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Malik A, Kamli MR, Sabir JSM, Rather IA, Phan LT, Kim CB, Manavalan B. APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features. Methods 2024:S1046-2023(24)00133-6. [PMID: 38944134 DOI: 10.1016/j.ymeth.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/08/2024] [Accepted: 05/19/2024] [Indexed: 07/01/2024] Open
Abstract
Asparagine peptide lyase (APL) is among the seven groups of proteases, also known as proteolytic enzymes, which are classified according to their catalytic residue. APLs are synthesized as precursors or propeptides that undergo self-cleavage through autoproteolytic reaction. At present, APLs are grouped into 10 families belonging to six different clans of proteases. Recognizing their critical roles in many biological processes including virus maturation, and virulence, accurate identification and characterization of APLs is indispensable. Experimental identification and characterization of APLs is laborious and time-consuming. Here, we developed APLpred, a novel support vector machine (SVM) based predictor that can predict APLs from the primary sequences. APLpred was developed using Boruta-based optimal features derived from seven encodings and subsequently trained using five machine learning algorithms. After evaluating each model on an independent dataset, we selected APLpred (an SVM-based model) due to its consistent performance during cross-validation and independent evaluation. We anticipate APLpred will be an effective tool for identifying APLs. This could aid in designing inhibitors against these enzymes and exploring their functions. The APLpred web server is freely available at https://procarb.org/APLpred/.
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Affiliation(s)
- Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul 03016, Republic of Korea
| | - Majid Rasool Kamli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Irfan Ahmad Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Le Thi Phan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea.
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea.
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Boral S, Sen S, Kushwaha T, Inampudi KK, De S. Extein residues regulate the catalytic function of Spl DnaX intein enzyme by restricting the near-attack conformations of the active-site residues. Protein Sci 2023; 32:e4699. [PMID: 37313648 PMCID: PMC10288555 DOI: 10.1002/pro.4699] [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: 03/23/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Intein enzymes catalyze the splicing of their flanking polypeptide chains and have found tremendous biotechnological applications. Their terminal residues form the catalytic core and participate in the splicing reaction. Hence, the neighboring N- and C-terminal extein residues influence the catalytic rate. As these extein residues vary depending on the substrate identity, we tested the influence of 20 amino acids at these sites in the Spl DnaX intein and observed significant variation of spliced product as well as N- and C-terminus cleavage product formation. We investigated the dependence of these reactions on the extein residues by molecular dynamics (MD) simulations on eight extein variants, and found that the conformational sampling of the active-site residues of the intein enzyme differed among these extein variants. We found that the extein variants that sample higher population of near-attack conformers (NACs) of the active-site residues undergo higher product formation in our activity assays. Ground state conformers that closely resemble the transition state are referred to as NACs. Very good correlation was observed between the NAC populations from the MD simulations of eight extein variants and the corresponding product formation from our activity assays. Furthermore, this molecular detail enabled us to elucidate the mechanistic roles of several conserved active-site residues in the splicing reaction. Overall, this study shows that the catalytic power of Spl DnaX intein enzyme, and most likely other inteins, depends on the efficiency of formation of NACs in the ground state, which is further modulated by the extein residues.
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Affiliation(s)
- Soumendu Boral
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Srijon Sen
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Tushar Kushwaha
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Krishna K. Inampudi
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Soumya De
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
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3
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Maksum IP, Yosua Y, Nabiel A, Pratiwi RD, Sriwidodo S, Soedjanaatmadja UM. Refolding of bioactive human epidermal growth factor from E. coli BL21(DE3) inclusion bodies & evaluations on its in vitro & in vivo bioactivity. Heliyon 2022; 8:e09306. [PMID: 35497033 PMCID: PMC9039848 DOI: 10.1016/j.heliyon.2022.e09306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/10/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Human epidermal growth factor (hEGF) is a mitogenic protein widely used in pharmaceutical and cosmetic industries, thus recombinant DNA technology has been applied to meet the high demand for hEGF. The overexpression of recombinant protein in E. coli often leads to the formation of inclusion bodies (IBs). Mild solubilisation preserves the native secondary protein structure in IBs, thereby the high recovery of active protein from IBs. The redox system also plays a pivotal role in the formation of disulphide bonds during refolding of disulphide bond-containing protein. This study aimed to recover hEGF from bacterial IBs through freeze-thawing solubilisation and glutathione-based oxidative refolding. CBD-Ssp DnaB-hEGF fusion protein was expressed as IBs in E. coli, washed with Triton X-100 and urea to remove most protein contaminants, then the solubilised fusion protein was obtained by freeze-thawing with the addition of 2 M urea. The solubilised protein was subsequently refolded by intein cleavage via a glutathione-based redox system. The refolded hEGF demonstrated heat-resistant properties, interacted with specific antibodies on ELISA, stimulated keratinocyte proliferation and possessed significant in vivo wound healing properties on the 8th day, confirming that hEGF was correctly folded. In summary, the protocol described is suitable for the recovery of refolded hEGF from bacterial IBs by mild solubilisation and oxidative refolding.
