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Iwaï H, Beyer HM, Johansson JEM, Li M, Wlodawer A. The three-dimensional structure of the Vint domain from Tetrahymena thermophila suggests a ligand-regulated cleavage mechanism by the HINT fold. FEBS Lett 2024; 598:864-874. [PMID: 38351630 DOI: 10.1002/1873-3468.14817] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 04/23/2024]
Abstract
Vint proteins have been identified in unicellular metazoans as a novel hedgehog-related gene family, merging the von Willebrand factor type A domain and the Hedgehog/INTein (HINT) domains. We present the first three-dimensional structure of the Vint domain from Tetrahymena thermophila corresponding to the auto-processing domain of hedgehog proteins, shedding light on the unique features, including an adduct recognition region (ARR). Our results suggest a potential binding between the ARR and sulfated glycosaminoglycans like heparin sulfate. Moreover, we uncover a possible regulatory role of the ARR in the auto-processing by Vint domains, expanding our understanding of the HINT domain evolution and their use in biotechnological applications. Vint domains might have played a crucial role in the transition from unicellular to multicellular organisms.
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Affiliation(s)
- Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Finland
| | | | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, MD, USA
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
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2
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Kolesnik VV, Nurtdinov RF, Oloruntimehin ES, Karabelsky AV, Malogolovkin AS. Optimization strategies and advances in the research and development of AAV-based gene therapy to deliver large transgenes. Clin Transl Med 2024; 14:e1607. [PMID: 38488469 PMCID: PMC10941601 DOI: 10.1002/ctm2.1607] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 03/18/2024] Open
Abstract
Adeno-associated virus (AAV)-based therapies are recognized as one of the most potent next-generation treatments for inherited and genetic diseases. However, several biological and technological aspects of AAV vectors remain a critical issue for their widespread clinical application. Among them, the limited capacity of the AAV genome significantly hinders the development of AAV-based gene therapy. In this context, genetically modified transgenes compatible with AAV are opening up new opportunities for unlimited gene therapies for many genetic disorders. Recent advances in de novo protein design and remodelling are paving the way for new, more efficient and targeted gene therapeutics. Using computational and genetic tools, AAV expression cassette and transgenic DNA can be split, miniaturized, shuffled or created from scratch to mediate efficient gene transfer into targeted cells. In this review, we highlight recent advances in AAV-based gene therapy with a focus on its use in translational research. We summarize recent research and development in gene therapy, with an emphasis on large transgenes (>4.8 kb) and optimizing strategies applied by biomedical companies in the research pipeline. We critically discuss the prospects for AAV-based treatment and some emerging challenges. We anticipate that the continued development of novel computational tools will lead to rapid advances in basic gene therapy research and translational studies.
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Affiliation(s)
- Valeria V. Kolesnik
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
| | - Ruslan F. Nurtdinov
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
| | - Ezekiel Sola Oloruntimehin
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
| | | | - Alexander S. Malogolovkin
- Martsinovsky Institute of Medical ParasitologyTropical and Vector‐Borne Diseases, Sechenov UniversityMoscowRussia
- Center for Translational MedicineSirius University of Science and TechnologySochiRussia
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3
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Mariano A, Di Cristofano S, Raimondo D, Scotto d'Abusco A. Split Gp41-1 intein splicing as a model to evaluate the cellular location of the oncosuppressor Maspin in an in vitro model of osteosarcoma. Cell Biochem Funct 2024; 42:e3987. [PMID: 38509770 DOI: 10.1002/cbf.3987] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/06/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Inteins are proteins involved in the protein splicing mechanism, an autoprocessing event, where sequences (exteins) separated by inteins become ligated each other after recombination. Two kinds of inteins have been described, contiguous inteins and split inteins. The former ones are transcribed and translated as a single peptide along with their exteins, while the latter are fragmented between two different genes and are transcribed and translated separately. The aim of this study is to establish a method to obtain a fluorescent eukaryotic protein to analyze its cellular localization, using the natural split gp41-1 inteins. We chose natural split inteins due to their distribution in all three domains of life. Two constructs were prepared, one containing the N-terminal split intein along with the N-moiety of the Red Fluorescent Protein (RFP) and a second construct containing the C-terminal of split intein, the C-moiety of RFP and the gene coding for Maspin, a tumor suppressor protein. The trans-splicing was verified by transfecting both N-terminal and C-terminal constructs into mammalian cells. The success of the recombination event was highlighted through the fluorescence produced by reconstituted RFP after recombination, along with the overlap of the red fluorescence produced by recombined RFP and the green fluorescence produced by the hybridization of the recombinant Maspin with a specific antibody. In conclusion, we opted to use this mechanism of recombination to obtain a fluorescent Maspin instead to express a large fusion protein, considering that it could interfere with Maspin's structure and function.
