1
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Foo GW, Leichthammer CD, Saita IM, Lukas ND, Batko IZ, Heinrichs DE, Edgell DR. Intein-based thermoregulated meganucleases for containment of genetic material. Nucleic Acids Res 2024; 52:2066-2077. [PMID: 38180814 PMCID: PMC10899782 DOI: 10.1093/nar/gkad1247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
Limiting the spread of synthetic genetic information outside of the intended use is essential for applications where biocontainment is critical. In particular, biocontainment of engineered probiotics and plasmids that are excreted from the mammalian gastrointestinal tract is needed to prevent escape and acquisition of genetic material that could confer a selective advantage to microbial communities. Here, we built a simple and lightweight biocontainment system that post-translationally activates a site-specific DNA endonuclease to degrade DNA at 18°C and not at higher temperatures. We constructed an orthogonal set of temperature-sensitive meganucleases (TSMs) by inserting the yeast VMA1 L212P temperature-sensitive intein into the coding regions of LAGLIDADG homing endonucleases. We showed that the TSMs eliminated plasmids carrying the cognate TSM target site from laboratory strains of Escherichia coli at the permissive 18°C but not at higher restrictive temperatures. Plasmid elimination is dependent on both TSM endonuclease activity and intein splicing. TSMs eliminated plasmids from E. coli Nissle 1917 after passage through the mouse gut when fecal resuspensions were incubated at 18°C but not at 37°C. Collectively, our data demonstrates the potential of thermoregulated meganucleases as a means of restricting engineered plasmids and probiotics to the mammalian gut.
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Affiliation(s)
- Gary W Foo
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | | | - Ibrahim M Saita
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - Nicholas D Lukas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - Izabela Z Batko
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - David E Heinrichs
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
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2
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Johnson LA, Mart RJ, Allemann RK. A Photoresponsive Homing Endonuclease for Programmed DNA Cleavage. ACS Synth Biol 2024; 13:195-205. [PMID: 38061193 PMCID: PMC10804406 DOI: 10.1021/acssynbio.3c00425] [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: 07/14/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 01/23/2024]
Abstract
Homing endonucleases are used in a wide range of biotechnological applications including gene editing, in gene drive systems, and for the modification of DNA structures, arrays, and prodrugs. However, controlling nuclease activity and sequence specificity remain key challenges when developing new tools. Here a photoresponsive homing endonuclease was engineered for optical control of DNA cleavage by partitioning DNA binding and nuclease domains of the monomeric homing endonuclease I-TevI into independent polypeptide chains. Use of the Aureochrome1a light-oxygen-voltage domain delivered control of dimerization with light. Illumination reduced the concentration needed to achieve 50% cleavage of the homing target site by 6-fold when compared to the dark state, resulting in an up to 9-fold difference in final yields between cleavage products. I-TevI nucleases with and without a native I-TevI zinc finger motif displayed different nuclease activity and sequence preference impacting the promiscuity of the nuclease domain. By harnessing an alternative DNA binding domain, target preference was reprogrammed only when the nuclease lacked the I-TevI zinc finger motif. This work establishes a first-generation photoresponsive platform for spatiotemporal activation of DNA cleavage.
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Affiliation(s)
- Luke A. Johnson
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
| | | | - Rudolf K. Allemann
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
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3
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Expression of Highly Active Bacterial Phospholipase A 2 in Yeast Using Intein-Mediated Delayed Protein Autoactivation. Appl Biochem Biotechnol 2020; 193:1351-1364. [PMID: 32388605 DOI: 10.1007/s12010-020-03333-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/23/2020] [Indexed: 10/24/2022]
Abstract
Phospholipase A2 (PLA2) has found extensive use in industry. However, recombinant PLA2 production in different expression systems is a difficult task because of its toxicity to cell membranes. We report here the development of an effective method for production of highly active PLA2 from Streptomyces violaceoruber strain A-2688 in the yeast Saccharomyces cerevisiae. The method is based on the use of the PRP8 mini-intein (from Penicillium chrysogenum) inserted into the phospholipase sequence with the purpose of temporal inactivation of the enzyme and its subsequent delayed autoactivation. We demonstrate that the most effective site for intein insertion is Ser76 of the mature phospholipase. As a result of intein-containing precursor secretion from yeast cells and its subsequent autocatalytic splicing, highly active enzyme accumulated in the yeast culture fluid. The properties of the obtained recombinant phospholipase A2 protein were similar to those of the native Streptomyces violaceoruber PLA2 protein. A possible evolutionary role of delayed autoactivation of intein-containing proteins is also discussed.
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4
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A promiscuous split intein with expanded protein engineering applications. Proc Natl Acad Sci U S A 2017; 114:8538-8543. [PMID: 28739907 DOI: 10.1073/pnas.1701083114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The protein trans-splicing (PTS) activity of naturally split inteins has found widespread use in chemical biology and biotechnology. However, currently used naturally split inteins suffer from an "extein dependence," whereby residues surrounding the splice junction strongly affect splicing efficiency, limiting the general applicability of many PTS-based methods. To address this, we describe a mechanism-guided protein engineering approach that imbues ultrafast DnaE split inteins with minimal extein dependence. The resulting "promiscuous" inteins are shown to be superior reagents for protein cyclization and protein semisynthesis, with the latter illustrated through the modification of native cellular chromatin. The promiscuous inteins reported here thus improve the applicability of existing PTS methods and should enable future efforts to engineer promiscuity into other naturally split inteins.
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5
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Coolbaugh M, Shakalli Tang M, Wood D. High-throughput purification of recombinant proteins using self-cleaving intein tags. Anal Biochem 2017; 516:65-74. [DOI: 10.1016/j.ab.2016.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022]
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6
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Lee J, Boersma A, Boudreau MA, Cheley S, Daltrop O, Li J, Tamagaki H, Bayley H. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry. ACS NANO 2016; 10:8843-50. [PMID: 27537396 PMCID: PMC5043417 DOI: 10.1021/acsnano.6b04663] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/18/2016] [Indexed: 05/27/2023]
Abstract
Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level.
