1
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Hunt JP, Free TJ, Galiardi J, Watt KM, Wood DW, Bundy BC. Streamlining the Detection of Human Thyroid Receptor Ligand Interactions with XL1-Blue Cell-Free Protein Synthesis and Beta-Galactosidase Fusion Protein Biosensors. Life (Basel) 2023; 13:1972. [PMID: 37895354 PMCID: PMC10608756 DOI: 10.3390/life13101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Thyroid receptor signaling controls major physiological processes and disrupted signaling can cause severe disorders that negatively impact human life. Consequently, methods to detect thyroid receptor ligands are of great toxicologic and pharmacologic importance. Previously, we reported thyroid receptor ligand detection with cell-free protein synthesis of a chimeric fusion protein composed of the human thyroid receptor beta (hTRβ) receptor activator and a β-lactamase reporter. Here, we report a 60% reduction in sensing cost by reengineering the chimeric fusion protein biosensor to include a reporter system composed of either the full-length beta galactosidase (β-gal), the alpha fragment of β-gal (β-gal-α), or a split alpha fragment of the β-gal (split β-gal-α). These biosensor constructs are deployed using E. coli XL1-Blue cell extract to (1) avoid the β-gal background activity abundant in BL21 cell extract and (2) facilitate β-gal complementation reporter activity to detect human thyroid receptor ligands. These results constitute a promising platform for high throughput screening and potentially the portable detection of human thyroid receptor ligands.
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Affiliation(s)
- J. Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Tyler J. Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Jackelyn Galiardi
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Kevin M. Watt
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84108, USA
| | - David W. Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
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2
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Pasch T, Schröder A, Kattelmann S, Eisenstein M, Pietrokovski S, Kümmel D, Mootz HD. Structural and biochemical analysis of a novel atypically split intein reveals a conserved histidine specific to cysteine-less inteins. Chem Sci 2023; 14:5204-5213. [PMID: 37206380 PMCID: PMC10189870 DOI: 10.1039/d3sc01200j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/23/2023] [Indexed: 05/21/2023] Open
Abstract
Protein trans-splicing mediated by a split intein reconstitutes a protein backbone from two parts. This virtually traceless autoprocessive reaction provides the basis for numerous protein engineering applications. Protein splicing typically proceeds through two thioester or oxyester intermediates involving the side chains of cysteine or serine/threonine residues. A cysteine-less split intein has recently attracted particular interest as it can splice under oxidizing conditions and is orthogonal to disulfide or thiol bioconjugation chemistries. Here, we report the split PolB16 OarG intein, a second such cysteine-independent intein. As a unique trait, it is atypically split with a short intein-N precursor fragment of only 15 amino acids, the shortest characterized to date, which was chemically synthesized to enable protein semi-synthesis. By rational engineering we obtained a high-yielding, improved split intein mutant. Structural and mutational analysis revealed the dispensability of the usually crucial conserved motif N3 (block B) histidine as an obvious peculiar property. Unexpectedly, we identified a previously unnoticed histidine in hydrogen-bond forming distance to the catalytic serine 1 as critical for splicing. This histidine has been overlooked so far in multiple sequence alignments and is highly conserved only in cysteine-independent inteins as a part of a newly discovered motif NX. The motif NX histidine is thus likely of general importance to the specialized environment in the active site required in this intein subgroup. Together, our study advances the toolbox as well as the structural and mechanistic understanding of cysteine-less inteins.
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Affiliation(s)
- Tim Pasch
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Alexander Schröder
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Sabrina Kattelmann
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Miriam Eisenstein
- Department of Molecular Genetics, Weizmann Institute of Science Rehovot 76100 Israel
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science Rehovot 76100 Israel
| | - Daniel Kümmel
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
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3
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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4
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Sekar G, Stevens AJ, Mostafavi AZ, Sashi P, Muir TW, Cowburn D. A Conserved Histidine Residue Drives Extein Dependence in an Enhanced Atypically Split Intein. J Am Chem Soc 2022; 144:19196-19203. [PMID: 36194550 PMCID: PMC10241006 DOI: 10.1021/jacs.2c08985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Split intein-mediated protein trans-splicing (PTS) is widely applied in chemical biology and biotechnology to carry out traceless and specific protein ligation. However, the external residues immediately flanking the intein (exteins) can reduce the splicing rate, thereby limiting certain applications of PTS. Splicing by a recently developed intein with atypical split architecture ("Cat") exhibits a stark dependence on the sequence of its N-terminal extein residues. Here, we further developed Cat using error-prone polymerase chain reaction (PCR) and a cell-based selection assay to produce Cat*, which exhibits greatly enhanced PTS activity in the presence of unfavorable N-extein residues. We then applied solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations to explore how the dynamics of a conserved B-block histidine residue (His78) contribute to this extein dependence. The enhanced extein tolerance of Cat* reported here should expand the applicability of atypically split inteins, and the mechanism highlights common principles that contribute to extein dependence.