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Affiliation(s)
- Alessia Mariano
- Department. of Biochemical Sciences, Sapienza University of Roma, Rome, Italy
| | | | - Domenico Raimondo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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4
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Lakshmanan RV, Agbandje-McKenna M, McKenna R. Feasibility of Domain Segmentation of B19V VP1u Using Intein Technology for Structural Studies. Protein Pept Lett 2024; 31:PPL-EPUB-137290. [PMID: 38243925 DOI: 10.2174/0109298665277211231214065419] [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] [Received: 08/30/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 01/22/2024]
Abstract
INTRODUCTION Parvovirus B19 (B19V) is a human pathogen, and the minor capsid protein of B19V possesses a unique N terminus called VP1u that plays a crucial role in the life cycle of the virus. OBJECTIVE The objective of this study was to develop a method for domain segmentation of B19 VP1u using intein technology, particularly its receptor binding domain (RBD) and phospholipase A2 (PLA2 ) domain. METHODS RBD and PLA2 domains of VP1u were each fused to the DnaE split inteins derived from the Nostoc punctiforme. Each of these precursor proteins was expressed in E. coli. Combining the purified precursors in equal molar ratios resulted in the formation of full-length VP1u. Furthermore, Circular Dichroism (CD) spectroscopy and PLA2 assays were used to probe the structure and activity of the newly formed protein. RESULTS The CD spectrum of the full length VP1u confirmed the secondary structure of protein, while the PLA2 assay indicated minimal disruption in enzymatic activity. CONCLUSION This method would allow for the selective incorporation of NMR-active isotopes into either of the VP1u domains, which can reduce signal overlap in NMR structural determination studies.
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Affiliation(s)
- Renuk Varayil Lakshmanan
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, USA
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5
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Gallot-Lavallée L, Jerlström-Hultqvist J, Zegarra-Vidarte P, Salas-Leiva DE, Stairs CW, Čepička I, Roger AJ, Archibald JM. Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes. Proc Natl Acad Sci U S A 2023; 120:e2306381120. [PMID: 38019867 DOI: 10.1073/pnas.2306381120] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Inteins are self-splicing protein elements found in viruses and all three domains of life. How the DNA encoding these selfish elements spreads within and between genomes is poorly understood, particularly in eukaryotes where inteins are scarce. Here, we show that the nuclear genomes of three strains of Anaeramoeba encode between 45 and 103 inteins, in stark contrast to four found in the most intein-rich eukaryotic genome described previously. The Anaeramoeba inteins reside in a wide range of proteins, only some of which correspond to intein-containing proteins in other eukaryotes, prokaryotes, and viruses. Our data also suggest that viruses have contributed to the spread of inteins in Anaeramoeba and the colonization of new alleles. The persistence of Anaeramoeba inteins might be partly explained by intragenomic movement of intein-encoding regions from gene to gene. Our intein dataset greatly expands the spectrum of intein-containing proteins and provides insights into the evolution of inteins in eukaryotes.
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Affiliation(s)
- Lucie Gallot-Lavallée
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jon Jerlström-Hultqvist
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala 751 24, Sweden
| | - Paula Zegarra-Vidarte
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala 751 24, Sweden
| | - Dayana E Salas-Leiva
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Courtney W Stairs
- Microbiology Group, Department of Biology, Lund University, Lund 223 62, Sweden
| | - Ivan Čepička
- Department of Zoology, Charles University, Prague 128 00, Czech Republic
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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López-Igual R, Dorado-Morales P, Mazel D. Increasing the Scalability of Toxin-Intein Orthogonal Combinations. ACS Synth Biol 2023; 12:618-623. [PMID: 36706324 PMCID: PMC9942249 DOI: 10.1021/acssynbio.2c00477] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Inteins are proteins embedded into host proteins from which they are excised in an autocatalytic reaction. Specifically, split inteins are separated into two independent fragments that reconstitute the host protein during the catalytic process. We recently developed a novel strategy for the specific killing of pathogenic and antibiotic resistant bacteria based on toxin-intein combinations. Bacterial type II toxin-antitoxin systems are protein modules in which the toxin can provoke cell death whereas the antitoxin inhibits toxin activity. Although our previous system was based on a split intein (iDnaE) and the CcdB toxin, we demonstrated that iDnaE is able to reconstitute four different toxins. To expand the applicability of our system by widening the repertoire of toxin-intein combinations for complex set-ups, we introduced a second intein, iDnaX, which was artificially split. We demonstrate that iDnaX is able to reconstitute the four toxins, and we manage to reduce its scar size to facilitate their use. In addition, we prove the orthogonality of both inteins (iDnaE and iDnaX) through a toxin reconstitution assay, thus opening the possibility for complex set-ups based on these toxin-intein modules. This could be used to develop specific antimicrobial and other biotechnological applications.