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Affiliation(s)
- Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
- Corresponding author.
| | - Yosua Yosua
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ahmad Nabiel
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Riyona Desvy Pratiwi
- Research Centre of Biotechnology, Indonesian Institute of Science, Bogor, Indonesia
| | - Sriwidodo Sriwidodo
- Department of Pharmaceutics & Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ukun M.S. Soedjanaatmadja
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
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SufB intein splicing in Mycobacterium tuberculosis is influenced by two remote conserved N-extein histidines. Biosci Rep 2022; 42:230724. [PMID: 35234249 PMCID: PMC8891592 DOI: 10.1042/bsr20212207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/11/2022] [Accepted: 01/27/2022] [Indexed: 11/24/2022] Open
Abstract
Inteins are auto-processing domains that implement a multistep biochemical reaction termed protein splicing, marked by cleavage and formation of peptide bonds. They excise from a precursor protein, generating a functional protein via covalent bonding of flanking exteins. We report the kinetic study of splicing and cleavage reaction in [Fe–S] cluster assembly protein SufB from Mycobacterium tuberculosis (Mtu). Although it follows a canonical intein splicing pathway, distinct features are added by extein residues present in the active site. Sequence analysis identified two conserved histidines in the N-extein region; His-5 and His-38. Kinetic analyses of His-5Ala and His-38Ala SufB mutants exhibited significant reductions in splicing and cleavage rates relative to the SufB wildtype (WT) precursor protein. Structural analysis and molecular dynamics (MD) simulations suggested that Mtu SufB displays a unique mechanism where two remote histidines work concurrently to facilitate N-terminal cleavage reaction. His-38 is stabilized by the solvent-exposed His-5, and can impact N–S acyl shift by direct interaction with the catalytic Cys1. Development of inteins as biotechnological tools or as pathogen-specific novel antimicrobial targets requires a more complete understanding of such unexpected roles of conserved extein residues in protein splicing.
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Panda S, Nanda A, Nasker SS, Sen D, Mehra A, Nayak S. Metal effect on intein splicing: A review. Biochimie 2021; 185:53-67. [PMID: 33727137 DOI: 10.1016/j.biochi.2021.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/08/2023]
Abstract
Inteins are intervening polypeptides that interrupt the functional domains of several important proteins across the three domains of life. Inteins excise themselves from the precursor protein, ligating concomitant extein residues in a process called protein splicing. Post-translational auto-removal of inteins remain critical for the generation of active proteins. The perspective of inteins in science is a robust field of research, however fundamental studies centralized upon splicing regulatory mechanism are imperative for addressing more intricate issues. Controlled engineering of intein splicing has many applications; intein inhibition can facilitate novel drug design, while activation of intein splicing is exploited in protein purification. This paper provides a comprehensive review of the past and recent advances in the splicing regulation via metal-intein interaction. We compare the behavior of different metal ions on diverse intein systems. Though metals such as Zn, Cu, Pt, Cd, Co, Ni exhibit intein inhibitory effect heterogeneously on different inteins, divalent metal ions such as Ca and Mg fail to do so. The observed diversity in the metal-intein interaction arises mostly due to intein polymorphism and variations in atomic structure of metals. A mechanistic understanding of intein regulation by metals in native as well as synthetically engineered intein systems may yield potent intein inhibitors via direct or indirect approach.
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Affiliation(s)
- Sunita Panda
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Ananya Nanda
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Sourya Subhra Nasker
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Debjani Sen
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Ashwaria Mehra
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Sasmita Nayak
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India.
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6
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Boral S, Maiti S, Basak AJ, Lee W, De S. Structural, Dynamic, and Functional Characterization of a DnaX Mini-intein Derived from Spirulina platensis Provides Important Insights into Intein-Mediated Catalysis of Protein Splicing. Biochemistry 2020; 59:4711-4724. [PMID: 33289560 DOI: 10.1021/acs.biochem.0c00828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein splicing is a self-catalyzed post-translational modification in which the intein enzyme excises itself from a precursor protein and ligates the flanking sequences to produce a mature protein. We report the solution structure of a 136-residue DnaX mini-intein enzyme derived from the cyanobacterium Spirulina platensis. This sequence adopts a well-defined globular structure and forms a horseshoe-shaped fold commonly found in the HINT (hedgehog intein) topology. Backbone dynamics and hydrogen exchange experiments revealed conserved motions on various time scales, which is proposed to be a characteristic of the intein fold. Interestingly, several dynamic motions were found in symmetrically equivalent positions within the protein structure, which might be a consequence of the symmetrical intein fold. In cell splicing activity showed that Spl DnaX mini-intein is a highly active enzyme. The precursor protein was not detected at any timepoint of the assay. Apart from the splicing reaction, catalytic cleavage at the N- and C-termini of the precursor protein was also observed. To determine the roles of the catalytic residues in splicing and cleavage reactions, all combinations of alanine mutations of these residues were generated and functionally characterized. This in-depth analysis revealed cooperativity between these catalytic residues, which suppresses the N- and C-terminal cleavage reactions and enhances the yield of the spliced product. Overall, this study provides a thorough structural, dynamic, and functional characterization of a new intein sequence and adds to the collection of these unique enzymes that have found tremendous applications in biochemistry and biotechnology.
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Affiliation(s)
- Soumendu Boral
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Snigdha Maiti
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Aditya J Basak
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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7
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Inteins in Science: Evolution to Application. Microorganisms 2020; 8:microorganisms8122004. [PMID: 33339089 PMCID: PMC7765530 DOI: 10.3390/microorganisms8122004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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8
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Hoffmann S, Terhorst TME, Singh RK, Kümmel D, Pietrokovski S, Mootz HD. Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein. Chembiochem 2020; 22:364-373. [PMID: 32813312 PMCID: PMC7891396 DOI: 10.1002/cbic.202000509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Indexed: 12/31/2022]
Abstract
Split inteins are indispensable tools for protein engineering because their ligation and cleavage reactions enable unique modifications of the polypeptide backbone. Three different classes of inteins have been identified according to the nature of the covalent intermediates resulting from the acyl rearrangements in the multistep protein‐splicing pathway. Class 3 inteins employ a characteristic internal cysteine for a branched thioester intermediate. A bioinformatic database search of non‐redundant protein sequences revealed the absence of split variants in 1701 class 3 inteins. We have discovered the first reported split class 3 intein in a metagenomics data set and report its biochemical, mechanistic and structural analysis. The AceL NrdHF intein exhibits low sequence conservation with other inteins and marked deviations in residues at conserved key positions, including a variation of the typical class‐3 WCT triplet motif. Nevertheless, functional analysis confirmed the class 3 mechanism of the intein and revealed excellent splicing yields within a few minutes over a wide range of conditions and with barely detectable cleavage side reactions. A high‐resolution crystal structure of the AceL NrdHF precursor and a mutagenesis study explained the importance and roles of several residues at the key positions. Tolerated substitutions in the flanking extein residues and a high affinity between the split intein fragments further underline the intein's future potential as a ligation tool.
