1
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Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard R, Gabir H, Patel T, Stetefeld J, Puglisi J, Söll D. tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut. Nucleic Acids Res 2024; 52:513-524. [PMID: 38100361 PMCID: PMC10810272 DOI: 10.1093/nar/gkad1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating >200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G-U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G-C base pairs (G3:C70 and G5:C68).
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jingji Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Alessandra Villa
- PDC-Center for High Performance Computing, KTH-Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Armaan Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, SE-171 65, Sweden
| | - Haben Gabir
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB T1K 2E1, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Joseph Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, 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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2
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Nunes LGA, Cain A, Comyns C, Hoffmann PR, Krahn N. Deciphering the Role of Selenoprotein M. Antioxidants (Basel) 2023; 12:1906. [PMID: 38001759 PMCID: PMC10668967 DOI: 10.3390/antiox12111906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
Selenocysteine (Sec), the 21st amino acid, is structurally similar to cysteine but with a sulfur to selenium replacement. This single change retains many of the chemical properties of cysteine but often with enhanced catalytic and redox activity. Incorporation of Sec into proteins is unique, requiring additional translation factors and multiple steps to insert Sec at stop (UGA) codons. These Sec-containing proteins (selenoproteins) are found in all three domains of life where they often are involved in cellular homeostasis (e.g., reducing reactive oxygen species). The essential role of selenoproteins in humans requires us to maintain appropriate levels of selenium, the precursor for Sec, in our diet. Too much selenium is also problematic due to its toxic effects. Deciphering the role of Sec in selenoproteins is challenging for many reasons, one of which is due to their complicated biosynthesis pathway. However, clever strategies are surfacing to overcome this and facilitate production of selenoproteins. Here, we focus on one of the 25 human selenoproteins, selenoprotein M (SELENOM), which has wide-spread expression throughout our tissues. Its thioredoxin motif suggests oxidoreductase function; however, its mechanism and functional role(s) are still being uncovered. Furthermore, the connection of both high and low expression levels of SELENOM to separate diseases emphasizes the medical application for studying the role of Sec in this protein. In this review, we aim to decipher the role of SELENOM through detailing and connecting current evidence. With multiple proposed functions in diverse tissues, continued research is still necessary to fully unveil the role of SELENOM.
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Affiliation(s)
- Lance G. A. Nunes
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813-5525, USA
| | - Antavius Cain
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA;
| | - Cody Comyns
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511-4902, USA
| | - Peter R. Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813-5525, USA
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511-4902, USA
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3
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Hoffman KS, Chung CZ, Mukai T, Krahn N, Jiang HK, Balasuriya N, O'Donoghue P, Söll D. Recoding UAG to selenocysteine in Saccharomyces cerevisiae. RNA 2023; 29:1400-1410. [PMID: 37279998 PMCID: PMC10573291 DOI: 10.1261/rna.079658.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
Unique chemical and physical properties are introduced by inserting selenocysteine (Sec) at specific sites within proteins. Recombinant and facile production of eukaryotic selenoproteins would benefit from a yeast expression system; however, the selenoprotein biosynthetic pathway was lost in the evolution of the kingdom Fungi as it diverged from its eukaryotic relatives. Based on our previous development of efficient selenoprotein production in bacteria, we designed a novel Sec biosynthesis pathway in Saccharomyces cerevisiae using Aeromonas salmonicida translation components. S. cerevisiae tRNASer was mutated to resemble A. salmonicida tRNASec to allow recognition by S. cerevisiae seryl-tRNA synthetase as well as A. salmonicida selenocysteine synthase (SelA) and selenophosphate synthetase (SelD). Expression of these Sec pathway components was then combined with metabolic engineering of yeast to enable the production of active methionine sulfate reductase enzyme containing genetically encoded Sec. Our report is the first demonstration that yeast is capable of selenoprotein production by site-specific incorporation of Sec.
