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Gharios R, Li A, Kopyeva I, Francis RM, DeForest CA. One-Step Purification and N-Terminal Functionalization of Bioactive Proteins via Atypically Split Inteins. Bioconjug Chem 2024; 35:750-757. [PMID: 38815180 PMCID: PMC11262789 DOI: 10.1021/acs.bioconjchem.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Site-specific installation of non-natural functionality onto proteins has enabled countless applications in biotechnology, chemical biology, and biomaterials science. Though the N-terminus is an attractive derivatization location, prior methodologies targeting this site have suffered from low selectivity, a limited selection of potential chemical modifications, and/or challenges associated with divergent protein purification/modification steps. In this work, we harness the atypically split VidaL intein to simultaneously N-functionalize and purify homogeneous protein populations in a single step. Our method─referred to as VidaL-tagged expression and protein ligation (VEPL)─enables modular and scalable production of N-terminally modified proteins with native bioactivity. Demonstrating its flexibility and ease of use, we employ VEPL to combinatorially install 4 distinct (multi)functional handles (e.g., biotin, alkyne, fluorophores) to the N-terminus of 4 proteins that span three different classes: fluorescent (Enhanced Green Fluorescent Protein, mCherry), enzymatic (β-lactamase), and growth factor (epidermal growth factor). Moving forward, we anticipate that VEPL's ability to rapidly generate and isolate N-modified proteins will prove useful across the growing fields of applied chemical biology.
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Affiliation(s)
- Ryan Gharios
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Annabella Li
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Irina Kopyeva
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - Ryan M Francis
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington 98105, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, Washington 98105, United States
- Institute for Protein Design, University of Washington, Seattle ,Washington 98105, United States
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Hume AJ, Deeney DJ, Smetana JS, Turcinovic J, Connor JH, Belfort M, Mühlberger E, Lennon CW. Improved protein splicing through viral passaging. mBio 2024; 15:e0098424. [PMID: 38780266 PMCID: PMC11237716 DOI: 10.1128/mbio.00984-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Intervening proteins (inteins) are translated as subdomains within host proteins and removed through an intein-driven splicing reaction where the flanking sequences (exteins) are joined with a peptide bond. Previously, we developed a self-removing translation reporter for labeling Ebola virus (EBOV). In this reporter, an intein (RadA) containing the fluorescent protein ZsGreen (ZsG) is inserted within the EBOV protein VP30. Upon VP30-RadA-ZsG expression from the viral genome, RadA-ZsG is removed from VP30 through the protein splicing activity of RadA, generating functional, non-tagged VP30 and functional ZsGreen. While incorporation of our VP30-RadA-ZsG fusion reporter into recombinant EBOV (rEBOV-RadA-ZsG) resulted in an infectious virus that expresses ZsG upon infection of cells, this virus displayed a replication defect compared to wild-type EBOV, which might be the result of insufficient RadA splicing. Here, we demonstrate that the serial passaging of rEBOV-RadA-ZsG in human cells led to an increase in replication efficiency compared to unpassaged rEBOV-RadA-ZsG. Sequencing of passaged viruses revealed intein-specific mutations. These mutations improve intein activity in both prokaryotic and eukaryotic systems, as well as in multiple extein contexts. Taken together, our findings offer a novel means to select for inteins with enhanced catalytic properties that appear independent of extein context and expression system.IMPORTANCEIntervening proteins (inteins) are self-removing protein elements that have been utilized to develop a variety of innovative protein engineering technologies. Here, we report the isolation of inteins with improved catalytic activity through viral passaging. Specifically, we inserted a highly active intein within an essential protein of Ebola virus and serially passaged this recombinant virus, which led to intein-specific hyper-activity mutations. The identified mutations showed improved intein activity within both bacterial and eukaryotic expression systems and in multiple extein contexts. These results present a new strategy for developing inteins with improved splicing activity.