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Affiliation(s)
- Simon Hoffmann
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Tobias M E Terhorst
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Rohit K Singh
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
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Li Z, Fu B, Green CM, Liu B, Zhang J, Lang Y, Chaturvedi S, Belfort M, Liao G, Li H. Cisplatin protects mice from challenge of Cryptococcus neoformans by targeting the Prp8 intein. Emerg Microbes Infect 2019; 8:895-908. [PMID: 31223062 PMCID: PMC6598491 DOI: 10.1080/22221751.2019.1625727] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/16/2019] [Indexed: 01/02/2023]
Abstract
The Prp8 intein is one of the most widespread eukaryotic inteins, present in important pathogenic fungi, including Cryptococcus and Aspergillus species. Because the processed Prp8 carries out essential and non-redundant cellular functions, a Prp8 intein inhibitor is a mechanistically novel antifungal agent. In this report, we demonstrated that cisplatin, an FDA-approved cancer drug, significantly arrested growth of Prp8 intein-containing fungi C. neoformans and C. gattii, but only poorly inhibited growth of intein-free Candida species. These results suggest that cisplatin arrests fungal growth through specific inhibition of the Prp8 intein. Cisplatin was also found to significantly inhibit growth of C. neoformans in a mouse model. Our results further showed that cisplatin inhibited Prp8 intein splicing in vitro in a dose-dependent manner by direct binding to the Prp8 intein. Crystal structures of the apo- and cisplatin-bound Prp8 inteins revealed that two degenerate cisplatin molecules bind at the intein active site. Mutation of the splicing-site residues led to loss of cisplatin binding, as well as impairment of intein splicing. Finally, we found that overexpression of the Prp8 intein in cryptococcal species conferred cisplatin resistance. Overall, these results indicate that the Prp8 intein is a novel antifungal target worth further investigation.
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Affiliation(s)
- Zhong Li
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Bin Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, People’s Republic of China
| | - Cathleen M. Green
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, USA
| | - Binbin Liu
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Jing Zhang
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Yuekun Lang
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Sudha Chaturvedi
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing, People’s Republic of China
| | - Hongmin Li
- New York State Department of Health, Wadsworth Center, Albany, NY, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
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Fang YT, Lai WS, Liu JH, Liu YC. Enhanced cecropin B2 production via chitin-binding domain and intein self-cleavage system. Biotechnol Appl Biochem 2018; 66:209-215. [PMID: 30471160 DOI: 10.1002/bab.1716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/23/2018] [Indexed: 11/06/2022]
Abstract
In this study, various constructs and hosts were used to produce high levels of cecropin B2 (cecB2). To mitigate cecB2's toxic inhibition of host cells, various cecB2 constructs were built. Results showed that the combination of a chitin-binding domain and an intein self-cleavage motif in front of cecropin B2, without a His-tag, was best for cecB2 expression. E. coli ER2566 was the best host, and 2YT was the best medium for cultivation. Under these conditions, a cecB2 yield of 98.2 mg/L could be obtained after purification. The purified cecB2 expressed a wide antimicrobial effect on most Gram-negative strains, including multidrug-resistant Acinetobactor baumannii and Staphylococcus aureus. This study provides a systematic approach to the efficient production of the antimicrobial peptide (AMP) cecB2 via the recombinant E. coli process, which is expected to be an efficient way for the production of other AMPs.
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Affiliation(s)
- Yi-Ting Fang
- Department of Chemical Engineering, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Wei-Shiang Lai
- Department of Chemical Engineering, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan, Republic of China.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Yung-Chuan Liu
- Department of Chemical Engineering, National Chung Hsing University, Taichung, Taiwan, Republic of China
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11
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Böcker JK, Dörner W, Mootz HD. Rational design of an improved photo-activatable intein for the production of head-to-tail cyclized peptides. Biol Chem 2018; 400:417-427. [DOI: 10.1515/hsz-2018-0367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/31/2018] [Indexed: 01/13/2023]
Abstract
Abstract
Head-to-tail cyclization of genetically encoded peptides and proteins can be achieved with the split intein circular ligation of peptides and proteins (SICLOPPS) method by inserting the desired polypeptide between the C- and N-terminal fragments of a split intein. To prevent the intramolecular protein splicing reaction from spontaneously occurring upon folding of the intein domain, we have previously rendered this process light-dependent in a photo-controllable variant of the M86 intein, using genetically encoded ortho-nitrobenzyltyrosine at a structurally important position. Here, we report improvements on this photo-intein with regard to expression yields and rate of cyclic peptide formation. The temporally defined photo-activation of the purified stable intein precursor enabled a kinetic analysis that identified the final resolution of the branched intermediate as the rate-determining individual reaction of the three steps catalyzed by the intein. With this knowledge, we prepared an R143H mutant with a block F histidine residue. This histidine is conserved in most inteins and helps catalyze the third step of succinimide formation. The engineered intein formed the cyclic peptide product up to 3-fold faster within the first 15 min after irradiation, underlining the potential of protein splicing pathway engineering. The broader utility of the intein was also shown by formation of the 14-mer sunflower trypsin inhibitor 1.