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Affiliation(s)
- Joongoo Lee
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Arnold
J. Boersma
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Marc A. Boudreau
- Department
of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Stephen Cheley
- Department
of Pharmacology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Oliver Daltrop
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Jianwei Li
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Hiroko Tamagaki
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Hagan Bayley
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
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7
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Li X, Jiang H, Luo Z, Chang YT, Zhang L. Development of a disaggregation-induced emission probe for the detection of RecA inteins from Mycobacterium tuberculosis. Chem Commun (Camb) 2016; 52:9086-8. [DOI: 10.1039/c6cc00439c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel fluorescent sensor with disaggregation-induced emission characteristics has been developed for the detection of RecA inteins from Mycobacterium tuberculosis.
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Affiliation(s)
- Xin Li
- Institute of Technical Biology and Agriculture Engineering
- Key Laboratory of Ion Beam Bioengineering
- Hefei Institutes of Physical Science
- Chinese Academy of Sciences
- Hefei
| | - Hao Jiang
- Hefei National Laboratory for Physical Science at the Microscale
- Core Facility Center for Life Sciences
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
| | - Zhaofeng Luo
- Hefei National Laboratory for Physical Science at the Microscale
- Core Facility Center for Life Sciences
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230026
| | - Young-Tae Chang
- Department of Chemistry
- National University of Singapore
- Singapore
| | - Liyun Zhang
- Institute of Technical Biology and Agriculture Engineering
- Key Laboratory of Ion Beam Bioengineering
- Hefei Institutes of Physical Science
- Chinese Academy of Sciences
- Hefei
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8
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Li Y. Split-inteins and their bioapplications. Biotechnol Lett 2015; 37:2121-37. [DOI: 10.1007/s10529-015-1905-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023]
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9
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Cronin M, Coolbaugh MJ, Nellis D, Zhu J, Wood DW, Nussinov R, Ma B. Dynamics differentiate between active and inactive inteins. Eur J Med Chem 2015; 91:51-62. [PMID: 25087201 PMCID: PMC4308580 DOI: 10.1016/j.ejmech.2014.07.094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/21/2014] [Accepted: 07/25/2014] [Indexed: 11/29/2022]
Abstract
The balance between stability and dynamics for active enzymes can be somewhat quantified by studies of intein splicing and cleaving reactions. Inteins catalyze the ligation of flanking host exteins while excising themselves. The potential for applications led to engineering of a mini-intein splicing domain, where the homing endonuclease domain of the Mycobacterium tuberculosis RecA (Mtu recA) intein was removed. The remaining domains were linked by several short peptides, but splicing activity in all was substantially lower than the full-length intein. Native splicing activity was restored in some cases by a V67L mutation. Using computations and experiments, we examine the impact of this mutation on the stability and conformational dynamics of the mini-intein splicing domain. Molecular dynamics simulations were used to delineate the factors that determine the active state, including the V67L mini-intein mutant, and peptide linker. We found that (1) the V67L mutation lowers the global fluctuations in all modeled mini-inteins, stabilizing the mini-intein constructs; (2) the connecting linker length affects intein dynamics; and (3) the flexibilities of the linker and intein core are higher in the active structure. We have observed that the interaction of the linker region and a turn region around residues 35-41 provides the pathway for the allostery interaction. Our experiments reveal that intein catalysis is characterized by non-linear Arrhenius plot, confirming the significant contribution of protein conformational dynamics to intein function. We conclude that while the V67L mutation stabilizes the global structure, cooperative dynamics of all intein regions appear more important for intein function than high stability. Our studies suggest that effectively quenching the conformational dynamics of an intein through engineered allosteric interactions could deactivate intein splicing or cleaving.
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Affiliation(s)
- Melissa Cronin
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Michael J Coolbaugh
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH 43210, USA
| | - David Nellis
- Biopharmaceutical Development Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jianwei Zhu
- School of Pharmacy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai 200240, China
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
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10
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Shi C, Tarimala A, Meng Q, Wood DW. A general purification platform for toxic proteins based on intein trans-splicing. Appl Microbiol Biotechnol 2014; 98:9425-35. [DOI: 10.1007/s00253-014-6080-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 08/15/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022]
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11
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Topilina NI, Mills KV. Recent advances in in vivo applications of intein-mediated protein splicing. Mob DNA 2014; 5:5. [PMID: 24490831 PMCID: PMC3922620 DOI: 10.1186/1759-8753-5-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/07/2014] [Indexed: 01/27/2023] Open
Abstract
Intein-mediated protein splicing has become an essential tool in modern biotechnology. Fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. Recent work has extended these in vitro applications to the cell or to whole organisms. We review recent advances in intein-mediated protein expression and modification, post-translational processing and labeling, protein regulation by conditional protein splicing, biosensors, and expression of trans-genes.
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Affiliation(s)
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, 1 College Street, Worcester, MA 01610, USA.