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Affiliation(s)
- Rocío López-Igual
- Institut
Pasteur, Université
de Paris, Unité Plasticité du Génome Bactérien,
et CNRS, UMR3525, 28 Rue
du Dr Roux, F-75015 Paris, France,Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 40, E-41092 Seville, Spain,
| | - Pedro Dorado-Morales
- Institut
Pasteur, Université
de Paris, Unité Plasticité du Génome Bactérien,
et CNRS, UMR3525, 28 Rue
du Dr Roux, F-75015 Paris, France
| | - Didier Mazel
- Institut
Pasteur, Université
de Paris, Unité Plasticité du Génome Bactérien,
et CNRS, UMR3525, 28 Rue
du Dr Roux, F-75015 Paris, France
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7
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Gosselin SP, Arsenault DR, Jennings CA, Gogarten JP. The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination. Genes (Basel) 2023; 14. [PMID: 36833214 DOI: 10.3390/genes14020288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction-modification systems). We found that the methylase family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages.
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Prabhala SV, Gierach I, Wood DW. The Evolution of Intein-Based Affinity Methods as Reflected in 30 years of Patent History. Front Mol Biosci 2022; 9:857566. [PMID: 35463948 PMCID: PMC9033041 DOI: 10.3389/fmolb.2022.857566] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/18/2022] Open
Abstract
Self-cleaving affinity tags, based on engineered intein protein domains, have been touted as a universal single step purification platform for tagless non-mAb proteins. These approaches provide all of the power and flexibility of tag-based affinity methods, but deliver a tagless target protein suitable for clinical applications without complex process development. This combination of features might accelerate and de-risk biopharmaceutical development by bridging early discovery to full-scale manufacturing under a single platform. Despite this profound promise, intein-based technologies have yet to reach their full potential. This review examines the evolution of intein-based purification methods in the light of several significant intein patents filed over the last 3 decades. Illustrated with actual key figures from each of the relevant patents, key advances are described with a focus on applications in basic research and biopharmaceutical production. Suggestions for extending intein-based purification systems to emerging therapies and non-protein applications are presented as concluding remarks.
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Affiliation(s)
- Sai Vivek Prabhala
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | | | - David W. Wood
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States,Protein Capture Science, Columbus, OH, United States,*Correspondence: David W. Wood,
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9
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Wang H, Wang L, Zhong B, Dai Z. Protein Splicing of Inteins: A Powerful Tool in Synthetic Biology. Front Bioeng Biotechnol 2022; 10:810180. [PMID: 35265596 PMCID: PMC8899391 DOI: 10.3389/fbioe.2022.810180] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
Inteins are protein segments that are capable of enabling the ligation of flanking extein into a new protein, a process known as protein splicing. Since its discovery, inteins have become powerful biotechnological tools for applications such as protein engineering. In the last 10 years, the development in synthetic biology has further endowed inteins with enhanced functions and diverse utilizations. Here we review these efforts and discuss the future directions.
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Affiliation(s)
- Hao Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lin Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Baihua Zhong
- Materials Interfaces Center, Institute of Advanced Materials Science and Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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10
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Woods D, LeSassier DS, Egbunam I, Lennon CW. Construction and Quantitation of a Selectable Protein Splicing Sensor Using Gibson Assembly and Spot Titers. Curr Protoc 2021; 1:e82. [PMID: 33739627 DOI: 10.1002/cpz1.82] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Inteins (intervening proteins) are translated within host proteins and removed through protein splicing. Conditional protein splicing (CPS), where the rate and accuracy of splicing are highly dependent on environmental cues, has emerged as a novel form of post-translational regulation. While CPS has been demonstrated for several inteins in vitro, a comprehensive understanding of inteins requires tools to quantitatively monitor their activity within the cellular context. Here, we describe a method for construction of a splicing-dependent system that can be used to quantitatively assay for conditions that modulate protein splicing. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Construction of an intein-containing KanR2 library using Gibson assembly Basic Protocol 2: Phenotype determination using quantitative spot titers Support Protocol 1: Preparation of LB agar plates for spot titers Support Protocol 2: Preparation and transformation of competent M. smegmatis cells.