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Affiliation(s)
- Jana K. Böcker
- Department of Chemistry and Pharmacy, Institute of Biochemistry , University of Münster , Wilhelm-Klemm-Str. 2 , D-48149 Münster , Germany
| | - Wolfgang Dörner
- Department of Chemistry and Pharmacy, Institute of Biochemistry , University of Münster , Wilhelm-Klemm-Str. 2 , D-48149 Münster , Germany
| | - Henning D. Mootz
- Department of Chemistry and Pharmacy, Institute of Biochemistry , University of Münster , Wilhelm-Klemm-Str. 2 , D-48149 Münster , Germany
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12
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Kelley DS, Lennon CW, Li Z, Miller MR, Banavali NK, Li H, Belfort M. Mycobacterial DnaB helicase intein as oxidative stress sensor. Nat Commun 2018; 9:4363. [PMID: 30341292 PMCID: PMC6195587 DOI: 10.1038/s41467-018-06554-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/10/2018] [Indexed: 11/09/2022] Open
Abstract
Inteins are widespread self-splicing protein elements emerging as potential post-translational environmental sensors. Here, we describe two inteins within one protein, the Mycobacterium smegmatis replicative helicase DnaB. These inteins, DnaBi1 and DnaBi2, have homology to inteins in pathogens, splice with vastly varied rates, and are differentially responsive to environmental stressors. Whereas DnaBi1 splicing is reversibly inhibited by oxidative and nitrosative insults, DnaBi2 is not. Using a reporter that measures splicing in a native intein-containing organism and western blotting, we show that H2O2 inhibits DnaBi1 splicing in M. smegmatis. Intriguingly, upon oxidation, the catalytic cysteine of DnaBi1 forms an intramolecular disulfide bond. We report a crystal structure of the class 3 DnaBi1 intein at 1.95 Å, supporting our findings and providing insight into this splicing mechanism. We propose that this cysteine toggle allows DnaBi1 to sense stress, pausing replication to maintain genome integrity, and then allowing splicing immediately when permissive conditions return.
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Affiliation(s)
- Danielle S Kelley
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
| | - Christopher W Lennon
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Michael R Miller
- Department of Chemistry, University at Albany, Albany, NY, 12222, USA
| | - Nilesh K Banavali
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Hongmin Li
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA.
| | - Marlene Belfort
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA.
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13
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Friedel K, Popp MA, Matern JCJ, Gazdag EM, Thiel IV, Volkmann G, Blankenfeldt W, Mootz HD. A functional interplay between intein and extein sequences in protein splicing compensates for the essential block B histidine. Chem Sci 2018; 10:239-251. [PMID: 30713635 PMCID: PMC6333167 DOI: 10.1039/c8sc01074a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/03/2018] [Indexed: 01/28/2023] Open
Abstract
Steric bulk can compensate for a catalytically critical histidine in an intein's active site and promote the N–S acyl shift.
Inteins remove themselves from a precursor protein by protein splicing. Due to the concomitant structural changes of the host protein, this self-processing reaction has enabled many applications in protein biotechnology and chemical biology. We show that the evolved M86 mutant of the Ssp DnaB intein displays a significantly improved tolerance towards non-native amino acids at the N-terminally flanking (–1) extein position compared to the parent intein, in the form of both an artificially trans-splicing split intein and the cis-splicing mini-intein. Surprisingly, side chains with increased steric bulk compared to the native Gly(–1) residue, including d-amino acids, were found to compensate for the essential block B histidine in His73Ala mutants in the initial N–S acyl shift of the protein splicing pathway. In the case of the M86 intein, large (–1) side chains can even rescue protein splicing activity as a whole. With the comparison of three crystal structures, namely of the M86 intein as well as of its Gly(–1)Phe and Gly(–1)Phe/His73Ala mutants, our data supports a model in which the intein's active site can exert a strain by varying mechanisms on the different angles of the scissile bond at the extein–intein junction to effect a ground-state destabilization. The compensatory mechanism of the block B histidine is the first example for the direct functional role of an extein residue in protein splicing. It sheds new light on the extein–intein interplay and on possible consequences of their co-evolution as well as on the laboratory engineering of improved inteins.
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Affiliation(s)
- Kristina Friedel
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Monika A Popp
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany
| | - Julian C J Matern
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Emerich M Gazdag
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany
| | - Ilka V Thiel
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Gerrit Volkmann
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Wulf Blankenfeldt
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics , Technische Universität Braunschweig , Spielmannstraße 7 , 38106 Braunschweig , Germany
| | - Henning D Mootz
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
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14
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Matern JCJ, Friedel K, Binschik J, Becher KS, Yilmaz Z, Mootz HD. Altered Coordination of Individual Catalytic Steps in Different and Evolved Inteins Reveals Kinetic Plasticity of the Protein Splicing Pathway. J Am Chem Soc 2018; 140:11267-11275. [PMID: 30111090 DOI: 10.1021/jacs.8b04794] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein splicing performed by inteins provides powerful opportunities to manipulate protein structure and function, however, detailed mechanistic knowledge of the multistep pathway to help engineering optimized inteins remains scarce. A typical intein has to coordinate three steps to maximize the product yield of ligated exteins. We have revealed a new type of coordination in the Ssp DnaB intein, in which the initial N- S acyl shift appears rate-limiting and acts as an up-regulation switch to dramatically accelerate the last step of succinimide formation, which is thus coupled to the first step. The structure-activity relationship at the N-terminal scissile bond was studied with atomic precision using a semisynthetic split intein. We show that the removal of the extein acyl group from the α-amino moiety of the intein's first residue is strictly required and sufficient for the up-regulation switch. Even an acetyl group as the smallest possible extein moiety completely blocked the switch. Furthermore, we investigated the M86 intein, a mutant with faster splicing kinetics previously obtained by laboratory evolution of the Ssp DnaB intein, and the individual impact of its eight mutations. The succinimide formation was decoupled from the first step in the M86 intein, but the acquired H143R mutation acts as a brake to prevent premature C-terminal cleavage and thereby maximizes splicing yields. Together, these results revealed a high degree of plasticity in the kinetic coordination of the splicing pathway. Furthermore, our study led to the rational design of improved M86 mutants with the highest yielding trans-splicing and fastest trans-cleavage activities.