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Affiliation(s)
- Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Adam J. Stevens
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Anahita Z. Mostafavi
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Pulikallu Sashi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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5
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Wall DA, Tarrant SP, Wang C, Mills KV, Lennon CW. Intein Inhibitors as Novel Antimicrobials: Protein Splicing in Human Pathogens, Screening Methods, and Off-Target Considerations. Front Mol Biosci 2021; 8:752824. [PMID: 34692773 PMCID: PMC8529194 DOI: 10.3389/fmolb.2021.752824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 01/20/2023] Open
Abstract
Protein splicing is a post-translational process by which an intervening polypeptide, or intein, catalyzes its own removal from the flanking polypeptides, or exteins, concomitant with extein ligation. Although inteins are highly abundant in the microbial world, including within several human pathogens, they are absent in the genomes of metazoans. As protein splicing is required to permit function of essential proteins within pathogens, inteins represent attractive antimicrobial targets. Here we review key proteins interrupted by inteins in pathogenic mycobacteria and fungi, exciting discoveries that provide proof of concept that intein activity can be inhibited and that this inhibition has an effect on the host organism's fitness, and bioanalytical methods that have been used to screen for intein activity. We also consider potential off-target inhibition of hedgehog signaling, given the similarity in structure and function of inteins and hedgehog autoprocessing domains.
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Affiliation(s)
- Diana A Wall
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Seanan P Tarrant
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States.,Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Christopher W Lennon
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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6
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Martin V, Egelund PHG, Johansson H, Thordal Le Quement S, Wojcik F, Sejer Pedersen D. Greening the synthesis of peptide therapeutics: an industrial perspective. RSC Adv 2020; 10:42457-42492. [PMID: 35516773 PMCID: PMC9057961 DOI: 10.1039/d0ra07204d] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Solid-phase peptide synthesis (SPPS) is generally the method of choice for the chemical synthesis of peptides, allowing routine synthesis of virtually any type of peptide sequence, including complex or cyclic peptide products. Importantly, SPPS can be automated and is scalable, which has led to its widespread adoption in the pharmaceutical industry, and a variety of marketed peptide-based drugs are now manufactured using this approach. However, SPPS-based synthetic strategies suffer from a negative environmental footprint mainly due to extensive solvent use. Moreover, most of the solvents used in peptide chemistry are classified as problematic by environmental agencies around the world and will soon need to be replaced, which in recent years has spurred a movement in academia and industry to make peptide synthesis greener. These efforts have been centred around solvent substitution, recycling and reduction, as well as exploring alternative synthetic methods. In this review, we focus on methods pertaining to solvent substitution and reduction with large-scale industrial production in mind, and further outline emerging technologies for peptide synthesis. Specifically, the technical requirements for large-scale manufacturing of peptide therapeutics are addressed.
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Affiliation(s)
- Vincent Martin
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Peter H G Egelund
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Henrik Johansson
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | | | - Felix Wojcik
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Daniel Sejer Pedersen
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
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7
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Hoffmann S, Terhorst TME, Singh RK, Kümmel D, Pietrokovski S, Mootz HD. Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein. Chembiochem 2020; 22:364-373. [PMID: 32813312 PMCID: PMC7891396 DOI: 10.1002/cbic.202000509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Indexed: 12/31/2022]
Abstract
Split inteins are indispensable tools for protein engineering because their ligation and cleavage reactions enable unique modifications of the polypeptide backbone. Three different classes of inteins have been identified according to the nature of the covalent intermediates resulting from the acyl rearrangements in the multistep protein‐splicing pathway. Class 3 inteins employ a characteristic internal cysteine for a branched thioester intermediate. A bioinformatic database search of non‐redundant protein sequences revealed the absence of split variants in 1701 class 3 inteins. We have discovered the first reported split class 3 intein in a metagenomics data set and report its biochemical, mechanistic and structural analysis. The AceL NrdHF intein exhibits low sequence conservation with other inteins and marked deviations in residues at conserved key positions, including a variation of the typical class‐3 WCT triplet motif. Nevertheless, functional analysis confirmed the class 3 mechanism of the intein and revealed excellent splicing yields within a few minutes over a wide range of conditions and with barely detectable cleavage side reactions. A high‐resolution crystal structure of the AceL NrdHF precursor and a mutagenesis study explained the importance and roles of several residues at the key positions. Tolerated substitutions in the flanking extein residues and a high affinity between the split intein fragments further underline the intein's future potential as a ligation tool.