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Affiliation(s)
- Kyle S Hoffman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Han-Kai Jiang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
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4
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Morosky P, Comyns C, Nunes LGA, Chung CZ, Hoffmann PR, Söll D, Vargas-Rodriguez O, Krahn N. Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins. Front Mol Biosci 2023; 10:1096261. [PMID: 36762212 PMCID: PMC9902344 DOI: 10.3389/fmolb.2023.1096261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
Post-translational modifications (PTMs) can occur on almost all amino acids in eukaryotes as a key mechanism for regulating protein function. The ability to study the role of these modifications in various biological processes requires techniques to modify proteins site-specifically. One strategy for this is genetic code expansion (GCE) in bacteria. The low frequency of post-translational modifications in bacteria makes it a preferred host to study whether the presence of a post-translational modification influences a protein's function. Genetic code expansion employs orthogonal translation systems engineered to incorporate a modified amino acid at a designated protein position. Selenoproteins, proteins containing selenocysteine, are also known to be post-translationally modified. Selenoproteins have essential roles in oxidative stress, immune response, cell maintenance, and skeletal muscle regeneration. Their complicated biosynthesis mechanism has been a hurdle in our understanding of selenoprotein functions. As technologies for selenocysteine insertion have recently improved, we wanted to create a genetic system that would allow the study of post-translational modifications in selenoproteins. By combining genetic code expansion techniques and selenocysteine insertion technologies, we were able to recode stop codons for insertion of N ε-acetyl-l-lysine and selenocysteine, respectively, into multiple proteins. The specificity of these amino acids for their assigned position and the simplicity of reverting the modified amino acid via mutagenesis of the codon sequence demonstrates the capacity of this method to study selenoproteins and the role of their post-translational modifications. Moreover, the evidence that Sec insertion technology can be combined with genetic code expansion tools further expands the chemical biology applications.
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Affiliation(s)
- Pearl Morosky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Cody Comyns
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Lance G. A. Nunes
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Peter R. Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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5
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Chung CZ, Söll D, Krahn N. Creating Selenocysteine-Specific Reporters Using Inteins. Methods Mol Biol 2023; 2676:69-86. [PMID: 37277625 DOI: 10.1007/978-1-0716-3251-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The selenium moiety in selenocysteine (Sec) imparts enhanced chemical properties to this amino acid and ultimately the protein in which it is inserted. These characteristics are attractive for designing highly active enzymes or extremely stable proteins and studying protein folding or electron transfer, to name a few. There are also 25 human selenoproteins, of which many are essential for our survival. The ability to create or study these selenoproteins is significantly hindered by the inability to easily produce them. Engineering translation has yielded simpler systems to facilitate site-specific insertion of Sec; however, Ser misincorporation remains problematic. Therefore, we have designed two Sec-specific reporters which promote high-throughput screening of Sec translation systems to overcome this barrier. This protocol outlines the workflow to engineer these Sec-specific reporters, with the application to any gene of interest and the ability to transfer this strategy to any organism.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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6
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Abstract
Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.
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Affiliation(s)
- Kexin Meng
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- *Correspondence: Natalie Krahn,
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7
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Chung CZ, Krahn N. The selenocysteine toolbox: A guide to studying the 21st amino acid. Arch Biochem Biophys 2022; 730:109421. [DOI: 10.1016/j.abb.2022.109421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
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8
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Krahn N, Söll D, Vargas-Rodriguez O. Diversification of aminoacyl-tRNA synthetase activities via genomic duplication. Front Physiol 2022; 13:983245. [PMID: 36060688 PMCID: PMC9437257 DOI: 10.3389/fphys.2022.983245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Intricate evolutionary events enabled the emergence of the full set of aminoacyl-tRNA synthetase (aaRS) families that define the genetic code. The diversification of aaRSs has continued in organisms from all domains of life, yielding aaRSs with unique characteristics as well as aaRS-like proteins with innovative functions outside translation. Recent bioinformatic analyses have revealed the extensive occurrence and phylogenetic diversity of aaRS gene duplication involving every synthetase family. However, only a fraction of these duplicated genes has been characterized, leaving many with biological functions yet to be discovered. Here we discuss how genomic duplication is associated with the occurrence of novel aaRSs and aaRS-like proteins that provide adaptive advantages to their hosts. We illustrate the variety of activities that have evolved from the primordial aaRS catalytic sites. This precedent underscores the need to investigate currently unexplored aaRS genomic duplications as they may hold a key to the discovery of exciting biological processes, new drug targets, important bioactive molecules, and tools for synthetic biology applications.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- *Correspondence: Oscar Vargas-Rodriguez,
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9
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Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res 2022; 50:10201-10211. [PMID: 35882385 PMCID: PMC9561287 DOI: 10.1093/nar/gkac576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNAUTu1, a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNAUTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.