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Affiliation(s)
- Julian C J Matern
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Kristina Friedel
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Jens Binschik
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Kira-Sophie Becher
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Zahide Yilmaz
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Henning D Mootz
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
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15
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Gordo V, Aparicio D, Pérez-Luque R, Benito A, Vilanova M, Usón I, Fita I, Ribó M. Structural Insights into Subunits Assembly and the Oxyester Splicing Mechanism of Neq pol Split Intein. Cell Chem Biol 2018; 25:871-879.e2. [PMID: 29754955 DOI: 10.1016/j.chembiol.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/28/2018] [Accepted: 04/08/2018] [Indexed: 11/28/2022]
Abstract
Split inteins are expressed as two separated subunits (N-intein and C-intein) fused to the corresponding exteins. The specific association of both intein subunits precedes protein splicing, which results in excision of the intein subunits and in ligation, by a peptide bond, of the concomitant exteins. Catalytically active intein precursors are typically too reactive for crystallization or even isolation. Neq pol is the trans-intein of the B-type DNA polymerase I split gene from hyperthermophile Nanoarchaeum equitans. We have determined the crystal structures of both the isolated NeqN and the complex of NeqN and NeqC subunits carrying the wild-type sequences, including the essential catalytic residues Ser1 and Thr+1, in addition to seven and three residues of the N- and C-exteins, respectively. These structures provide detailed information on the unique oxyester chemistry of the splicing mechanism of Neq pol and of the extensive rearrangements that occur in NeqN during the association step.
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Affiliation(s)
- Verónica Gordo
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Antoni Benito
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Maria Vilanova
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain; ICREA Lluís Companys 23, 08003 Barcelona, Spain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain.
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain.
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16
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Li X, Zhang XL, Cai YM, Zhang L, Lin Y, Meng Q. Site specific labeling of two proteins in one system by atypical split inteins. Int J Biol Macromol 2018; 109:921-931. [DOI: 10.1016/j.ijbiomac.2017.11.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/06/2017] [Accepted: 11/12/2017] [Indexed: 01/25/2023]
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17
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Mujika JI, Lopez X. Unveiling the Catalytic Role of B-Block Histidine in the N–S Acyl Shift Step of Protein Splicing. J Phys Chem B 2017; 121:7786-7796. [DOI: 10.1021/acs.jpcb.7b04276] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. I. Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi Spain
| | - X. Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi Spain
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18
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Engineered Ssp DnaX inteins for protein splicing with flanking proline residues. Saudi J Biol Sci 2017; 26:854-859. [PMID: 31049014 PMCID: PMC6486613 DOI: 10.1016/j.sjbs.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 07/19/2017] [Accepted: 07/19/2017] [Indexed: 11/23/2022] Open
Abstract
Inteins are internal protein sequences capable of catalyzing a protein splicing reaction by self-excising from a precursor protein and simultaneously joining the flanking sequences with a peptide bond. Split inteins have separate pieces (N-intein and C-intein) that reassemble non-covalently to catalyze a protein trans-splicing reaction joining two polypeptides. Protein splicing has become increasingly useful tools in many fields of biological research and biotechnology. However, natural and engineered inteins have failed previously to function when being flanked by proline residue at the -1 or +2 positions, which limits general uses of inteins. In this study, different engineered inteins were tested. We found that engineered Ssp DnaX mini-intein and split inteins could carry out protein splicing with proline at the +2 positions or at both -1 and +2 positions. Under in vivo conditions in E. coli cells, the mini-intein, S1 split intein, and S11 split intein spliced efficiently, whereas the S0 split intein did not splice with proline at both -1 and +2 positions. The S1 and S11 split inteins also trans-spliced efficiently in vitro with proline at the +2 positions or at both -1 and +2 positions, but the S0 split intein trans-spliced inefficiently with proline at the +2 position and did not trans-splice with proline at both -1 and +2 positions. These findings contribute significantly to the toolbox of intein-based technologies by allowing the use of inteins in proteins having proline at the splicing point.
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19
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Neugebauer M, Böcker JK, Matern JCJ, Pietrokovski S, Mootz HD. Development of a screening system for inteins active in protein splicing based on intein insertion into the LacZα-peptide. Biol Chem 2017; 398:57-67. [PMID: 27632429 DOI: 10.1515/hsz-2016-0229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/23/2016] [Indexed: 11/15/2022]
Abstract
Protein splicing by inteins has found diverse applications in biotechnology, protein chemistry and chemical biology. Inteins display a wide range of efficiencies and rates unpredictable from their amino acid sequences. Here, we identified positions T22S and S35 in the LacZα peptide as intein insertion sites that strictly require protein splicing, in contrast to cleavage side-reactions, to allow for complementation of β-galactosidase activity. Both the cis-variant of the M86 mutant of the Ssp DnaB intein and a split form undergoing protein trans-splicing gave rise to formation of blue colonies in the β-galactosidase read-out. Furthermore, we report the two novel, naturally split VidaL T4Lh-1 and VidaL UvsX-2 inteins whose N-terminal fragments consist of only 15 and 16 amino acids, respectively. Initial biochemical characterization with the LacZα host system of these inteins further underlines its utility. Finally, we used the LacZα host system to rapidly identify amino acid substitutions from a small randomized library at the structurally conserved intein position 2 next to the catalytic center, that are tolerated for protein splicing activity of the M86 intein. These findings demonstrate the potential of the system for initial testing and directed evolution of inteins.