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Affiliation(s)
- Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, Massachusetts, USA
| | - Dylan J Deeney
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - John S Smetana
- Department of Biological Sciences, Murray State University, Murray, Kentucky, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, Massachusetts, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Christopher W Lennon
- Department of Biological Sciences, Murray State University, Murray, Kentucky, USA
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Clifford R, Lindman S, Zhu J, Luo E, Delmar J, Tao Y, Ren K, Lara A, Cayatte C, McTamney P, O'Connor E, Öhman J. Production of native recombinant proteins using a novel split intein affinity technology. J Chromatogr A 2024; 1724:464908. [PMID: 38669943 DOI: 10.1016/j.chroma.2024.464908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Affinity tags are frequently engineered into recombinant proteins to facilitate purification. Although this technique is powerful, removal of the tag is desired because the tag can interfere with biological activity and can potentially increase the immunogenicity of therapeutic proteins. Tag removal is complex, as it requires adding expensive protease enzymes. To overcome this limitation, split intein based affinity purification systems have been developed in which a CC-intein tag is engineered into a protein of interest for binding to a NC-intein peptide ligand fixed to a chromatographic support. Tag removal in these systems is achieved by creating an active intein-complex during protein capture, which triggers a precise self-cleavage reaction. In this work, we show applications of a new split intein system, Cytiva™ ProteinSelect™. One advantage of the new system is that the NC-intein ligand can be robustly produced and conjugated to large volumes of resin for production of gram scale proteins. SARS-CoV-2 spike protein receptor binding domain and a Bispecific T Cell Engager in this work were successfully captured on the affinity resin and scaled 10-fold. Another advantage of this system is the ability to sanitize the resin with sodium hydroxide without loosing the 10-20 g/L binding capacity. Binding studies with IL-1b and IFNAR-1 ECD showed that the resin can be regenerated and sanitized for up to 50 cycles without loosing binding capacity. Additionally, after several cycles of sanitization, binding capacity was retained for the SARS-CoV-2 spike protein receptor binding domain and a Bispecific T Cell Engager. As with other split intein systems, optimization was needed to achieve ideal expression and recovery. The N-terminal amino acid sequence of the protein of interest required engineering to enable the cleavage reaction. Additionally, ensuring the stability of the CC-intein tag was important to prevent premature cleavage or truncation. Controlling the hold time of the expression product and the prevention of protease activity prior to purification was needed. These results demonstrate the feasibility of the Cytiva™ ProteinSelect™ system to be used in academic and industrial research and development laboratories for the purification of novel proteins expressed in either bacterial or mammalian systems.
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Affiliation(s)
- Robert Clifford
- Purification Process Sciences, Process and Analytical Sciences, R&D Biopharmaceuticals, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | | | - Jie Zhu
- Cell Culture & Fermentation Sciences, R&D Biopharmaceuticals, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Ethan Luo
- Cell Culture & Fermentation Sciences, R&D Biopharmaceuticals, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Jared Delmar
- Physicochemical Development, Process and Analytical Sciences, R&D Biopharmaceuticals, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Yeqing Tao
- Physicochemical Development, Process and Analytical Sciences, R&D Biopharmaceuticals, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Kuishu Ren
- Virology and Targeted Therapeutics, Virology and Vaccine Discovery, Vaccines & Immune Therapies Unit, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Abigail Lara
- Immune Engagers, Early ICC Discovery, R&D Oncology, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Corinne Cayatte
- Immune Engagers, Early ICC Discovery, R&D Oncology, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Patrick McTamney
- Virology and Targeted Therapeutics, Virology and Vaccine Discovery, Vaccines & Immune Therapies Unit, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA
| | - Ellen O'Connor
- Purification Process Sciences, Process and Analytical Sciences, R&D Biopharmaceuticals, AstraZeneca LLC, One Medimmune Way, Gaithersburg, MD 20878, USA.