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12
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Guan D, Ramirez M, Chen Z. Split intein mediated ultra‐rapid purification of tagless protein (SIRP). Biotechnol Bioeng 2013; 110:2471-81. [DOI: 10.1002/bit.24913] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/15/2013] [Accepted: 03/22/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Dongli Guan
- Department of Chemical Engineering, 3122 TAMU, Artie McFerrinTexas A&M UniversityCollege StationTX 77843
| | - Miguel Ramirez
- Department of Chemical Engineering, 3122 TAMU, Artie McFerrinTexas A&M UniversityCollege StationTX 77843
| | - Zhilei Chen
- Department of Chemical Engineering, 3122 TAMU, Artie McFerrinTexas A&M UniversityCollege StationTX 77843
- Department of Microbial and Molecular PathogenesisTexas A&M Health Science CenterCollege StationTX
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13
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Lin Y, Li M, Song H, Xu L, Meng Q, Liu XQ. Protein trans-splicing of multiple atypical split inteins engineered from natural inteins. PLoS One 2013; 8:e59516. [PMID: 23593141 PMCID: PMC3620165 DOI: 10.1371/journal.pone.0059516] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/15/2013] [Indexed: 11/30/2022] Open
Abstract
Protein trans-splicing by split inteins has many uses in protein production and research. Splicing proteins with synthetic peptides, which employs atypical split inteins, is particularly useful for site-specific protein modifications and labeling, because the synthetic peptide can be made to contain a variety of unnatural amino acids and chemical modifications. For this purpose, atypical split inteins need to be engineered to have a small N-intein or C-intein fragment that can be more easily included in a synthetic peptide that also contains a small extein to be trans-spliced onto target proteins. Here we have successfully engineered multiple atypical split inteins capable of protein trans-splicing, by modifying and testing more than a dozen natural inteins. These included both S1 split inteins having a very small (11–12 aa) N-intein fragment and S11 split inteins having a very small (6 aa) C-intein fragment. Four of the new S1 and S11 split inteins showed high efficiencies (85–100%) of protein trans-splicing both in E. coli cells and in vitro. Under in vitro conditions, they exhibited reaction rate constants ranging from ∼1.7×10−4 s−1 to ∼3.8×10−4 s−1, which are comparable to or higher than those of previously reported atypical split inteins. These findings should facilitate a more general use of trans-splicing between proteins and synthetic peptides, by expanding the availability of different atypical split inteins. They also have implications on understanding the structure-function relationship of atypical split inteins, particularly in terms of intein fragment complementation.
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Affiliation(s)
- Ying Lin
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
| | - Mengmeng Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
| | - Huiling Song
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lingling Xu
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, P.R. China
- * E-mail: (QM); (XQL)
| | - Xiang-Qin Liu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail: (QM); (XQL)
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14
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Song H, Meng Q, Liu XQ. Protein trans-splicing of an atypical split intein showing structural flexibility and cross-reactivity. PLoS One 2012; 7:e45355. [PMID: 23024818 PMCID: PMC3443213 DOI: 10.1371/journal.pone.0045355] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/20/2012] [Indexed: 11/18/2022] Open
Abstract
Inteins catalyze a protein splicing reaction to excise the intein from a precursor protein and join the flanking sequences (exteins) with a peptide bond. In a split intein, the intein fragments (IN and IC) can reassemble non-covalently to catalyze a trans-splicing reaction that joins the exteins from separate polypeptides. An atypical split intein having a very small IN and a large IC is particularly useful for joining synthetic peptides with recombinant proteins, which can be a generally useful method of introducing site-specific chemical labeling or modifications into proteins. However, a large IC derived from an Ssp DnaX intein was found recently to undergo spontaneous C-cleavage, which raised questions regarding its structure-function and ability to trans-splice. Here, we show that this IC could undergo trans-splicing in the presence of IN, and the trans-splicing activity completely suppressed the C-cleavage activity. We also found that this IC could trans-splice with small IN sequences derived from two other inteins, showing a cross-reactivity of this atypical split intein. Furthermore, we found that this IC could trans-splice even when the IN sequence was embedded in a nearly complete intein sequence, suggesting that the small IN could project out of the central pocket of the intein to become accessible to the IC. Overall, these findings uncovered a new atypical split intein that can be valuable for peptide-protein trans-splicing, and they also revealed an interesting structural flexibility and cross-reactivity at the active site of this intein.
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Affiliation(s)
- Huiling Song
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People’s Republic of China
- * E-mail: (QM); (XQL)
| | - Xiang-Qin Liu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail: (QM); (XQL)
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15
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Ferrari E, Soloviev M, Niranjan D, Arsenault J, Gu C, Vallis Y, O'Brien J, Davletov B. Assembly of protein building blocks using a short synthetic peptide. Bioconjug Chem 2012; 23:479-84. [PMID: 22299630 PMCID: PMC3309608 DOI: 10.1021/bc2005208] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Combining proteins or their defined domains offers new
enhanced
functions. Conventionally, two proteins are either fused into a single
polypeptide chain by recombinant means or chemically cross-linked.
However, these strategies can have drawbacks such as poor expression
(recombinant fusions) or aggregation and inactivation (chemical cross-linking),
especially in the case of large multifunctional proteins. We developed
a new linking method which allows site-oriented, noncovalent, yet
irreversible stapling of modified proteins at neutral pH and ambient
temperature. This method is based on two distinct polypeptide linkers
which self-assemble in the presence of a specific peptide staple allowing
on-demand and irreversible combination of protein domains. Here we
show that linkers can either be expressed or be chemically conjugated
to proteins of interest, depending on the source of the proteins.
We also show that the peptide staple can be shortened to 24 amino
acids still permitting an irreversible combination of functional proteins.
The versatility of this modular technique is demonstrated by stapling
a variety of proteins either in solution or to surfaces.
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Affiliation(s)
- Enrico Ferrari
- MRC Laboratory of Molecular Biology, Hills Road, CB2 0QH Cambridge, United Kingdom
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16
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Shemella P, Topilina N, Soga I, Pereira B, Belfort G, Belfort M, Nayak S. Electronic structure of neighboring extein residue modulates intein C-terminal cleavage activity. Biophys J 2011; 100:2217-25. [PMID: 21539790 PMCID: PMC3149237 DOI: 10.1016/j.bpj.2011.02.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 01/25/2011] [Accepted: 02/04/2011] [Indexed: 11/27/2022] Open
Abstract
Protein splicing is an autocatalytic reaction where an intervening element (intein) is excised and the remaining two flanking sequences (exteins) are joined. The reaction requires specific conserved residues, and activity may be affected by both the intein and the extein sequence. Predicting how sequence will affect activity is a challenging task. Based on first-principles density functional theory and multiscale quantum mechanics/molecular mechanics, we report C-terminal cleavage reaction rates for five mutations at the first residue of the C-extein (+1), and describe molecular properties that may be used as predictors for future mutations. Independently, we report on experimental characterization of the same set of mutations at the +1 residue resulting in a wide range of C-terminal cleavage activities. With some exceptions, there is general agreement between computational rates and experimental cleavage, giving molecular insight into previous claims that the +1 extein residue affects intein catalysis. These data suggest utilization of attenuating +1 mutants for intein-mediated protein manipulations because they facilitate precursor accumulation in vivo for standard purification schemes. A more detailed analysis of the "+1 effect" will also help to predict sequence-defined effects on insertion points of the intein into proteins of interest.