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Affiliation(s)
- Simon Hoffmann
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Tobias M E Terhorst
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Rohit K Singh
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
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8
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Oeemig JS, Beyer HM, Aranko AS, Mutanen J, Iwaï H. Substrate specificities of inteins investigated by QuickDrop-cassette mutagenesis. FEBS Lett 2020; 594:3338-3355. [PMID: 32805768 DOI: 10.1002/1873-3468.13909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 01/21/2023]
Abstract
Inteins catalyze self-excision from host precursor proteins while concomitantly ligating the flanking substrates (exteins) with a peptide bond. Noncatalytic extein residues near the splice junctions, such as the residues at the -1 and +2 positions, often strongly influence the protein-splicing efficiency. The substrate specificities of inteins have not been studied for many inteins. We developed a convenient mutagenesis platform termed "QuickDrop"-cassette mutagenesis for investigating the influences of 20 amino acid types at the -1 and +2 positions of different inteins. We elucidated 17 different profiles of the 20 amino acid dependencies across different inteins. The substrate specificities will accelerate our understanding of the structure-function relationship at the splicing junctions for broader applications of inteins in biotechnology and molecular biosciences.
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Affiliation(s)
- Jesper S Oeemig
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - A Sesilja Aranko
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Justus Mutanen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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9
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Abstract
Split inteins are privileged molecular scaffolds for the chemical modification of proteins. Though efficient for in vitro applications, these polypeptide ligases have not been utilized for the semisynthesis of proteins in live cells. Here, we biochemically and structurally characterize the naturally split intein VidaL. We show that this split intein, which features the shortest known N-terminal fragment, supports rapid and efficient protein trans-splicing under a range of conditions, enabling semisynthesis of modified proteins both in vitro and in mammalian cells. The utility of this protein engineering system is illustrated through the traceless assembly of multidomain proteins whose biophysical properties render them incompatible with a single expression system, as well as by the semisynthesis of dual posttranslationally modified histone proteins in live cells. We also exploit the domain swapping function of VidaL to effect simultaneous modification and translocation of the nuclear protein HP1α in live cells. Collectively, our studies highlight the VidaL system as a tool for the precise chemical modification of cellular proteins with spatial and temporal control.
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10
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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11
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Unbiased libraries in protein directed evolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140321. [DOI: 10.1016/j.bbapap.2019.140321] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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12
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Beyer HM, Iwaï H. Off-Pathway-Sensitive Protein-Splicing Screening Based on a Toxin/Antitoxin System. Chembiochem 2019; 20:1933-1938. [PMID: 30963690 PMCID: PMC6771659 DOI: 10.1002/cbic.201900139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Indexed: 02/04/2023]
Abstract
Protein‐splicing domains are frequently used engineering tools that find application in the in vivo and in vitro ligation of protein domains. Directed evolution is among the most promising technologies used to advance this technology. However, the available screening systems for protein‐splicing activity are associated with bottlenecks such as the selection of pseudo‐positive clones arising from off‐pathway reaction products or fragment complementation. Herein, we report a stringent screening method for protein‐splicing activity in cis and trans, that exclusively selects productively splicing domains. By fusing splicing domains to an intrinsically disordered region of the antidote from the Escherichia coli CcdA/CcdB type II toxin/antitoxin system, we linked protein splicing to cell survival. The screen allows selecting novel cis‐ and trans‐splicing inteins catalyzing productive highly efficient protein splicing, for example, from directed‐evolution approaches or the natural intein sequence space.
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Affiliation(s)
- Hannes M Beyer
- Research Program in Structural Biology and Biophysics, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
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13
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Bachmann AL, Mootz HD. N-terminal chemical protein labeling using the naturally split GOS-TerL intein. J Pept Sci 2017; 23:624-630. [PMID: 28332258 DOI: 10.1002/psc.2996] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/07/2022]
Abstract
Chemoselective and regioselective chemical protein labeling is of great importance, yet no current technique is sufficiently general and simple to perform. Protein trans-splicing by split inteins can be used to ligate short tags with chemical labels to either the N or the C terminus of a protein. The CysTag approach exploits split intein fragments without a cysteine fused with such a short tag containing a single cysteine that is easily amenable to selective modification using classical cysteine bioconjugation. Labeling of the protein of interest is achieved through transfer of the pre-labeled tag by protein trans-splicing. This protocol keeps other cysteines unmodified. While split inteins for C-terminal CysTag labeling were previously reported, no high-yielding and naturally split intein for N-terminal labeling has been available. In this work, the recently discovered GOS-TerL intein was explored as the only known naturally split intein that both lacks a cysteine in its N-terminal fragment and is active under ambient conditions. Thioredoxin as a model protein and a camelid nanobody were labeled with a synthetic fluorophore by transferring the pre-labeling CysTag in the protein trans-splicing reaction with yields of about 50 to 90%. The short N-terminal intein fragment was also chemically synthesized with a tag to enable protein labeling by semi-synthetic protein trans-splicing. Our results expand the scope of the CysTag labeling strategy, which achieves selective chemical modification without the requirement for sophisticated biorthogonal functional groups and rather builds on the plethora of commercially available reagents directed at the thiol side chain of cysteine. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Anne-Lena Bachmann
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
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