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Affiliation(s)
| | | | | | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Miri Krupkin
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA
| | - Ziao Fu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Francisco J Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 24, Sweden
| | - Junhong Choi
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 24, Sweden
| | | | - Dieter Söll
- Correspondence may also be addressed to Dieter Söll.
| | - Joseph Puglisi
- To whom correspondence should be addressed. Tel: +1 650 498 4397;
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10
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Chung CZ, Söll D, Krahn N. Using selenocysteine-specific reporters to screen for efficient tRNA Sec variants. Methods Enzymol 2022; 662:63-93. [PMID: 35101219 DOI: 10.1016/bs.mie.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The unique properties of selenocysteine (Sec) have generated an interest in the scientific community to site-specifically incorporate Sec into a protein of choice. Current technologies have rewired the natural Sec-specific translation factor-dependent selenoprotein biosynthesis pathway by harnessing the canonical elongation factor (EF-Tu) to simplify the requirements for Sec incorporation in Escherichia coli. This strategy is versatile and can be applied to Sec incorporation at any position in a protein of interest. However, selenoprotein production is still limited by yield and serine misincorporation. This protocol outlines a method in E. coli to design and optimize tRNA libraries which can be selected and screened for by the use of Sec-specific intein-based reporters. This provides a fast and simple way to engineer tRNAs with enhanced Sec-incorporation ability.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States.
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
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11
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Abstract
Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.
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Affiliation(s)
- Armaan Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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12
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Chung CZ, Krahn N, Crnković A, Söll D. Intein-based Design Expands Diversity of Selenocysteine Reporters. J Mol Biol 2021; 434:167199. [PMID: 34411545 PMCID: PMC8847544 DOI: 10.1016/j.jmb.2021.167199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 12/27/2022]
Abstract
The presence of selenocysteine in a protein confers many unique properties that make the production of recombinant selenoproteins desirable. Targeted incorporation of Sec into a protein of choice is possible by exploiting elongation factor Tu-dependent reassignment of UAG codons, a strategy that has been continuously improved by a variety of means. Improving selenoprotein yield by directed evolution requires selection and screening markers that are titratable, have a high dynamic range, enable high-throughput screening, and can discriminate against nonspecific UAG decoding. Current screening techniques are limited to a handful of reporters where a cysteine (Cys) or Sec residue normally affords activity. Unfortunately, these existing Cys/Sec-dependent reporters lack the dynamic range of more ubiquitous reporters or suffer from other limitations. Here we present a versatile strategy to adapt established reporters for specific Sec incorporation. Inteins are intervening polypeptides that splice themselves from the precursor protein in an autocatalytic splicing reaction. Using an intein that relies exclusively on Sec for splicing, we show that this intein cassette can be placed in-frame within selection and screening markers, affording reporter activity only upon successful intein splicing. Furthermore, because functional splicing can only occur when a catalytic Sec is present, the amount of synthesized reporter directly measures UAG-directed Sec incorporation. Importantly, we show that results obtained with intein-containing reporters are comparable to the Sec incorporation levels determined by mass spectrometry of isolated recombinant selenoproteins. This result validates the use of these intein-containing reporters to screen for evolved components of a translation system yielding increased selenoprotein amounts.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511, USA.