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Affiliation(s)
- Daniel Woods
- Wadsworth Center, New York State Department of Health, Albany, New York
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11
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Nanda A, Nasker SS, Mehra A, Panda S, Nayak S. Inteins in Science: Evolution to Application. Microorganisms 2020; 8:E2004. [PMID: 33339089 DOI: 10.3390/microorganisms8122004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022] Open
Abstract
Inteins are mobile genetic elements that apply standard enzymatic strategies to excise themselves post-translationally from the precursor protein via protein splicing. Since their discovery in the 1990s, recent advances in intein technology allow for them to be implemented as a modern biotechnological contrivance. Radical improvement in the structure and catalytic framework of cis- and trans-splicing inteins devised the development of engineered inteins that contribute to various efficient downstream techniques. Previous literature indicates that implementation of intein-mediated splicing has been extended to in vivo systems. Besides, the homing endonuclease domain also acts as a versatile biotechnological tool involving genetic manipulation and control of monogenic diseases. This review orients the understanding of inteins by sequentially studying the distribution and evolution pattern of intein, thereby highlighting a role in genetic mobility. Further, we include an in-depth summary of specific applications branching from protein purification using self-cleaving tags to protein modification, post-translational processing and labelling, followed by the development of intein-based biosensors. These engineered inteins offer a disruptive approach towards research avenues like biomaterial construction, metabolic engineering and synthetic biology. Therefore, this linear perspective allows for a more comprehensive understanding of intein function and its diverse applications.
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12
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Abstract
Multiobjective optimization of microbial chassis for the production of xenobiotic compounds requires the implementation of metabolic control strategies that permit dynamic distribution of cellular resources between biomass and product formation. We addressed this need in a previous study by engineering the T7 RNA polymerase to be thermally responsive. The modified polymerase is activated only after the temperature of the host cell falls below 18 °C, and Escherichia coli cells that employ the protein to transcribe the heterologous lycopene biosynthetic pathway exhibit impressive improvements in productivity. We have expanded our toolbox of metabolic switches in the current study by engineering a version of the T7 RNA polymerase that drives the transition between biomass and product formation upon stimulation with red light. The engineered polymerase is expressed as two distinct polypeptide chains. Each chain comprises one of two photoactive components from Arabidopsis thaliana, phytochrome B (PhyB) and phytochrome-integrating factor 3 (PIF3), as well as the N- or C-terminus domains of both, the vacuolar ATPase subunit (VMA) intein of Saccharomyces cerevisiae and the polymerase. Red light drives photodimerization of PhyB and PIF3, which then brings together the N- and C-terminus domains of the VMA intein. Trans-splicing of the intein follows suit and produces an active form of the polymerase that subsequently transcribes any sequence that is under the control of a T7 promoter. The photodimerization also involves a third element, the cyanobacterial chromophore phycocyanobilin (PCB), which too is expressed heterologously by E. coli. We deployed this version of the T7 RNA polymerase to control the production of lycopene in E. coli and observed tight control of pathway expression. We tested a variety of expression configurations to identify one that imposes the lowest metabolic burden on the strain, and we subsequently optimized key parameters such as the source, moment, and duration of photostimulation. We also identified targets for future refinement of the circuit. In summary, our work is a significant advance for the field and greatly expands on previous work by other groups that have used optogenetic circuits to control heterologous metabolism in prokaryotic hosts.
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Affiliation(s)
- Adhithi R. Raghavan
- Department of Chemical and Biological Engineering & School of Biomedical Engineering, The University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Kevin Salim
- Department of Chemical and Biological Engineering & School of Biomedical Engineering, The University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Vikramaditya G. Yadav
- Department of Chemical and Biological Engineering & School of Biomedical Engineering, The University of British Columbia, Vancouver, V6T 1Z3, Canada
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13
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Hofmann T, Krah S, Sellmann C, Zielonka S, Doerner A. Greatest Hits-Innovative Technologies for High Throughput Identification of Bispecific Antibodies. Int J Mol Sci 2020; 21:E6551. [PMID: 32911608 PMCID: PMC7554978 DOI: 10.3390/ijms21186551] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Recent years have shown a tremendous increase and diversification in antibody-based therapeutics with advances in production techniques and formats. The plethora of currently investigated bi- to multi-specific antibody architectures can be harnessed to elicit a broad variety of specific modes of actions in oncology and immunology, spanning from enhanced selectivity to effector cell recruitment, all of which cannot be addressed by monospecific antibodies. Despite continuously growing efforts and methodologies, the identification of an optimal bispecific antibody as the best possible combination of two parental monospecific binders, however, remains challenging, due to tedious cloning and production, often resulting in undesired extended development times and increased expenses. Although automated high throughput screening approaches have matured for pharmaceutical small molecule development, it was only recently that protein bioconjugation technologies have been developed for the facile generation of bispecific antibodies in a 'plug and play' manner. In this review, we provide an overview of the most relevant methodologies for bispecific screening purposes-the DuoBody concept, paired light chain single cell production approaches, Sortase A and Transglutaminase, the SpyTag/SpyCatcher system, and inteins-and elaborate on the benefits as well as drawbacks of the different technologies.