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Affiliation(s)
- Philip T. Shemella
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | | | - Ikko Soga
- Wadsworth Center, New York State Department of Health, Albany, New York
| | - Brian Pereira
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
- Wadsworth Center, New York State Department of Health, Albany, New York
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Marlene Belfort
- Wadsworth Center, New York State Department of Health, Albany, New York
| | - Saroj K. Nayak
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
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17
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Karagoz GE, Sinnige T, Hsieh O, Rudiger SGD. Expressed protein ligation for a large dimeric protein. Protein Eng Des Sel 2011; 24:495-501. [DOI: 10.1093/protein/gzr007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Robbins JB, Smith D, Belfort M. Redox-responsive zinc finger fidelity switch in homing endonuclease and intron promiscuity in oxidative stress. Curr Biol 2011; 21:243-8. [PMID: 21256016 DOI: 10.1016/j.cub.2011.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 12/10/2010] [Accepted: 01/04/2011] [Indexed: 12/24/2022]
Abstract
It is well understood how mobile introns home to allelic sites, but how they are stimulated to transpose to ectopic locations on an evolutionary timescale is unclear. Here we show that a group I intron can move to degenerate sites under oxidizing conditions. The phage T4 td intron endonuclease, I-TevI, is responsible for this infidelity. We demonstrate that I-TevI, which promotes mobility and is subject to autorepression and translational control, is also regulated posttranslationally by a redox mechanism. Redox regulation is exercised by a zinc finger (ZF) in a linker that connects the catalytic domain of I-TevI to the DNA binding domain. Four cysteines coordinate Zn(2+) in the ZF, which ensures that I-TevI cleaves its DNA substrate at a fixed distance, 23-25 nucleotides upstream of the intron insertion site. We show that the fidelity of I-TevI cleavage is controlled by redox-responsive Zn(2+) cycling. When the ZF is mutated, or after exposure of the wild-type I-TevI to H(2)O(2), intron homing to degenerate sites is increased, likely because of indiscriminate DNA cleavage. These results suggest a mechanism for rapid intron dispersal, joining recent descriptions of the activation of biomolecular processes by oxidative stress through cysteine chemistry.
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Affiliation(s)
- Justin B Robbins
- Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA
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19
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Pereira B, Shemella PT, Amitai G, Belfort G, Nayak SK, Belfort M. Spontaneous proton transfer to a conserved intein residue determines on-pathway protein splicing. J Mol Biol 2010; 406:430-42. [PMID: 21185311 DOI: 10.1016/j.jmb.2010.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 12/16/2010] [Indexed: 02/06/2023]
Abstract
The discovery of inteins, which are protein-splicing elements, has stimulated interest for various applications in chemical biology, bioseparations, drug delivery, and sensor development. However, for inteins to effectively contribute to these applications, an increased mechanistic understanding of cleavage and splicing reactions is required. While the multistep chemical reaction that leads to splicing is often explored and utilized, it is not clear how the intein navigates through the reaction space. The sequence of reaction steps must progress in concert in order to yield efficient splicing while minimizing off-pathway cleavage reactions. In this study, we demonstrate that formation of a previously identified branched intermediate is the critical step for determining splicing over cleavage products. By combining experimental assays and quantum mechanical simulations, we identify the electrostatic interactions that are important to the dynamics of the reaction steps. We illustrate, via an animated simulation trajectory, a proton transfer from the first C-terminal extein residue to a conserved aspartate, which synchronizes the multistep enzymatic reaction that is key to splicing. This work provides new insights into the complex interplay between critical active-site residues in the protein splicing mechanism, thereby facilitating biotechnological application while shedding light on multistep enzyme activity.
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Affiliation(s)
- Brian Pereira
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
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20
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Gibb EA, Edgell DR. Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron. Mol Microbiol 2010; 78:35-46. [PMID: 20497330 DOI: 10.1111/j.1365-2958.2010.07216.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The td group I intron interrupting the thymidylate synthase (TS) gene of phage T4 is a mobile intron that encodes the homing endonuclease I-TevI. Efficient RNA splicing of the intron is required to restore function of the TS gene, while expression of I-TevI from within the intron is required to initiate intron mobility. Three distinct layers of regulation temporally limit I-TevI expression to late in the T4 infective cycle, yet the biological rationale for stringent regulation has not been tested. Here, we deleted key control elements to deregulate I-TevI expression at early and middle times post T4 infection. Strikingly, we found that deregulation of I-TevI, or of a catalytically inactive variant, generated a thymidine-dependent phenotype that is caused by a reduction in td intron splicing. Prematurely terminating I-TevI translation restores td splicing, full-length TS synthesis, and rescues the thymidine-dependent phenotype. We suggest that stringent translational control of I-TevI evolved to prevent the ribosome from disrupting key structural elements of the td intron that are required for splicing and TS function at early and middle times post T4 infection. Analogous translational regulatory mechanisms in unrelated intron-open reading frame arrangements may also function to limit deleterious consequences on splicing and host gene function.