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20
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Ramsoomair CK, Yakely AE, Urbanski LM, Karanja K, Giaccone ZT, Siegart NM, Wang C, Gomez AV, Reitter JN, Mills KV. Coordination of the third step of protein splicing in two cyanobacterial inteins. FEBS Lett 2017. [PMID: 28649707 DOI: 10.1002/1873-3468.12730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The third step of protein splicing is cyclization of Asn coupled to peptide bond cleavage. In two related cyanobacterial inteins, this step is facilitated by Asn or Gln. For a Synechococcus sp. PCC7002 intein, the isolated third step of protein splicing is more efficient with its native Asn than with substitution to Gln. For a Trichodesmium erythraeum intein, its native Gln facilitates the third step as efficiently as with Asn. Despite these differences, the yield of splicing is not affected, suggesting that the third step is influenced by mechanism-linked conformational changes. A conserved catalytic His and the penultimate residue also play roles in promoting side-chain cyclization.
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Affiliation(s)
| | - Anthony E Yakely
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Laura M Urbanski
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Kevin Karanja
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | | | - Nicolle M Siegart
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Chunyu Wang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.,Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Alvin V Gomez
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Julie N Reitter
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
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21
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Abstract
Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific. Strikingly, despite this phage specificity, inteins localize to functional motifs shared with bacteria, such that intein-containing genes have similar roles, like hydrolase activity and nucleic acid binding, indicating a global commonality among intein-hosting proteins. Additionally, there are multiple insertion points within active centers, implying independent invasion events, with regulatory implications. Several phage inteins were shown to be splicing competent and to encode functional homing endonucleases, important for mobility. Further, bioinformatic analysis supports the potential for phages as facilitators of intein movement among mycobacteria and related genera. Analysis of catalytic intein residues finds the highly conserved penultimate histidine inconsistently maintained among mycobacteriophages. Biochemical characterization of a noncanonical phage intein shows that this residue influences precursor accumulation, suggesting that splicing has been tuned in phages to modulate generation of important proteins. Together, this work expands our understanding of phage-based intein dissemination and evolution and implies that phages provide a context for evolution of splicing-based regulation. Inteins are mobile protein splicing elements found in critical genes across all domains of life. Mycobacterial inteins are of particular interest because of their occurrence in pathogenic species, such as Mycobacterium tuberculosis and Mycobacterium leprae, which harbor inteins in important proteins. We have discovered a similarity in activities of intein-containing proteins among mycobacteriophages and their intein-rich actinobacterial hosts, with implications for both posttranslational regulation by inteins and phages participating in horizontal intein transfer. Our demonstration of multiple insertion points within active centers of phage proteins implies independent invasion events, indicating the importance of intein maintenance at specific functional sites. The variable conservation of a catalytic splicing residue, leading to profoundly altered splicing rates, points to the regulatory potential of inteins and to mycobacteriophages playing a role in intein evolution. Collectively, these results suggest inteins as posttranslational regulators and mycobacteriophages as both vehicles for intein distribution and incubators for intein evolution.
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22
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Chan H, Pearson CS, Green CM, Li Z, Zhang J, Belfort G, Shekhtman A, Li H, Belfort M. Exploring Intein Inhibition by Platinum Compounds as an Antimicrobial Strategy. J Biol Chem 2016; 291:22661-22670. [PMID: 27609519 DOI: 10.1074/jbc.m116.747824] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/29/2016] [Indexed: 01/10/2023] Open
Abstract
Inteins, self-splicing protein elements, interrupt genes and proteins in many microbes, including the human pathogen Mycobacterium tuberculosis Using conserved catalytic nucleophiles at their N- and C-terminal splice junctions, inteins are able to excise out of precursor polypeptides. The splicing of the intein in the mycobacterial recombinase RecA is specifically inhibited by the widely used cancer therapeutic cisplatin, cis-[Pt(NH3)2Cl2], and this compound inhibits mycobacterial growth. Mass spectrometric and crystallographic studies of Pt(II) binding to the RecA intein revealed a complex in which two platinum atoms bind at N- and C-terminal catalytic cysteine residues. Kinetic analyses of NMR spectroscopic data support a two-step binding mechanism in which a Pt(II) first rapidly interacts reversibly at the N terminus followed by a slower, first order irreversible binding event involving both the N and C termini. Notably, the ligands of Pt(II) compounds that are required for chemotherapeutic efficacy and toxicity are no longer bound to the metal atom in the intein adduct. The lack of ammine ligands and need for phosphine represent a springboard for future design of platinum-based compounds targeting inteins. Because the intein splicing mechanism is conserved across a range of pathogenic microbes, developing these drugs could lead to novel, broad range antimicrobial agents.