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13
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Moya-Torres A, Gupta M, Heide F, Krahn N, Legare S, Nikodemus D, Imhof T, Meier M, Koch M, Stetefeld J. Homogenous overexpression of the extracellular matrix protein Netrin-1 in a hollow fiber bioreactor. Appl Microbiol Biotechnol 2021; 105:6047-6057. [PMID: 34342709 PMCID: PMC8390410 DOI: 10.1007/s00253-021-11438-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/24/2021] [Accepted: 07/03/2021] [Indexed: 12/14/2022]
Abstract
The production of recombinant proteins for functional and biophysical studies, especially in the field of structural determination, still represents a challenge as high quality and quantities are needed to adequately perform experiments. This is in part solved by optimizing protein constructs and expression conditions to maximize the yields in regular flask expression systems. Still, work flow and effort can be substantial with no guarantee to obtain improvements. This study presents a combination of workflows that can be used to dramatically increase protein production and improve processing results, specifically for the extracellular matrix protein Netrin-1. This proteoglycan is an axon guidance cue which interacts with various receptors to initiate downstream signaling cascades affecting cell differentiation, proliferation, metabolism, and survival. We were able to produce large glycoprotein quantities in mammalian cells, which were engineered for protein overexpression and secretion into the media using the controlled environment provided by a hollow fiber bioreactor. Close monitoring of the internal bioreactor conditions allowed for stable production over an extended period of time. In addition to this, Netrin-1 concentrations were monitored in expression media through biolayer interferometry which allowed us to increase Netrin-1 media concentrations tenfold over our current flask systems while preserving excellent protein quality and in solution behavior. Our particular combination of genetic engineering, cell culture system, protein purification, and biophysical characterization permitted us to establish an efficient and continuous production of high-quality protein suitable for structural biology studies that can be translated to various biological systems. KEY POINTS: • Hollow fiber bioreactor produces substantial yields of homogenous Netrin-1 • Biolayer interferometry allows target protein quantitation in expression media • High production yields in the bioreactor do not impair Netrin-1 proteoglycan quality.
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Affiliation(s)
- Aniel Moya-Torres
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Monika Gupta
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Scott Legare
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Denise Nikodemus
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Imhof
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Center for Molecular Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
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14
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Abstract
Selenoproteins contain the 21st amino acid, selenocysteine. Selenocysteine is the only amino acid that is synthesized on its cognate tRNA, and it is inserted at specific recoded UGA stop codons via a complex translation system. Although highly similar to cysteine, selenocysteine has unique properties, including a stronger nucleophilic ability and lower reduction potential. Efforts to site-specifically incorporate selenocysteine to create recombinant selenoproteins involve a recoded UAG stop codon and expression of the necessary selenocysteine translation machinery. This article presents a protocol for expressing and purifying selenoproteins in Escherichia coli. © 2021 Wiley Periodicals LLC. Basic Protocol: Recombinant selenoprotein production in E. coli using a rewired translation system.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Corwin Miller
- Department of Biosciences, Rice University, Houston, Texas
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Department of Chemistry, Yale University, New Haven, Connecticut
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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15
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Evans RM, Krahn N, Murphy BJ, Lee H, Armstrong FA, Söll D. Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance. Proc Natl Acad Sci U S A 2021; 118:e2100921118. [PMID: 33753519 PMCID: PMC8020662 DOI: 10.1073/pnas.2100921118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In [NiFe]-hydrogenases, the active-site Ni is coordinated by four cysteine-S ligands (Cys; C), two of which are bridging to the Fe(CO)(CN)2 fragment. Substitution of a single Cys residue by selenocysteine (Sec; U) occurs occasionally in nature. Using a recent method for site-specific Sec incorporation into proteins, each of the four Ni-coordinating cysteine residues in the oxygen-tolerant Escherichia coli [NiFe]-hydrogenase-1 (Hyd-1) has been replaced by U to identify its importance for enzyme function. Steady-state solution activity of each Sec-substituted enzyme (on a per-milligram basis) is lowered, although this may reflect the unquantified presence of recalcitrant inactive/immature/misfolded forms. Protein film electrochemistry, however, reveals detailed kinetic data that are independent of absolute activities. Like native Hyd-1, the variants have low apparent KMH2 values, do not produce H2 at pH 6, and display the same onset overpotential for H2 oxidation. Mechanistically important differences were identified for the C576U variant bearing the equivalent replacement found in native [NiFeSe]-hydrogenases, its extreme O2 tolerance (apparent KMH2 and Vmax [solution] values relative to native Hyd-1 of 0.13 and 0.04, respectively) implying the importance of a selenium atom in the position cis to the site where exogenous ligands (H-, H2, O2) bind. Observation of the same unusual electrocatalytic signature seen earlier for the proton transfer-defective E28Q variant highlights the direct role of the chalcogen atom (S/Se) at position 576 close to E28, with the caveat that Se is less effective than S in facilitating proton transfer away from the Ni during H2 oxidation by this enzyme.