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Affiliation(s)
- Ewan A Gibb
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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21
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Kleinstiver BP, Fernandes AD, Gloor GB, Edgell DR. A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI. Nucleic Acids Res 2010; 38:2411-27. [PMID: 20061372 PMCID: PMC2853131 DOI: 10.1093/nar/gkp1223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 12/18/2009] [Accepted: 12/20/2009] [Indexed: 11/14/2022] Open
Abstract
Insight into protein structure and function is best obtained through a synthesis of experimental, structural and bioinformatic data. Here, we outline a framework that we call MUSE (mutual information, unigenic evolution and structure-guided elucidation), which facilitated the identification of previously unknown residues that are relevant for function of the GIY-YIG homing endonuclease I-BmoI. Our approach synthesizes three types of data: mutual information analyses that identify co-evolving residues within the GIY-YIG catalytic domain; a unigenic evolution strategy that identifies hyper- and hypo-mutable residues of I-BmoI; and interpretation of the unigenic and co-evolution data using a homology model. In particular, we identify novel positions within the GIY-YIG domain as functionally important. Proof-of-principle experiments implicate the non-conserved I71 as functionally relevant, with an I71N mutant accumulating a nicked cleavage intermediate. Moreover, many additional positions within the catalytic, linker and C-terminal domains of I-BmoI were implicated as important for function. Our results represent a platform on which to pursue future studies of I-BmoI and other GIY-YIG-containing proteins, and demonstrate that MUSE can successfully identify novel functionally critical residues that would be ignored in a traditional structure-function analysis within an extensively studied small domain of approximately 90 amino acids.
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Affiliation(s)
- Benjamin P. Kleinstiver
- Department of Biochemistry, Schulich School of Medicine & Dentistry and Department of Applied Mathematics, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Andrew D. Fernandes
- Department of Biochemistry, Schulich School of Medicine & Dentistry and Department of Applied Mathematics, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Gregory B. Gloor
- Department of Biochemistry, Schulich School of Medicine & Dentistry and Department of Applied Mathematics, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - David R. Edgell
- Department of Biochemistry, Schulich School of Medicine & Dentistry and Department of Applied Mathematics, The University of Western Ontario, London, ON N6A 5C1, Canada
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22
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Hiraga K, Soga I, Dansereau JT, Pereira B, Derbyshire V, Du Z, Wang C, Van Roey P, Belfort G, Belfort M. Selection and structure of hyperactive inteins: peripheral changes relayed to the catalytic center. J Mol Biol 2009; 393:1106-17. [PMID: 19744499 DOI: 10.1016/j.jmb.2009.08.074] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 08/27/2009] [Accepted: 08/31/2009] [Indexed: 02/05/2023]
Abstract
Inteins are phylogenetically diverse self-splicing proteins that are of great functional, evolutionary, biotechnological, and medical interest. To address the relationship between intein structure and function, particularly with respect to regulating the splicing reaction, and to groom inteins for application, we developed a phage display system to extend current in vivo selection for enhanced intein function to selection in vitro. We thereby isolated inteins that can function under excursions in temperature, pH, and denaturing environment. Remarkably, most mutations mapped to the surface of the intein, remote from the active site. We chose two mutants with enhanced splicing activity for crystallography, one of which was also subjected to NMR analysis. These studies define a "ripple effect", whereby mutations in peripheral non-catalytic residues can cause subtle allosteric changes in the active-site environment in a way that facilitates intein activity. Altered salt-bridge formation and chemical shift changes of the mutant inteins provide a molecular rationale for their phenotypes. These fundamental insights will advance the utility of inteins in chemical biology, biotechnology, and medicine.
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Affiliation(s)
- Kaori Hiraga
- Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12208, USA
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23
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Purification of green fluorescent protein using a two-intein system. Appl Microbiol Biotechnol 2008; 77:1175-80. [DOI: 10.1007/s00253-007-1233-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2007] [Revised: 09/27/2007] [Accepted: 09/28/2007] [Indexed: 10/22/2022]
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24
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Robbins JB, Stapleton M, Stanger MJ, Smith D, Dansereau JT, Derbyshire V, Belfort M. Homing endonuclease I-TevIII: dimerization as a means to a double-strand break. Nucleic Acids Res 2007; 35:1589-600. [PMID: 17289754 PMCID: PMC1865063 DOI: 10.1093/nar/gkl1170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Homing endonucleases are unusual enzymes, capable of recognizing lengthy DNA sequences and cleaving site-specifically within genomes. Many homing endonucleases are encoded within group I introns, and such enzymes promote the mobility reactions of these introns. Phage T4 has three group I introns, within the td, nrdB and nrdD genes. The td and nrdD introns are mobile, whereas the nrdB intron is not. Phage RB3 is a close relative of T4 and has a lengthier nrdB intron. Here, we describe I-TevIII, the H-N-H endonuclease encoded by the RB3 nrdB intron. In contrast to previous reports, we demonstrate that this intron is mobile, and that this mobility is dependent on I-TevIII, which generates 2-nt 3' extensions. The enzyme has a distinct catalytic domain, which contains the H-N-H motif, and DNA-binding domain, which contains two zinc fingers required for interaction with the DNA substrate. Most importantly, I-TevIII, unlike the H-N-H endonucleases described so far, makes a double-strand break on the DNA homing site by acting as a dimer. Through deletion analysis, the dimerization interface was mapped to the DNA-binding domain. The unusual propensity of I-TevIII to dimerize to achieve cleavage of both DNA strands underscores the versatility of the H-N-H enzyme family.