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Affiliation(s)
- Tim Hofmann
- Advanced Cell Culture Technologies, Merck Life Sciences KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany;
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany; (S.K.); (C.S.); (S.Z.)
| | - Carolin Sellmann
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany; (S.K.); (C.S.); (S.Z.)
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany; (S.K.); (C.S.); (S.Z.)
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany; (S.K.); (C.S.); (S.Z.)
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14
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Liu Y, Duan Z, Fang J, Zhang F, Xiao J, Zhang WB. Cellular Synthesis and X-ray Crystal Structure of a Designed Protein Heterocatenane. Angew Chem Int Ed Engl 2020; 59:16122-16127. [PMID: 32506656 DOI: 10.1002/anie.202005490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 04/17/2020] [Indexed: 01/24/2023]
Abstract
Herein, we report the biosynthesis of protein heterocatenanes using a programmed sequence of multiple post-translational processing events including intramolecular chain entanglement, in situ backbone cleavage, and spontaneous cyclization. The approach is general, autonomous, and can obviate the need for any additional enzymes. The catenane topology was convincingly proven using a combination of SDS-PAGE, LC-MS, size exclusion chromatography, controlled proteolytic digestion, and protein crystallography. The X-ray crystal structure clearly shows two mechanically interlocked protein rings with intact folded domains. It opens new avenues in the nascent field of protein-topology engineering.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Zelin Duan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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15
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Abstract
The gene that allows budding yeast cells to switch their mating type evolved from a newly discovered family of genes named weird HO.
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Affiliation(s)
- Laura N Rusche
- Department of Biological Science, University of Buffalo, The State University of New York, New York, United States
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16
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Coughlan AY, Lombardi L, Braun-Galleani S, Martos AA, Galeote V, Bigey F, Dequin S, Byrne KP, Wolfe KH. The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family. eLife 2020; 9:55336. [PMID: 32338594 PMCID: PMC7282813 DOI: 10.7554/elife.55336] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/24/2020] [Indexed: 01/07/2023] Open
Abstract
The mating-type switching endonuclease HO plays a central role in the natural life cycle of Saccharomyces cerevisiae, but its evolutionary origin is unknown. HO is a recent addition to yeast genomes, present in only a few genera close to Saccharomyces. Here we show that HO is structurally and phylogenetically related to a family of unorthodox homing genetic elements found in Torulaspora and Lachancea yeasts. These WHO elements home into the aldolase gene FBA1, replacing its 3' end each time they integrate. They resemble inteins but they operate by a different mechanism that does not require protein splicing. We show that a WHO protein cleaves Torulaspora delbrueckii FBA1 efficiently and in an allele-specific manner, leading to DNA repair by gene conversion or NHEJ. The DNA rearrangement steps during WHO element homing are very similar to those during mating-type switching, and indicate that HO is a domesticated WHO-like element. In the same way as a sperm from a male and an egg from a female join together to form an embryo in most animals, yeast cells have two sexes that coordinate how they reproduce. These are called “mating types” and, rather than male or female, an individual yeast cell can either be mating type “a” or “alpha”. Every yeast cell contains the genes for both mating types, and each cell’s mating type is determined by which of those genes it has active. Only one mating type gene can be ‘on’ at a time, but some yeast species can swap mating type on demand by switching the corresponding genes ‘on’ or ‘off’. This switch is unusual. Rather than simply activate one of the genes it already has, the yeast cell keeps an inactive version of each mating type gene tucked away, makes a copy of the gene it wants to be active and pastes that copy into a different location in its genome. To do all of this yeast need another gene called HO. This gene codes for an enzyme that cuts the DNA at the location of the active mating type gene. This makes an opening that allows the cell to replace the ‘a’ gene with the ‘alpha’ gene, or vice versa. This system allows yeast cells to continue mating even if all the cells in a colony start off as the same mating type. But, cutting into the DNA is risky, and can damage the health of the cell. So, why did yeast cells evolve a system that could cause them harm? To find out where the HO gene came from, Coughlan et al. searched through all the available genomes from yeast species for other genes with similar sequences and identified a cluster which they nicknamed “weird HO” genes, or WHO genes for short. Testing these genes revealed that they also code for enzymes that make cuts in the yeast genome, but the way the cell repairs the cuts is different. The WHO genes are jumping genes. When the enzyme encoded by a WHO gene makes a cut in the genome, the yeast cell copies the gene into the gap, allowing the gene to ‘jump’ from one part of the genome to another. It is possible that this was the starting point for the evolution of the HO gene. Changes to a WHO gene could have allowed it to cut into the mating type region of the yeast genome, giving the yeast an opportunity to ‘domesticate’ it. Over time, the yeast cell stopped the WHO gene from jumping into the gap and started using the cut to change its mating type. Understanding how cells adapt genes for different purposes is a key question in evolutionary biology. There are many other examples of domesticated jumping genes in other organisms, including in the human immune system. Understanding the evolution of HO not only sheds light on how yeast mating type switching evolved, but on how other species might harness and adapt their genes.