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Affiliation(s)
- Rhiannon M Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Bonnie J Murphy
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Harrison Lee
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom;
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Chemistry, Yale University, New Haven, CT 06520
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16
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Abstract
Transfer RNA (tRNA) is the central molecule in genetically encoded protein synthesis. Most tRNA species were found to be very similar in structure: the well-known cloverleaf secondary structure and L-shaped tertiary structure. Furthermore, the length of the acceptor arm, T-arm, and anticodon arm were found to be closely conserved. Later research discovered naturally occurring, active tRNAs that did not fit the established 'canonical' tRNA structure. This review discusses the non-canonical structures of some well-characterized natural tRNA species and describes how these structures relate to their role in translation. Additionally, we highlight some newly discovered tRNAs in which the structure-function relationship is not yet fully understood.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Jonathan T Fischer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
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17
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Abstract
Within the broad field of synthetic biology, genetic code expansion (GCE) techniques enable creation of proteins with an expanded set of amino acids. This may be invaluable for applications in therapeutics, bioremediation, and biocatalysis. Central to GCE are aminoacyl-tRNA synthetases (aaRSs) as they link a non-canonical amino acid (ncAA) to their cognate tRNA, allowing ncAA incorporation into proteins on the ribosome. The ncAA-acylating aaRSs and their tRNAs should not cross-react with 20 natural aaRSs and tRNAs in the host, i.e., they need to function as an orthogonal translating system. All current orthogonal aaRS•tRNA pairs have been engineered from naturally occurring molecules to change the aaRS's amino acid specificity or assign the tRNA to a liberated codon of choice. Here we discuss the importance of orthogonality in GCE, laboratory techniques employed to create designer aaRSs and tRNAs, and provide an overview of orthogonal aaRS•tRNA pairs for GCE purposes.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.
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18
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Abstract
Genetic code expansion (GCE) has revolutionized the field of protein chemistry. Over the past several decades more than 150 different noncanonical amino acids (ncAAs) have been co-translationally installed into proteins within various host organisms. The vast majority of these ncAAs have been incorporated between the start and stop codons within an open reading frame. This requires that the ncAA be able to form a peptide bond at the α-amine, limiting the types of molecules that can be genetically encoded. In contrast, the α-amine of the initiating amino acid is not required for peptide bond formation. Therefore, including the initiator position in GCE allows for co-translational insertion of more diverse molecules that are modified, or completely lacking an α-amine. This review explores various methods which have been used to initiate protein synthesis with diverse molecules both in vitro and in vivo.
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Affiliation(s)
- Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - 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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19
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Tharp JM, Krahn N, Varshney U, Söll D. Front Cover: Hijacking Translation Initiation for Synthetic Biology (ChemBioChem 10/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jeffery M. Tharp
- Department of Molecular Biophysics and BiochemistryYale University New Haven CT 06520 USA
| | - Natalie Krahn
- Department of Molecular Biophysics and BiochemistryYale University New Haven CT 06520 USA
| | - Umesh Varshney
- Department of Microbiology and Cell BiologyIndian Institute of Science Bangalore 560012 India
| | - Dieter Söll
- Department of Molecular Biophysics and BiochemistryYale University New Haven CT 06520 USA
- Department of ChemistryYale University New Haven CT 06520 USA
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20
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Koul A, Gemmill D, Lubna N, Meier M, Krahn N, Booy EP, Stetefeld J, Patel TR, McKenna SA. Structural and Hydrodynamic Characterization of Dimeric Human Oligoadenylate Synthetase 2. Biophys J 2020; 118:2726-2740. [PMID: 32413313 PMCID: PMC7264852 DOI: 10.1016/j.bpj.2020.04.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/15/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Oligoadenylate synthetases (OASs) are a family of interferon-inducible enzymes that require double-stranded RNA (dsRNA) as a cofactor. Upon binding dsRNA, OAS undergoes a conformational change and is activated to polymerize ATP into 2'-5'-oligoadenylate chains. The OAS family consists of several isozymes, with unique domain organizations to potentially interact with dsRNA of variable length, providing diversity in viral RNA recognition. In addition, oligomerization of OAS isozymes, potentially OAS1 and OAS2, is hypothesized to be important for 2'-5'-oligoadenylate chain building. In this study, we present the solution conformation of dimeric human OAS2 using an integrated approach involving small-angle x-ray scattering, analytical ultracentrifugation, and dynamic light scattering techniques. We also demonstrate OAS2 dimerization using immunoprecipitation approaches in human cells. Whereas mutation of a key active-site aspartic acid residue prevents OAS2 activity, a C-terminal mutation previously hypothesized to disrupt OAS self-association had only a minor effect on OAS2 activity. Finally, we also present the solution structure of OAS1 monomer and dimer, comparing their hydrodynamic properties with OAS2. In summary, our work presents the first, to our knowledge, dimeric structural models of OAS2 that enhance our understanding of the oligomerization and catalytic function of OAS enzymes.