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Affiliation(s)
- Justin B. Robbins
- Wadsworth Center, New York State Department of Health, Center for Medical Science and Department of Biomedical Sciences, School of Public Health, SUNY, 150 New Scotland Avenue, Albany, NY 12208
| | - Michelle Stapleton
- Wadsworth Center, New York State Department of Health, Center for Medical Science and Department of Biomedical Sciences, School of Public Health, SUNY, 150 New Scotland Avenue, Albany, NY 12208
| | - Matthew J. Stanger
- Wadsworth Center, New York State Department of Health, Center for Medical Science and Department of Biomedical Sciences, School of Public Health, SUNY, 150 New Scotland Avenue, Albany, NY 12208
| | - Dorie Smith
- Wadsworth Center, New York State Department of Health, Center for Medical Science and Department of Biomedical Sciences, School of Public Health, SUNY, 150 New Scotland Avenue, Albany, NY 12208
| | - John T. Dansereau
- Wadsworth Center, New York State Department of Health, Center for Medical Science and Department of Biomedical Sciences, School of Public Health, SUNY, 150 New Scotland Avenue, Albany, NY 12208
| | - Victoria Derbyshire
- Wadsworth Center, New York State Department of Health, Center for Medical Science and Department of Biomedical Sciences, School of Public Health, SUNY, 150 New Scotland Avenue, Albany, NY 12208
| | - Marlene Belfort
- Wadsworth Center, New York State Department of Health, Center for Medical Science and Department of Biomedical Sciences, School of Public Health, SUNY, 150 New Scotland Avenue, Albany, NY 12208
- *To whom correspondence should be addressed. +518 473 3345+518 474 3181
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25
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Sharma SS, Chong S, Harcum SW. Intein-mediated protein purification of fusion proteins expressed under high-cell density conditions in E. coli. J Biotechnol 2006; 125:48-56. [PMID: 16546284 DOI: 10.1016/j.jbiotec.2006.01.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 01/10/2006] [Accepted: 01/19/2006] [Indexed: 01/05/2023]
Abstract
The intein-mediated purification system has the potential to significantly reduce the recovery costs of industrial recombinant proteins. The ability of inteins to catalyze a controllable peptide bond cleavage reaction can be used to separate a recombinant protein from its affinity tag during affinity purification. Inteins have been combined with a chitin-binding domain to serve as a self-cleaving affinity tag, facilitating highly selective capture of the fusion protein on an inexpensive substrate--chitin (IMPACT) system, New England Biolabs, Beverly, MA). This purification system has been used successfully at a lab scale in low cell density cultures, but has not been examined comprehensively under high-cell density conditions in defined medium. In this study, the intein-mediated purification of three commercially relevant proteins expressed under high-cell density conditions in E. coli was studied. Additionally, losses during the purification process were quantified. The data indicate that the intein fusion proteins expressed under high cell density fermentations were stable in vivo after induction for a significant duration, and the intein fusion proteins could undergo thiol or pH and temperature initiated cleavage reaction in vitro. Thus, the intein-mediated protein purification system potentially could be employed for the production of recombinant proteins at the industrial-scale.
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Affiliation(s)
- Shamik S Sharma
- Department of Chemical Engineering, 127 Earle Hall, Clemson University, Clemson, SC 29634, USA
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26
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Muralidharan V, Muir TW. Protein ligation: an enabling technology for the biophysical analysis of proteins. Nat Methods 2006; 3:429-38. [PMID: 16721376 DOI: 10.1038/nmeth886] [Citation(s) in RCA: 304] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biophysical techniques such as fluorescence spectroscopy and nuclear magnetic resonance (NMR) spectroscopy provide a window into the inner workings of proteins. These approaches make use of probes that can either be naturally present within the protein or introduced through a labeling procedure. In general, the more control one has over the type, location and number of probes in a protein, then the more information one can extract from a given biophysical analysis. Recently, two related approaches have emerged that allow proteins to be labeled with a broad range of physical probes. Expressed protein ligation (EPL) and protein trans-splicing (PTS) are both intein-based approaches that permit the assembly of a protein from smaller synthetic and/or recombinant pieces. Here we provide some guidelines for the use of EPL and PTS, and highlight how the dovetailing of these new protein chemistry methods with standard biophysical techniques has improved our ability to interrogate protein function, structure and folding.
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Affiliation(s)
- Vasant Muralidharan
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, New York 10021, USA
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27
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Katragadda M, Lambris JD. Expression of compstatin in Escherichia coli: incorporation of unnatural amino acids enhances its activity. Protein Expr Purif 2005; 47:289-95. [PMID: 16406678 DOI: 10.1016/j.pep.2005.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2005] [Revised: 11/11/2005] [Accepted: 11/18/2005] [Indexed: 10/25/2022]
Abstract
Compstatin, a 13-residue cyclic peptide, is a complement inhibitor that shows therapeutic potential. Several previous approaches have improved the activity of this peptide several-fold. In the present study, we have expressed and purified compstatin from Escherichia coli in an effort to increase its potency and to generate it in high yield in a more economical fashion. An intein-based expression system was used to express compstatin in fusion with chitin-binding domain and Ssp DnaB intein, which were later cleaved from the expressed molecule at room temperature and pH 7.0 to yield pure compstatin in one step. The expressed compstatin showed activity similar to the synthetic compstatin in an ELISA-based assay. The same expression system and purification strategy were used to incorporate three tryptophan analogs, 6-fluoro-tryptophan, 5-hydroxy-tryptophan, and 7-aza-tryptophan, into compstatin. Interestingly, incorporation of 6-fluoro-tryptophan increased the activity three-fold relative to wild-type compstatin; in contrast, incorporation of 5-hydroxy- or 7-aza-tryptophan rendered compstatin less active than the wild-type form.