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Affiliation(s)
- Hon Chan
- From the Department of Biological Sciences and RNA Institute and.,Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - C Seth Pearson
- From the Department of Biological Sciences and RNA Institute and.,Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Cathleen M Green
- From the Department of Biological Sciences and RNA Institute and
| | - Zhong Li
- Laboratory of Computational and Structural Biology, Wadsworth Center, New York State Department of Health, Albany, New York 12208, and
| | - Jing Zhang
- Laboratory of Computational and Structural Biology, Wadsworth Center, New York State Department of Health, Albany, New York 12208, and
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Alex Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222
| | - Hongmin Li
- Laboratory of Computational and Structural Biology, Wadsworth Center, New York State Department of Health, Albany, New York 12208, and.,Department of Biomedical Sciences, University at Albany, State University of New York, Albany, New York 12201
| | - Marlene Belfort
- From the Department of Biological Sciences and RNA Institute and
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23
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Abstract
Split intein circular ligation of peptides and proteins (SICLOPPS) is a genetically encoded method for the intracellular production of cyclic peptide libraries of around 100 million (10(8)) members that utilizes the Synechocystis sp PCC6803 (Ssp) DnaE split inteins. However, Ssp inteins are relatively slow splicing and intolerant of amino acid variation around the splice junction, potentially limiting the utility and composition of SICLOPPS libraries. In contrast, Nostoc punctiforme (Npu) DnaE split inteins not only splice significantly faster, they are also much more tolerant of amino acid variation around their splice junctions. Here, we report the use of engineered Npu inteins in SICLOPPS for the generation of cyclic peptide libraries and cyclic proteins. Despite their superior splicing characteristics, however, we observed a high level of toxicity from the Npu SICLOPPS constructs in E. coli. The observed toxicity was overcome though incorporation of an SsrA tag to target the spliced Npu inteins to the ClpXP complex for degradation. The resulting traceless Npu SICLOPPS inteins showed no toxicity to E. coli, demonstrating their potential for the production of cyclic peptide libraries for use in a variety of high-throughput screens.
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Affiliation(s)
- Jaime E. Townend
- Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Ali Tavassoli
- Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
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24
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Takahashi T, Saito A. Interaction-dependent native chemical ligation and protein trans-splicing (IDNCL-PTS) for detection and visualization of ligand-protein interactions. ChemistrySelect 2016. [DOI: 10.1002/slct.201600443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tsuyoshi Takahashi
- Graduate School of Science and Technology; Gunma University; 1-5-1, Tenjin-cho, Kiryu Gunma 376-8515 Japan
| | - Akinori Saito
- Graduate School of Science and Technology; Gunma University; 1-5-1, Tenjin-cho, Kiryu Gunma 376-8515 Japan
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25
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26
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Komiya C, Aihara K, Morishita K, Ding H, Inokuma T, Shigenaga A, Otaka A. Development of an Intein-Inspired Amide Cleavage Chemical Device. J Org Chem 2015; 81:699-707. [DOI: 10.1021/acs.joc.5b02399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chiaki Komiya
- Institute of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Keisuke Aihara
- Institute of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Ko Morishita
- Institute of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Hao Ding
- Institute of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Tsubasa Inokuma
- Institute of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Akira Shigenaga
- Institute of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
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27
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Bosmans RPG, Hendriksen WE, Verheijden M, Eelkema R, Jonkheijm P, van Esch JH, Brunsveld L. Supramolecular Protein Immobilization on Lipid Bilayers. Chemistry 2015; 21:18466-73. [DOI: 10.1002/chem.201502461] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 01/08/2023]
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28
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Bachmann AL, Mootz HD. An Unprecedented Combination of Serine and Cysteine Nucleophiles in a Split Intein with an Atypical Split Site. J Biol Chem 2015; 290:28792-804. [PMID: 26453311 DOI: 10.1074/jbc.m115.677237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 11/06/2022] Open
Abstract
Protein splicing mediated by inteins is a self-processive reaction leading to the excision of the internal intein domain from a precursor protein and the concomitant ligation of the flanking sequences, the extein-N and extein-C parts, thereby reconstituting the host protein. Most inteins employ a splicing pathway in which the upstream scissile peptide bond is consecutively rearranged into two thioester or oxoester intermediates before intein excision and rearrangement into the new peptide bond occurs. The catalytically critical amino acids involved at the two splice junctions are cysteine, serine, or threonine. Notably, the only potential combination not observed so far in any of the known or engineered inteins corresponds to the transesterification from an oxoester to a thioester, which suggested that this formal uphill reaction with regard to the thermodynamic stability might be incompatible with intein-mediated catalysis. We show that corresponding mutations also led to inactive gp41-1 and AceL-TerL inteins. We report the novel GOS-TerL split intein identified from metagenomic databases as the first intein harboring the combination of Ser1 and Cys+1 residues. Mutational analysis showed that its efficient splicing reaction indeed follows the shift from oxoester to thioester and thus represents a rare diversion from the canonical pathway. Furthermore, the GOS-TerL intein has an atypical split site close to the N terminus. The Int(N) fragment could be shortened from 37 to 28 amino acids and exchanged with the 25-amino acid Int(N) fragment from the AceL-TerL intein, indicating a high degree of promiscuity of the Int(C) fragment of the GOS-TerL intein.
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Affiliation(s)
- Anne-Lena Bachmann
- From the Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, 48149 Münster, Germany
| | - Henning D Mootz
- From the Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, 48149 Münster, Germany
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29
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Abstract
Protein splicing in trans by split inteins has increasingly become a powerful protein-engineering tool for protein ligation, both in vivo and in vitro. Over 100 naturally occurring and artificially engineered split inteins have been reported for protein ligation using protein trans-splicing. Here, we review the current status of the reported split inteins in order to delineate an empirical or rational strategy for constructing new split inteins suitable for various applications in biotechnology and chemical biology.