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Affiliation(s)
- Amit Koul
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Darren Gemmill
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Nikhat Lubna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Natalie Krahn
- Department of Molecular Biology and Biochemistry, Yale University, New Haven, Connecticut
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Northwest Calgary, Alberta, Canada; Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, Alberta, Canada.
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.
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21
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Ghaffari N, Jardon MA, Krahn N, Butler M, Kennard M, Turner RFB, Gopaluni B, Piret JM. Effects of cysteine, asparagine, or glutamine limitations in Chinese hamster ovary cell batch and fed‐batch cultures. Biotechnol Prog 2020; 36:e2946. [DOI: 10.1002/btpr.2946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Navid Ghaffari
- Michael Smith LaboratoriesThe University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological EngineeringThe University of British Columbia Vancouver British Columbia Canada
| | - Mario A. Jardon
- Michael Smith Genome Sciences CentreBC Cancer Research Centre Vancouver British Columbia Canada
| | - Natalie Krahn
- Department of MicrobiologyUniversity of Manitoba Winnipeg Manitoba Canada
| | - Michael Butler
- Department of MicrobiologyUniversity of Manitoba Winnipeg Manitoba Canada
- National Institute for Bioprocessing Research and Training Dublin Ireland
| | - Malcolm Kennard
- Michael Smith LaboratoriesThe University of British Columbia Vancouver British Columbia Canada
| | - Robin F. B. Turner
- Michael Smith LaboratoriesThe University of British Columbia Vancouver British Columbia Canada
- Department of Electrical and Computer EngineeringThe University of British Columbia Vancouver British Columbia Canada
- Department of ChemistryThe University of British Columbia Vancouver British Columbia Canada
| | - Bhushan Gopaluni
- Department of Chemical and Biological EngineeringThe University of British Columbia Vancouver British Columbia Canada
| | - James M. Piret
- Michael Smith LaboratoriesThe University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological EngineeringThe University of British Columbia Vancouver British Columbia Canada
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22
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Krahn N, Meier M, Reuten R, Koch M, Stetefeld J, Patel TR. Solution Structure of C. elegans UNC-6: A Nematode Paralogue of the Axon Guidance Protein Netrin-1. Biophys J 2019; 116:2121-2130. [PMID: 31103237 DOI: 10.1016/j.bpj.2019.04.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 12/14/2022] Open
Abstract
UNCoordinated-6 (UNC-6) was the first member of the netrin family to be discovered in Caenorhabditis elegans. With homology to human netrin-1, it is a key signaling molecule involved in directing axon migration in nematodes. Similar to netrin-1, UNC-6 interacts with multiple receptors (UNC-5 and UNC-40, specifically) to guide axon migration in development. As a result of the distinct evolutionary path of UNC-6 compared to vertebrate netrins, we decided to employ an integrated approach to study its solution behavior and compare it to the high-resolution structure we previously published on vertebrate netrins. Dynamic light scattering and analytical ultracentrifugation on UNC-6 (with and without its C-domain) solubilized in a low-ionic strength buffer suggested that UNC-6 forms high-order oligomers. An increase in the buffer ionic strength resulted in a more homogeneous preparation of UNC-6, that was used for subsequent solution x-ray scattering experiments. Our biophysical analysis of UNC-6 ΔC solubilized in a high-ionic strength buffer suggested that it maintains a similar head-to-stalk arrangement as netrins -1 and -4. This phenomenon is thought to play a role in the signaling behavior of UNC-6 and its ability to move throughout the extracellular matrix.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Raphael Reuten
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Medical Faculty, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Joerg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; DiscoveryLab and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
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23