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Affiliation(s)
- Madan Katragadda
- Protein Chemistry Laboratory, Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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28
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Skretas G, Wood DW. A Bacterial Biosensor of Endocrine Modulators. J Mol Biol 2005; 349:464-74. [PMID: 15878176 DOI: 10.1016/j.jmb.2005.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 04/04/2005] [Accepted: 04/05/2005] [Indexed: 12/22/2022]
Abstract
The nuclear hormone receptors comprise one of the largest classes of protein targets for drug discovery, as their function has been linked to a variety of serious diseases, including several forms of cancer. Identifying novel compounds with the ability to modulate the function of these targets could lead to the development of effective therapeutics. In vivo sensors of ligand binding have emerged as tools that can greatly accelerate the lead identification process, allowing new drugs to be discovered more rapidly and cheaply. In this work, a novel sensor of nuclear hormone binding has been developed in Escherichia coli by constructing a fusion of the ligand-binding domain of the human estrogen receptor with a thymidylate synthase enzyme (TS). Expression of this fusion protein in TS-deficient bacterial cells resulted in growth phenotypes that were dependent on the presence of estrogen. Subsequent replacement of the estrogen receptor with the ligand-binding domain of the human thyroid hormone receptor led to specific thyroid hormone-enhanced growth that was insensitive to estrogen. This biosensor was then challenged with a small library of estrogen and thyroid hormone analogues, and it was observed that levels of cell growth correlate well with ligand-binding affinity. Remarkably, this simple biosensor was able to discriminate between agonistic and antagonistic activities, as combinations of estrogen agonists had an additive impact on cell growth, whereas known estrogen antagonists were found to neutralize agonist effects. This system constitutes a technique for facile selection of lead compounds with potential medical applications.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, Princeton University, Engineering Quadrangle, Olden St., Princeton, NJ 08544, USA
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29
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Miao J, Wu W, Spielmann T, Belfort M, Derbyshire V, Belfort G. Single-step affinity purification of toxic and non-toxic proteins on a fluidics platform. LAB ON A CHIP 2005; 5:248-253. [PMID: 15726200 DOI: 10.1039/b413292k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Single-step fusion-based affinity purification of proteins with pH-controllable linkers was carried out in a fluidic device. The linkers were previously derived from self-splicing protein elements called inteins. Two different linkers were generated to solve two distinct separation problems: one for rapid single-step affinity purification of a wide range of proteins, and the other specifically for the purification of cytotoxic proteins. Scale-down factors of 185 resulted in separations in a 27 microl bed-volume. A rotating CD format was chosen because of its simplicity in effecting fluid movement through centrifugal force without the complications associated with electro-osmosis and other pumping methods. The design and fabrication of the fluidic device and the protein purification process are described. This work, which demonstrates the purification of active proteins by two distinct fluidic separations, is widely applicable to small-scale massively parallel proteomic separations.
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Affiliation(s)
- Jun Miao
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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30
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Morassutti C, De Amicis F, Bandiera A, Marchetti S. Expression of SMAP-29 cathelicidin-like peptide in bacterial cells by intein-mediated system. Protein Expr Purif 2005; 39:160-8. [PMID: 15642466 DOI: 10.1016/j.pep.2004.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Revised: 11/10/2004] [Indexed: 10/26/2022]
Abstract
In this work, the intein fusion approach was used for expression and purification of cathelicidin-like peptide SMAP-29 from Escherichia coli cultures. To overcome the high toxicity of the antimicrobial peptide against host cells, both C- and N-terminal fusions with Sce VMA intein were evaluated. The fusion of SMAP-29 with the N-terminus of intein had a dramatic lethal effect. In contrast, chimeric constructs harboring SMAP-29 linked to the C-terminus of intein displayed no significant inhibition of bacterial growth. Expression of intein-SMAP fusion protein was then induced in ER2566 E. coli strain by IPTG addition and different experimental conditions were tested in order to optimize the recovery of the soluble protein complex. Peptide purification was carried out by affinity chromatography: the chitin binding domain linked to intein was used to immobilize the chimeric protein on a chitin column and intein-mediated splicing of target peptide was obtained by thiol addition. Microbroth dilution assay showed that recombinant SMAP-29 displayed a high, dose-dependent bactericidal activity. These data demonstrate that the fusion of SMAP-29 with C-intein was able to inactivate the antimicrobial properties of the cathelicidin peptide allowing the expression of fusion protein in the host cell. The intein-mediated purification supplied an effective way to recover the fusion partner in its proper biologically active form.
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Affiliation(s)
- Carla Morassutti
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, via delle Scienze, 208-33100 Udine, Italy.
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31
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Abstract
Inteins are the protein analogs of self-splicing RNA introns, as they post-translationally excise themselves from a variety of protein hosts. Intein insertion abolishes, in general, the activity of its host protein, which is subsequently restored upon intein excision. These protein elements therefore have the potential to be used as general molecular "switches" for the control of arbitrary target proteins. Based on rational design, an intein-based protein switch has been constructed whose splicing activity is conditionally triggered in vivo by the presence of thyroid hormone or synthetic analogs. This modified intein was used in Escherichia coli to demonstrate that a number of different proteins can be inactivated by intein insertion and then reactivated by the addition of thyroid hormone via ligand-induced splicing. This conditional activation was also found to occur in a dose-dependent manner. Rational protein engineering was then combined with genetic selection to evolve an additional intein whose activity is controlled by the presence of synthetic estrogen ligands. The ability to regulate protein function post-translationally through the use of ligand-controlled intein splicing will most likely find applications in metabolic engineering, drug discovery and delivery, biosensing, molecular computation, as well as many additional areas of biotechnology.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, Princeton University, Engineering Quadrangle, Olden St., Princeton, NJ 08544, USA
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32
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Evans TC, Xu MQ, Pradhan S. Protein splicing elements and plants: from transgene containment to protein purification. ANNUAL REVIEW OF PLANT BIOLOGY 2005; 56:375-92. [PMID: 15862101 DOI: 10.1146/annurev.arplant.56.032604.144242] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Protein splicing elements, termed inteins, have been discovered in all the domains of life. Basic research on inteins has led to a greater understanding of how they mediate the protein splicing process. Because inteins are natural protein engineering elements they have been harnessed for use in a number of applications, including protein purification, protein semisynthesis, and in vivo and in vitro protein modifications. This review focuses on the use of inteins in plants. A split-gene technique utilizes inteins to reconstitute the activity of a transgene product with the goal of limiting the spread of transgenes from a genetically modified plant to a weedy relative. Furthermore, merging the intein tag for protein purification with the large protein yields possible with plants has the potential to produce pharmaceutically important proteins. Finally, relevant techniques that may be used in plants in the future are discussed.
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Affiliation(s)
- Thomas C Evans
- New England Biolabs, Inc., Beverly, Massachusetts 01915, USA.
