrate range of TrpRS; this implies that the sequence of the anticodon affects the TrpRS amino acid binding pocket. These results highlight again that inherent AARS polyspecificity will be a major challenge in the aim of incorporating multiple different amino acids site-specifically into proteins.
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Affiliation(s)
- Chenguang Fan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
| | - Joanne M L Ho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
| | - Napon Chirathivat
- 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)
| | - Yane-Shih Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
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44
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Suppression of amber codons in Caulobacter crescentus by the orthogonal Escherichia coli histidyl-tRNA synthetase/tRNAHis pair. PLoS One 2013; 8:e83630. [PMID: 24386240 PMCID: PMC3875453 DOI: 10.1371/journal.pone.0083630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 11/05/2013] [Indexed: 11/19/2022] Open
Abstract
While translational read-through of stop codons by suppressor tRNAs is common in many bacteria, archaea and eukaryotes, this phenomenon has not yet been observed in the α-proteobacterium Caulobacter crescentus. Based on a previous report that C. crescentus and Escherichia coli tRNAHis have distinctive identity elements, we constructed E. coli tRNAHisCUA, a UAG suppressor tRNA for C. crescentus. By examining the expression of three UAG codon- containing reporter genes (encoding a β-lactamase, the fluorescent mCherry protein, or the C. crescentus xylonate dehydratase), we demonstrated that the E. coli histidyl-tRNA synthetase/tRNAHisCUA pair enables in vivo UAG suppression in C. crescentus. E. coli histidyl-tRNA synthetase (HisRS) or tRNAHisCUA alone did not achieve suppression; this indicates that the E. coli HisRS/tRNAHisCUA pair is orthogonal in C. crescentus. These results illustrate that UAG suppression can be achieved in C. crescentus with an orthogonal aminoacyl-tRNA synthetase/suppressor tRNA pair.
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45
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High-yield, zero-leakage expression system with a translational switch using site-specific unnatural amino Acid incorporation. Appl Environ Microbiol 2013; 80:1718-25. [PMID: 24375139 DOI: 10.1128/aem.03417-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synthetic biologists construct complex biological circuits by combinations of various genetic parts. Many genetic parts that are orthogonal to one another and are independent of existing cellular processes would be ideal for use in synthetic biology. However, our toolbox is still limited with respect to the bacterium Escherichia coli, which is important for both research and industrial use. The site-specific incorporation of unnatural amino acids is a technique that incorporates unnatural amino acids into proteins using a modified exogenous aminoacyl-tRNA synthetase/tRNA pair that is orthogonal to any native pairs in a host and is independent from other cellular functions. Focusing on the orthogonality and independency that are suitable for the genetic parts, we designed novel AND gate and translational switches using the unnatural amino acid 3-iodo-l-tyrosine incorporation system in E. coli. A translational switch was turned on after addition of 3-iodo-l-tyrosine in the culture medium within minutes and allowed tuning of switchability and translational efficiency. As an application, we also constructed a gene expression system that produced large amounts of proteins under induction conditions and exhibited zero-leakage expression under repression conditions. Similar translational switches are expected to be applicable also for eukaryotes such as yeasts, nematodes, insects, mammalian cells, and plants.
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46
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Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ. Genomically recoded organisms expand biological functions. Science 2013; 342:357-60. [PMID: 24136966 PMCID: PMC4924538 DOI: 10.1126/science.1241459] [Citation(s) in RCA: 600] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We describe the construction and characterization of a genomically recoded organism (GRO). We replaced all known UAG stop codons in Escherichia coli MG1655 with synonymous UAA codons, which permitted the deletion of release factor 1 and reassignment of UAG translation function. This GRO exhibited improved properties for incorporation of nonstandard amino acids that expand the chemical diversity of proteins in vivo. The GRO also exhibited increased resistance to T7 bacteriophage, demonstrating that new genetic codes could enable increased viral resistance.