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Affiliation(s)
- Aisling Y Coughlan
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Lisa Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | | | - Alexandre Ar Martos
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Virginie Galeote
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bigey
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Kevin P Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
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17
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Ciragan A, Backlund SM, Mikula KM, Beyer HM, Samuli Ollila OH, Iwaï H. NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein. Front Chem 2020; 8:136. [PMID: 32266203 PMCID: PMC7098700 DOI: 10.3389/fchem.2020.00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 11/22/2022] Open
Abstract
The growing understanding of partially unfolded proteins increasingly points to their biological relevance in allosteric regulation, complex formation, and protein design. However, the structural characterization of disordered proteins remains challenging. NMR methods can access both the dynamics and structures of such proteins, yet suffering from a high degeneracy of NMR signals. Here, we overcame this bottleneck utilizing a salt-inducible split intein to produce segmentally isotope-labeled samples with the native sequence, including the ligation junction. With this technique, we investigated the NMR structure and conformational dynamics of TonB from Helicobacter pylori in the presence of a proline-rich low complexity region. Spin relaxation experiments suggest that the several nano-second time scale dynamics of the C-terminal domain (CTD) is almost independent of the faster pico-to-nanosecond dynamics of the low complexity central region (LCCR). Our results demonstrate the utility of segmental isotopic labeling for proteins with heterogenous dynamics such as TonB and could advance NMR studies of other partially unfolded proteins.
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Affiliation(s)
- Annika Ciragan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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18
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Pech-Canul AC, Carrillo-Campos J, Ballinas-Casarrubias ML, Solis-Oviedo RL, Hernández-Rascón SK, Hernández-Ochoa LR, Gutiérrez-Méndez N, García-Triana A. Functional Expression and One-Step Protein Purification of Manganese Peroxidase 1 (rMnP1) from Phanerochaete chrysosporium Using the E. coli-Expression System. Int J Mol Sci 2020; 21:E416. [PMID: 31936493 DOI: 10.3390/ijms21020416] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/14/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022] Open
Abstract
Manganese peroxidases (MnP) from the white-rot fungi Phanerochaete chrysosporium catalyse the oxidation of Mn2+ to Mn3+, a strong oxidizer able to oxidize a wide variety of organic compounds. Different approaches have been used to unravel the enzymatic properties and potential applications of MnP. However, these efforts have been hampered by the limited production of native MnP by fungi. Heterologous expression of MnP has been achieved in both eukaryotic and prokaryotic expression systems, although with limited production and many disadvantages in the process. Here we described a novel molecular approach for the expression and purification of manganese peroxidase isoform 1 (MnP1) from P. chrysosporium using an E. coli-expression system. The proposed strategy involved the codon optimization and chemical synthesis of the MnP1 gene for optimised expression in the E. coli T7 shuffle host. Recombinant MnP1 (rMnP1) was expressed as a fusion protein, which was recovered from solubilised inclusion bodies. rMnP1 was purified from the fusion protein using intein-based protein purification techniques and a one-step affinity chromatography. The designated strategy allowed production of an active enzyme able to oxidize guaiacol or Mn2+.
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19
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Gale GAR, Schiavon Osorio AA, Mills LA, Wang B, Lea-Smith DJ, McCormick AJ. Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology. Microorganisms 2019; 7:E409. [PMID: 31569579 PMCID: PMC6843473 DOI: 10.3390/microorganisms7100409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community.