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D'Eall C, Pon RA, Rossotti MA, Krahn N, Spearman M, Callaghan D, van Faassen H, Hussack G, Stetefeld J, Butler M, Durocher Y, Zhang J, Henry KA, Tanha J. Modulating antibody-dependent cellular cytotoxicity of epidermal growth factor receptor-specific heavy-chain antibodies through hinge engineering. Immunol Cell Biol 2019; 97:526-537. [PMID: 30680791 DOI: 10.1111/imcb.12238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/22/2019] [Accepted: 01/22/2019] [Indexed: 01/20/2023]
Abstract
Human IgG1 and IgG3 antibodies (Abs) can mediate Ab-dependent cellular cytotoxicity (ADCC), and engineering of the Ab Fc (point mutation; defucosylation) has been shown to affect ADCC by modulating affinity for FcRγIIIa. In the absence of a CH 1 domain, many camelid heavy-chain Abs (HCAbs) naturally bear very long and flexible hinge regions connecting their VH H and CH 2 domains. To better understand the influence of hinge length and structure on HCAb ADCC, we produced a series of hinge-engineered epidermal growth factor receptor (EGFR)-specific chimeric camelid VH H-human Fc Abs and characterized their affinities for recombinant EGFR and FcRγIIIa, their binding to EGFR-positive tumor cells, and their ability to elicit ADCC. In the case of one chimeric HCAb (EG2-hFc), we found that variants bearing longer hinges (IgG3 or camelid hinge regions) showed dramatically improved ADCC in comparison with a variant bearing the human IgG1 hinge, in similar fashion to a variant with reduced CH 2 fucosylation. Conversely, an EG2-hFc variant bearing a truncated human IgG1 upper hinge region failed to elicit ADCC. However, there was no consistent association between hinge length and ADCC for four similarly engineered chimeric HCAbs directed against distinct EGFR epitopes. These findings demonstrate that the ADCC of some HCAbs can be modulated simply by varying the length of the Ab hinge. Although this effect appears to be heavily epitope-dependent, this strategy may be useful to consider during the design of VH H-based therapeutic Abs for cancer.
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Affiliation(s)
- Calvin D'Eall
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Robert A Pon
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Martin A Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Natalie Krahn
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Maureen Spearman
- Department of Microbiology, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Deborah Callaghan
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Michael Butler
- Department of Microbiology, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Ave, Montréal, QC, H4P 2R2, Canada
| | - Jianbing Zhang
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
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24
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Reuten R, Krahn N, McDougall M, Nikodemus D, Meier M, Koch M, Stetefeld J, Patel TR. Solution Structures of Wildtype and Deglycosylated Neuropilin 1. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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25
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Krahn N, Spearman M, Meier M, Dorion-Thibaudeau J, McDougall M, Patel TR, De Crescenzo G, Durocher Y, Stetefeld J, Butler M. Inhibition of glycosylation on a camelid antibody uniquely affects its FcγRI binding activity. Eur J Pharm Sci 2017; 96:428-439. [DOI: 10.1016/j.ejps.2016.09.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 09/13/2016] [Accepted: 09/30/2016] [Indexed: 11/27/2022]
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26
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Grandin M, Meier M, Delcros JG, Nikodemus D, Reuten R, Patel TR, Goldschneider D, Orriss G, Krahn N, Boussouar A, Abes R, Dean Y, Neves D, Bernet A, Depil S, Schneiders F, Poole K, Dante R, Koch M, Mehlen P, Stetefeld J. Structural Decoding of the Netrin-1/UNC5 Interaction and its Therapeutical Implications in Cancers. Cancer Cell 2016; 29:173-85. [PMID: 26859457 DOI: 10.1016/j.ccell.2016.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/02/2015] [Accepted: 01/05/2016] [Indexed: 12/17/2022]
Abstract
Netrin-1 has been shown to be up-regulated in a fraction of human cancers as a mechanism to allow these tumors to escape the pro-apoptotic activity of some of its main dependence receptors, the UNC5 homologs (UNC5H). Here we identify the V-2 domain of netrin-1 to be important for its interaction with the Ig1/Ig2 domains of UNC5H2. We generate a humanized anti-netrin-1 antibody that disrupts the interaction between netrin-1 and UNC5H2 and triggers death of netrin-1-expressing tumor cells in vitro. We also present evidence that combining the anti-netrin-1 antibody with epidrugs such as decitabine could be effective in treating tumors showing no or modest netrin-1 expression. These results support that this antibody is a promising drug candidate.