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Affiliation(s)
- Marc J. Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexis J. Rovner
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daniel B. Goodman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical Engineering and Medical Physics, Harvard–Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - Adrian D. Haimovich
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Gleb Kuznetsov
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Harris H. Wang
- Department of Systems Biology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Joshua A. Mosberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph M. Jacobson
- Center for Bits and Atoms, MIT, Cambridge, MA 02139, USA
- MIT Media Lab, MIT, Cambridge, MA 02139, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
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47
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Jeudy S, Abergel C, Claverie JM, Legendre M. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. PLoS Genet 2012; 8:e1003122. [PMID: 23271980 PMCID: PMC3521657 DOI: 10.1371/journal.pgen.1003122] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/12/2012] [Indexed: 12/04/2022] Open
Abstract
Mimivirus and Megavirus are the best characterized representatives of an expanding new family of giant viruses infecting Acanthamoeba. Their most distinctive features, megabase-sized genomes carried in particles of size comparable to that of small bacteria, fill the gap between the viral and cellular worlds. These giant viruses are also uniquely equipped with genes coding for central components of the translation apparatus. The presence of those genes, thought to be hallmarks of cellular organisms, revived fundamental interrogations on the evolutionary origin of these viruses and the link they might have with the emergence of eukaryotes. In this work, we focused on the Mimivirus-encoded translation termination factor gene, the detailed primary structure of which was elucidated using computational and experimental approaches. We demonstrated that the translation of this protein proceeds through two internal stop codons via two distinct recoding events: a frameshift and a readthrough, the combined occurrence of which is unique to these viruses. Unexpectedly, the viral gene carries an autoregulatory mechanism exclusively encountered in bacterial termination factors, though the viral sequence is related to the eukaryotic/archaeal class-I release factors. This finding is a hint that the virally-encoded translation functions may not be strictly redundant with the one provided by the host. Lastly, the perplexing occurrence of a bacterial-like regulatory mechanism in a eukaryotic/archaeal homologous gene is yet another oddity brought about by the study of giant viruses. Giant viruses, such as Mimivirus and Megavirus, have huge near-micron-sized particles and possess more genes than several cellular organisms. Furthermore their genomes encode functions not supposed to be in a virus, such as components of the protein translation apparatus. Since Lwoff in 1957, viruses are defined as ultimate obligate intracellular parasites from their need to hijack the peptide synthesis machinery of their host to replicate. We looked at the Mimivirus and Megavirus proteins that recognize the stop codons, the translation termination factors. We found that these genes contain two internal stop codons, meaning that their translation bypasses two distinct stop codons to produce a functional translation termination factor. These types of autoregulatory mechanisms are found in bacterial termination factors, although it involves only a single internal stop codon and not two, and are absent from their eukaryotic and archaeal homologs. Despite these bacterial-like features, giant viruses' termination factors have sequences that do not resemble bacterial genes but are clearly related to the eukaryotic and archaeal termination factors. Thus, giant viruses' termination factors surprisingly combine elements from eukaryotes/archaea and bacteria.
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Affiliation(s)
- Sandra Jeudy
- CNRS, Aix-Marseille Université, IGS UMR7256, Marseille, France
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48
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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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49
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Heinemann IU, Rovner AJ, Aerni HR, Rogulina S, Cheng L, Olds W, Fischer JT, Söll D, Isaacs FJ, Rinehart J. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett 2012; 586:3716-22. [PMID: 22982858 DOI: 10.1016/j.febslet.2012.08.031] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 10/27/2022]
Abstract
Genetically encoded phosphoserine incorporation programmed by the UAG codon was achieved by addition of engineered elongation factor and an archaeal aminoacyl-tRNA synthetase to the normal Escherichia coli translation machinery (Park et al., 2011) Science 333, 1151). However, protein yield suffers from expression of the orthogonal phosphoserine translation system and competition with release factor 1 (RF-1). In a strain lacking RF-1, phosphoserine phosphatase, and where seven UAG codons residing in essential genes were converted to UAA, phosphoserine incorporation into GFP and WNK4 was significantly elevated, but with an accompanying loss in cellular fitness and viability.
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Affiliation(s)
- Ilka U Heinemann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8144, USA
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50
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A Concept for Selection of Codon-Suppressor tRNAs Based on Read-Through Ribosome Display in an In Vitro Compartmentalized Cell-Free Translation System. J Nucleic Acids 2012; 2012:538129. [PMID: 22928090 PMCID: PMC3425794 DOI: 10.1155/2012/538129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 06/29/2012] [Indexed: 11/24/2022] Open
Abstract
Here is presented a concept for in vitro selection of suppressor tRNAs. It uses a pool of dsDNA templates in compartmentalized water-in-oil micelles. The template contains a transcription/translation trigger, an amber stop codon, and another transcription trigger for the anticodon- or anticodon loop-randomized gene for tRNASer. Upon transcription are generated two types of RNAs, a tRNA and a translatable mRNA (mRNA-tRNA). When the tRNA suppresses the stop codon (UAG) of the mRNA, the full-length protein obtained upon translation remains attached to the mRNA (read-through ribosome display) that contains the sequence of the tRNA. In this way, the active suppressor tRNAs can be selected (amplified) and their sequences read out. The enriched anticodon (CUA) was complementary to the UAG stop codon and the enriched anticodon-loop was the same as that in the natural tRNASer.
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