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33
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Edgell DR, Stanger MJ, Belfort M. Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene. J Mol Biol 2004; 343:1231-41. [PMID: 15491609 DOI: 10.1016/j.jmb.2004.09.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 08/25/2004] [Accepted: 09/02/2004] [Indexed: 12/01/2022]
Abstract
To maximize spread of their host intron or intein, many homing endonucleases recognize nucleotides that code for important and conserved amino acid residues of the target gene. Here, we examine the cleavage requirements for I-TevI, which binds a stretch of thymidylate synthase (TS) DNA that codes for functionally critical residues in the TS active site. Using an in vitro selection scheme, we identified two base-pairs in the I-TevI cleavage site region as important for cleavage efficiency. These were confirmed by comparison of I-TevI cleavage efficiencies on mutant and on wild-type substrates. We also showed that nicking of the bottom strand by I-TevI is not affected by mutation of residues surrounding the bottom-strand cleavage site, unlike other homing endonucleases. One of these two base-pairs is universally conserved in all TS sequences, and is identical with a previously identified cleavage determinant of I-BmoI, a related GIY-YIG endonuclease that binds a homologous stretch of TS-encoding DNA. The other base-pair is conserved only in a subset of TS genes that includes the I-TevI, but not the I-BmoI, target sequence. Both the I-TevI and I-BmoI cleavage site requirements correspond to functionally critical residues involved in an extensive hydrogen bond network within the TS active site. Remarkably, these cleavage requirements correlate with TS phylogeny in bacteria, suggesting that each endonuclease has individually adapted to efficiently cleave distinct TS substrates.
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Affiliation(s)
- David R Edgell
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health, PO Box 22002, Albany, NY 12201-2002, USA.
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34
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Zeidler MP, Tan C, Bellaiche Y, Cherry S, Häder S, Gayko U, Perrimon N. Temperature-sensitive control of protein activity by conditionally splicing inteins. Nat Biotechnol 2004; 22:871-6. [PMID: 15184905 DOI: 10.1038/nbt979] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Accepted: 03/22/2004] [Indexed: 11/09/2022]
Abstract
Conditional or temperature-sensitive (TS) alleles represent useful tools with which to investigate gene function. Indeed, much of our understanding of yeast has relied on temperature-sensitive mutations which, when available, also provide important insights into other model systems. However, the rarity of temperature-sensitive alleles and difficulty in identifying them has limited their use. Here we describe a system to generate temperature-sensitive alleles based on conditionally active inteins. We have identified temperature-sensitive splicing variants of the yeast Saccharomyces cerevisiae vacuolar ATPase subunit (VMA) intein inserted within Gal4 and transferred these into Gal80. We show that Gal80-intein(TS) is able to efficiently provide temporal regulation of the Gal4/upstream activation sequence (UAS) system in a temperature-dependent manner in Drosophila melanogaster. Given the minimal host requirements necessary for temperature-sensitive intein splicing, this technique has the potential to allow the generation and use of conditionally active inteins in multiple host proteins and model systems, thereby widening the use of temperature-sensitive alleles for functional protein analysis.
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Affiliation(s)
- Martin P Zeidler
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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Abstract
The introduction of noncanonical amino acids and biophysical probes into peptides and proteins, and total or segmental isotopic labelling has the potential to greatly aid the determination of protein structure, function and protein-protein interactions. To obtain a peptide as large as possible by solid-phase peptide synthesis, native chemical ligation was introduced to enable synthesis of proteins of up to 120 amino acids in length. After the discovery of inteins, with their self-splicing properties and their application in protein synthesis, the semisynthetic methodology, expressed protein ligation, was developed to circumvent size limitation problems. Today, diverse expression vectors are available that allow the production of N- and C-terminal fragments that are needed for ligation to produce large amounts and high purity protein(s) (protein alpha-thioesters and peptides or proteins with N-terminal Cys). Unfortunately, expressed protein ligation is still limited mainly by the requirement of a Cys residue. Of course, additional Cys residues can be introduced into the sequence by site directed mutagenesis or synthesis, however, those mutations may disturb protein structure and function. Recently, alternative ligation approaches have been developed that do not require Cys residues. Accordingly, it is theoretically possible to obtain each modified protein using ligation strategies.
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Affiliation(s)
- Ralf David
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany
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Edgell DR, Stanger MJ, Belfort M. Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI. Curr Biol 2003; 13:973-8. [PMID: 12781137 DOI: 10.1016/s0960-9822(03)00340-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Homing endonucleases initiate mobility of their host group I introns by binding to and cleaving lengthy recognition sequences that are typically centered on the intron insertion site (IS) of intronless alleles. Because the intron interrupts the endonucleases' recognition sequence, intron-containing alleles are immune to cleavage by their own endonuclease. I-TevI and I-BmoI are related GIY-YIG endonucleases that bind a homologous stretch of thymidylate synthase (TS)-encoding DNA but use different strategies to distinguish intronless from intron-containing substrates. I-TevI discriminates between substrates at the level of DNA binding, as its recognition sequence is centered on the intron IS. I-BmoI, in contrast, possesses a very asymmetric recognition sequence with respect to the intron IS, binds both intron-containing and intronless TS-encoding substrates, but efficiently cleaves only intronless substrate. Here, we show that I-BmoI is extremely tolerant of multiple substitutions around its cleavage sites and has a low specific activity. However, a single G-C base pair, at position -2 of a 39-base pair recognition sequence, is a major determinant for cleavage efficiency and distinguishes intronless from intron-containing alleles. Strikingly, this G-C base pair is universally conserved in phylogenetically diverse TS-coding sequences; this finding suggests that I-BmoI has evolved exquisite cleavage requirements to maximize the potential to spread to variant intronless alleles, while minimizing cleavage at its own intron-containing allele.
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Affiliation(s)
- David R Edgell
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health, P.O. Box 22002, Albany, NY 12201-2002, USA.
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Schwartz EC, Muir TW, Tyszkiewicz AB. “The splice is right”: how protein splicing is opening new doors in protein science. Chem Commun (Camb) 2003:2087-90. [PMID: 13678154 DOI: 10.1039/b304989m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Edmund C Schwartz
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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