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Affiliation(s)
- Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - Alejandra A Schiavon Osorio
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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20
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Abstract
Semisynthetic cyclic peptides containing both non-proteinogenic building blocks, as the synthetic part, and a genetically encoded sequence amenable to DNA-based randomization hold great potential to expand the chemical space in the quest for novel bioactive peptides. Key to an efficient selection of novel binders to biomacromolecules is a robust method to link their genotype and phenotype. A novel bacterial cell surface display technology has been developed to present cyclic peptides composed of synthetic and genetically encoded fragments in their backbones. The fragments were combined by protein trans-splicing and intramolecular oxime ligation. To this end, a split intein half and an unnatural amino acid were displayed with the genetically encoded part on the surface of Escherichia coli. Addition of the synthetic fragment equipped with the split intein partner and an aminooxy moiety, as well as the application of a pH-shift protocol, resulted in the onsurface formation of the semisynthetic cyclic peptide. This approach will serve for the generation of cyclic peptide libraries suitable for selection by fluorescence-activated cell sorting, and more generally enables chemical modification of proteins on the bacterial surface.
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Affiliation(s)
- Shubhendu Palei
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Kira S Becher
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
| | - Christian Nienberg
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
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21
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Pavankumar TL. Inteins: Localized Distribution, Gene Regulation, and Protein Engineering for Biological Applications. Microorganisms 2018; 6:E19. [PMID: 29495613 PMCID: PMC5874633 DOI: 10.3390/microorganisms6010019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/24/2018] [Accepted: 02/25/2018] [Indexed: 11/25/2022] Open
Abstract
Inteins are self-splicing polypeptides with an ability to excise themselves from flanking host protein regions with remarkable precision; in the process, they ligate flanked host protein fragments. Inteins are distributed sporadically across all three domains of life (bacteria, archaea, and unicellular eukaryotes). However, their apparent localized distribution in DNA replication, repair, and recombination proteins (the 3Rs), particularly in bacteria and archaea, is enigmatic. Our understanding of the localized distribution of inteins in the 3Rs, and their possible regulatory role in such distribution, is still only partial. Nevertheless, understanding the chemistry of post-translational self-splicing of inteins has opened up opportunities for protein chemists to modify, manipulate, and bioengineer proteins. Protein-splicing technology is adapted to a wide range of applications, starting with untagged protein purification, site-specific protein labeling, protein biotinylation, isotope incorporation, peptide cyclization, as an antimicrobial target, and so on. This review is focused on the chemistry of splicing; the localized distribution of inteins, particularly in the 3Rs and their possible role in regulating host protein function; and finally, the use of protein-splicing technology in various protein engineering applications.
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Affiliation(s)
- Theetha L Pavankumar
- Department of Microbiology and Molecular Genetics, Briggs Hall, One Shields Ave, University of California, Davis, CA 95616, USA.
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22
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Schmelas C, Grimm D. Split Cas9, Not Hairs - Advancing the Therapeutic Index of CRISPR Technology. Biotechnol J 2018; 13:e1700432. [PMID: 29316283 DOI: 10.1002/biot.201700432] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 11/02/2017] [Revised: 12/28/2017] [Indexed: 02/06/2023]
Abstract
The discovery that the bacterial CRISPR/Cas9 system can be translated into mammalian cells continues to have an unprecedented impact on the biomedical research community, as it largely facilitates efforts to experimentally interrogate or therapeutically modify the cellular genome. In particular, CRISPR promises the ability to correct disease-associated genetic defects, or to target and destroy invading foreign DNA, in a simple, efficient, and selective manner directly in affected human cells or tissues. Here, we highlight a set of exciting new strategies that aim at further increasing the therapeutic index of CRISPR technologies, by reducing the size of Cas9 expression cassettes and thus enhancing their compatibility with viral gene delivery vectors. Specifically, we discuss the concept of splitCas9 whereby the Cas9 holo-protein is segregated into two parts that are expressed individually and reunited in the cell by various means, including use of 1) the gRNA as a scaffold for Cas9 assembly; 2) the rapamycin-controlled FKBP/FRB system; 3) the light-regulated Magnet system; or 4) inteins. We describe how these avenues, despite pursuing the identical aim, differ in critical features comprising the extent of spatio-temporal control of CRISPR activity, and discuss additional improvements to their efficiency or specificity that should foster their clinical translation.