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Affiliation(s)
- Mélodie Grandin
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Markus Meier
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB RT3 2N2, Canada
| | - Jean Guy Delcros
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Denise Nikodemus
- Center for Biochemistry, Institute for Dental Research and Oral Musculoskeletal Research, University of Cologne, 50931 Cologne, Germany; Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon 1749-016, Portugal
| | - Raphael Reuten
- Center for Biochemistry, Institute for Dental Research and Oral Musculoskeletal Research, University of Cologne, 50931 Cologne, Germany
| | - Trushar R Patel
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB RT3 2N2, Canada; Department of Microbiology, University of Manitoba, 144 Dysart Road, Winnipeg, MB RT3 2N2, Canada
| | - David Goldschneider
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France; Netris Pharma, Centre Léon Bérard, 69008 Lyon, France
| | - George Orriss
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB RT3 2N2, Canada
| | - Natalie Krahn
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB RT3 2N2, Canada
| | - Amina Boussouar
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Riad Abes
- Netris Pharma, Centre Léon Bérard, 69008 Lyon, France
| | - Yann Dean
- Netris Pharma, Centre Léon Bérard, 69008 Lyon, France
| | - David Neves
- Netris Pharma, Centre Léon Bérard, 69008 Lyon, France
| | - Agnes Bernet
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France; Netris Pharma, Centre Léon Bérard, 69008 Lyon, France
| | | | - Fiona Schneiders
- Center for Biochemistry, Institute for Dental Research and Oral Musculoskeletal Research, University of Cologne, 50931 Cologne, Germany
| | - Kate Poole
- Department of Neuroscience, Max-Delbrück Center for Molecular Medicine, Robert-Rössle Straβe 10, Berlin 13092, Germany
| | - Robert Dante
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Manuel Koch
- Center for Biochemistry, Institute for Dental Research and Oral Musculoskeletal Research, University of Cologne, 50931 Cologne, Germany; Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon 1749-016, Portugal
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France.
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB RT3 2N2, Canada.
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Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM. Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 2014; 186:98-109. [PMID: 25014402 DOI: 10.1016/j.jbiotec.2014.05.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/08/2014] [Accepted: 05/23/2014] [Indexed: 01/17/2023]
Abstract
The impact of operating conditions on the glycosylation pattern of humanized camelid monoclonal antibody, EG2-hFc produced by Chinese hamster ovary (CHO) cells has been evaluated by a combination of experiments and modeling. Cells were cultivated under different levels of glucose and glutamine concentrations with the goal of investigating the effect of nutrient depletion levels and ammonia build up on the cell growth and the glycoprofiles of the monoclonal antibody (Mab). The effect of average pH reduction on glycosylation level during the entire culture time or during a specific time span was also investigated. The relative abundance of glycan structures was quantified by hydrophilic interaction liquid chromatography (HILIC) and the galactosylation index (GI) and the sialylation index (SI) were determined. Lower initial concentrations of glutamine resulted in lower glucose consumption and lower cell yield but increased GI and SI levels when compared to cultures started with higher initial glutamine levels. Similarly, reducing the average pH of culture resulted in lower growth but higher SI and GI levels. These findings indicate that there is a tradeoff between cell growth, resulting Mab productivity and the achievement of desirable higher glycosylation levels. A dynamic model, based on a metabolic flux analysis (MFA), is proposed to describe the metabolism of nutrients, cell growth and Mab productivity. Finally, existing software (GLYCOVIS) that describes the glycosylation pathways was used to illustrate the impact of extracellular species on the glycoprofiles.
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Affiliation(s)
| | - Kaveh Ohadi
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
| | - Maureen Spearman
- Microbiology Department, University of Manitoba, Winnipeg, MB, Canada.
| | - Natalie Krahn
- Microbiology Department, University of Manitoba, Winnipeg, MB, Canada.
| | - Murray Moo-Young
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
| | - Jeno M Scharer
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
| | - Mike Butler
- Microbiology Department, University of Manitoba, Winnipeg, MB, Canada.
| | - Hector M Budman
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
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