| | - Johan Öhman
- Cytiva, Björkgatan 30, Uppsala, 753 23, Sweden
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Schneider RF, Hallstrom K, DeMott C, McDonough KA. Conditional protein splicing of the Mycobacterium tuberculosis RecA intein in its native host. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589443. [PMID: 38659745 PMCID: PMC11042385 DOI: 10.1101/2024.04.15.589443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The recA gene, encoding Recombinase A (RecA) is one of three Mycobacterium tuberculosis (Mtb) genes encoding an in-frame intervening protein sequence (intein) that must splice out of precursor host protein to produce functional protein. Ongoing debate about whether inteins function solely as selfish genetic elements or benefit their host cells requires understanding of interplay between inteins and their hosts. We measured environmental effects on native RecA intein splicing within Mtb using a combination of western blots and promoter reporter assays. RecA splicing was stimulated in bacteria exposed to DNA damaging agents or by treatment with copper in hypoxic, but not normoxic, conditions. Spliced RecA was processed by the Mtb proteasome, while free intein was degraded efficiently by other unknown mechanisms. Unspliced precursor protein was not observed within Mtb despite its accumulation during ectopic expression of Mtb recA within E. coli. Surprisingly, Mtb produced free N-extein in some conditions, and ectopic expression of Mtb N-extein activated LexA in E. coli. These results demonstrate that the bacterial environment greatly impacts RecA splicing in Mtb, underscoring the importance of studying intein splicing in native host environments and raising the exciting possibility of intein splicing as a novel regulatory mechanism in Mtb.
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Affiliation(s)
- Ryan F. Schneider
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
| | | | | | - Kathleen A. McDonough
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
- Wadsworth Center, New York Department of Health
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Lu W, Shi R, Li X, Ma S, Yang D, Shang D, Xia Q. A review on complete silk gene sequencing and de novo assembly of artificial silk. Int J Biol Macromol 2024; 264:130444. [PMID: 38417762 DOI: 10.1016/j.ijbiomac.2024.130444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Silk, especially spider and insect silk, is a highly versatile biomaterial with potential applications in biomedicine, materials science, and biomimetic engineering. The primary structure of silk proteins is the basis for the mechanical properties of silk fibers. Biotechnologies such as single-molecule sequencing have facilitated an increasing number of reports on new silk genes and assembled silk proteins. Therefore, this review aims to provide a comprehensive overview of the recent advances in representative spider and insect silk proteins, focusing on identification methods, sequence characteristics, and de novo design and assembly. The review discusses three identification methods for silk genes: polymerase chain reaction (PCR)-based sequencing, PCR-free cloning and sequencing, and whole-genome sequencing. Moreover, it reveals the main spider and insect silk proteins and their sequences. Subsequent de novo assembly of artificial silk is covered and future research directions in the field of silk proteins, including new silk genes, customizable artificial silk, and the expansion of silk production and applications are discussed. This review provides a basis for the genetic aspects of silk production and the potential applications of artificial silk in material science and biomedical engineering.
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Affiliation(s)
- Wei Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Run Shi
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Xue Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Daiying Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Deli Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China.
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Son A, Smetana JS, Horowitz S, Lennon CW. An intein-based biosensor to measure protein stability in vivo. Protein Sci 2024; 33:e4925. [PMID: 38380775 PMCID: PMC10880411 DOI: 10.1002/pro.4925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/10/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Biosensors to measure protein stability in vivo are valuable tools for a variety of applications. Previous work has demonstrated that a tripartite design, whereby a protein of interest (POI) is inserted within a reporter, can link POI stability to reporter activity. Inteins are translated within other proteins and excised in a self-mediated protein splicing reaction. Here, we developed a novel folding biosensor where a POI is inserted within an intein, which is subsequently translated within an antibiotic resistance marker. We showed that protein splicing is required for antibiotic resistance and that housing a stable POI within the intein, compared to an unstable variant, results in a 100,000-fold difference in survival. Further, using a fluorescent protein that matures slowly as the POI, we developed a reporter with two simultaneous readouts for protein folding. Finally, we showed that co-expression of GroEL can significantly increase the activity of both reporters, further verifying that protein folding factors can act on the POI in the biosensor. As a whole, our work provides a new twist on the traditional tripartite approach to measuring protein stability in vivo.
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Affiliation(s)
- Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy AgingUniversity of DenverDenverColoradoUSA
| | - John S. Smetana
- Department of Biological SciencesMurray State UniversityMurrayKentuckyUSA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy AgingUniversity of DenverDenverColoradoUSA
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