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Affiliation(s)
- Carolin Schmelas
- Heidelberg University Hospital, Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany
| | - Dirk Grimm
- Heidelberg University Hospital, Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner site Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany
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23
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Iwaï H, Mikula KM, Oeemig JS, Zhou D, Li M, Wlodawer A. Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins. J Mol Biol 2017; 429:3942-3956. [PMID: 29055778 PMCID: PMC6309676 DOI: 10.1016/j.jmb.2017.10.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/29/2017] [Accepted: 10/12/2017] [Indexed: 11/19/2022]
Abstract
Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains. Despite the lack of obvious mutualism between HEN and HINT domains, HEN domains are persistently found at one specific site in inteins, indicating their potential functional role in protein splicing. Here we report crystal structures of inactive and active mini-inteins derived from inteins residing in the transcription factor IIB of Methanococcus jannaschii and Methanocaldococcus vulcanius, revealing a novel modified HINT fold that might provide new insights into the mutualism between the HEN and HINT domains. We propose an evolutionary model of inteins and a functional role of HEN domains in inteins.
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Affiliation(s)
- Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland.
| | - Kornelia M Mikula
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland
| | - Jesper S Oeemig
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland
| | - Dongwen Zhou
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mi Li
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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24
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Abstract
Synthetic control strategies using signaling peptides to regulate and coordinate cellular behaviors in multicellular organisms and synthetic consortia remain largely underdeveloped because of the complexities necessitated by heterologous peptide expression. Using recombinant proteins that exploit split intein-mediated reactions, we presented here a new strategy for reconstituting functional signaling peptides capable of eliciting desired cellular responses in S. cerevisiae. These designs can potentially be tailored to any signaling peptides to be reconstituted, as the split inteins are promiscuous and both the peptides and the reactions are amenable to changes by directed evolution and other protein engineering tools, thereby offering a general strategy to implement synthetic control strategies in a large variety of applications.
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Affiliation(s)
- Ka-Hei Siu
- Department of Chemical and
Biomolecular Engineering, University of Delaware, 150 Academy
Street, Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and
Biomolecular Engineering, University of Delaware, 150 Academy
Street, Newark, Delaware 19716, United States
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25
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Ciragan A, Aranko AS, Tascon I, Iwaï H. Salt-inducible Protein Splicing in cis and trans by Inteins from Extremely Halophilic Archaea as a Novel Protein-Engineering Tool. J Mol Biol 2016; 428:4573-4588. [PMID: 27720988 DOI: 10.1016/j.jmb.2016.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 07/23/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 10/20/2022]
Abstract
Intervening protein sequences (inteins) from extremely halophilic haloarchaea can be inactive under low salinity but could be activated by increasing the salt content to a specific concentration for each intein. The halo-obligatory inteins confer high solubility under both low and high salinity conditions. We showed the broad utility of salt-dependent protein splicing in cis and trans by demonstrating backbone cyclization, self-cleavage for purification, and scarless protein ligation for segmental isotopic labeling. Artificially split MCM2 intein derived from Halorhabdus utahensis remained highly soluble and was capable of protein trans-splicing with excellent ligation kinetics by reassembly under high salinity conditions. Importantly, the MCM2 intein has the active site residue of Ser at the +1 position, which remains in the ligated product, instead of Cys as found in many other efficient split inteins. Since Ser is more abundant than Cys in proteins, the novel split intein could widen the applications of segmental labeling in protein NMR spectroscopy and traceless protein ligation by exploiting a Ser residue in the native sequences as the +1 position of the MCM2 intein. The split halo-obligatory intein was successfully used to demonstrate the utility in NMR investigation of intact proteins by producing segmentally isotope-labeled intact TonB protein from Helicobacter pylori.
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Affiliation(s)
- Annika Ciragan
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - A Sesilja Aranko
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Igor Tascon
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.
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26
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Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. Front Chem 2015; 3:26. [PMID: 25905098 PMCID: PMC4389572 DOI: 10.3389/fchem.2015.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/23/2015] [Indexed: 12/02/2022] Open
Abstract
Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.
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Affiliation(s)
- Frank H Schumann
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Ranjani Varadan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Praveen P Tayakuniyil
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Jennifer H Grossman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles, CA, USA ; Department of Chemistry, University of Southern California Los Angeles, CA, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
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27
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Abstract
This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed 118 genomes representing 26 genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified 24 proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein's life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN); smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena), Bacteriodetes (Salinibacter), Betaproteobacteria (Delftia, Acidovorax), Firmicutes (Halanaerobium), Actinobacteria (Longispora), and Deinococcus-Thermus-group.
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Affiliation(s)
- Shannon M Soucy
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Matthew S Fullmer
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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