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Affiliation(s)
- A Sesilja Aranko
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute-Frederick, MD 21702, USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland
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30
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Jiang A, Jin W, Zhao F, Tang Y, Sun Z, Liu JN. Split Ssp DnaB mini-intein-mediated production of recombinant human glucagon-like peptide-1/7-36. Biotechnol Appl Biochem 2015; 62:309-15. [DOI: 10.1002/bab.1274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/22/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Aiqin Jiang
- Institute of Molecular Medicine; Nanjing University; Nanjing People's Republic of China
| | - Wenbo Jin
- Institute of Molecular Medicine; Nanjing University; Nanjing People's Republic of China
| | - Feng Zhao
- Institute of Molecular Medicine; Nanjing University; Nanjing People's Republic of China
| | - Yanchun Tang
- Institute of Molecular Medicine; Nanjing University; Nanjing People's Republic of China
| | - Ziyong Sun
- Institute of Molecular Medicine; Nanjing University; Nanjing People's Republic of China
| | - Jian-Ning Liu
- Institute of Molecular Medicine; Nanjing University; Nanjing People's Republic of China
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31
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Böcker JK, Friedel K, Matern JCJ, Bachmann AL, Mootz HD. Generation of a Genetically Encoded, Photoactivatable Intein for the Controlled Production of Cyclic Peptides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409848] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Böcker JK, Friedel K, Matern JCJ, Bachmann AL, Mootz HD. Generation of a Genetically Encoded, Photoactivatable Intein for the Controlled Production of Cyclic Peptides. Angew Chem Int Ed Engl 2014; 54:2116-20. [DOI: 10.1002/anie.201409848] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/04/2014] [Indexed: 01/19/2023]
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33
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Aranko AS, Oeemig JS, Zhou D, Kajander T, Wlodawer A, Iwaï H. Structure-based engineering and comparison of novel split inteins for protein ligation. MOLECULAR BIOSYSTEMS 2014; 10:1023-34. [PMID: 24574026 DOI: 10.1039/c4mb00021h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein splicing is an autocatalytic process involving self-excision of an internal protein domain, the intein, and concomitant ligation of the two flanking sequences, the exteins, with a peptide bond. Protein splicing can also take place in trans by naturally split inteins or artificially split inteins, ligating the exteins on two different polypeptide chains into one polypeptide chain. Protein trans-splicing could work in foreign contexts by replacing the native extein sequences with other protein sequences. Protein ligation using protein trans-splicing increasingly becomes a useful tool for biotechnological applications such as semi-synthesis of proteins, segmental isotopic labeling, and in vivo protein engineering. However, only a few split inteins have been successfully applied for protein ligation. Naturally split inteins have been widely used, but they are cross-reactive to each other, limiting their applications to multiple-fragment ligation. Based on the three-dimensional structures including two newly determined intein structures, we derived 21 new split inteins from four highly efficient cis-splicing inteins, in order to develop novel split inteins suitable for protein ligation. We systematically compared trans-splicing of 24 split inteins and tested the cross-activities among them to identify orthogonal split intein fragments that could be used in chemical biology and biotechnological applications.
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Affiliation(s)
- A Sesilja Aranko
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FIN-00014, Finland.
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34
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Abstract
The first crystal trans-structure of a naturally occurring split intein has been determined for the Npu (Nostoc punctiforme PCC73102) DnaE split intein. Guided by this structure, the residues NArg50 and CSer35, well conserved in DnaE split inteins, are identified to be critical in the trans-splicing of Npu DnaE split intein. An in vitro splicing assay demonstrates that NArg50 and CSer35 play synergistic roles in modulating its intein activity. The C-terminal CAsn36 exhibits two orientations of its side chain and interacts with both NArg50 and CSer35 through hydrogen bonding. These interactions likely facilitate the cyclization of asparagine in the course of protein splicing. The mutation of either residue reduces intein activity, and correlates with the low activity of the Ssp (Cyanobacterium synechocystis sp. strain PCC6803) DnaE split intein. On the other hand, NArg50 also forms a hydrogen bond with the highly conserved F-block CAsp17, thus influencing the N-S acyl shift during N-terminal cleavage. Sequence alignments show that residues NArg50 and CSer35 are rather conserved in those split inteins that lack a penultimate histidine residue. The conserved non-catalytic residues of split inteins modulate the efficiency of protein trans-splicing by hydrogen-bond interactions with the catalytic residues at the splice junction.
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35
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Eryilmaz E, Shah NH, Muir TW, Cowburn D. Structural and dynamical features of inteins and implications on protein splicing. J Biol Chem 2014; 289:14506-11. [PMID: 24695731 DOI: 10.1074/jbc.r113.540302] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein splicing is a posttranslational modification where intervening proteins (inteins) cleave themselves from larger precursor proteins and ligate their flanking polypeptides (exteins) through a multistep chemical reaction. First thought to be an anomaly found in only a few organisms, protein splicing by inteins has since been observed in microorganisms from all domains of life. Despite this broad phylogenetic distribution, all inteins share common structural features such as a horseshoe-like pseudo two-fold symmetric fold, several canonical sequence motifs, and similar splicing mechanisms. Intriguingly, the splicing efficiencies and substrate specificity of different inteins vary considerably, reflecting subtle changes in the chemical mechanism of splicing, linked to their local structure and dynamics. As intein chemistry has widespread use in protein chemistry, understanding the structural and dynamical aspects of inteins is crucial for intein engineering and the improvement of intein-based technologies.
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Affiliation(s)
- Ertan Eryilmaz
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
| | - Neel H Shah
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - Tom W Muir
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - David Cowburn
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
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36
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Abstract
Inteins are nature's escape artists; they facilitate their excision from flanking polypeptides (exteins) concomitant with extein ligation to produce a mature host protein. Splicing requires sequential nucleophilic displacement reactions catalyzed by strategies similar to proteases and asparagine lyases. Inteins require precise reaction coordination rather than rapid turnover or tight substrate binding because they are single turnover enzymes with covalently linked substrates. This has allowed inteins to explore alternative mechanisms with different steps or to use different methods for activation and coordination of the steps. Pressing issues include understanding the underlying details of catalysis and how the splicing steps are controlled.
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Affiliation(s)
- Kenneth V Mills
- From the Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610
| | - Margaret A Johnson
- the Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, and
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37
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Thiel IV, Volkmann G, Pietrokovski S, Mootz HD. An Atypical Naturally Split Intein Engineered for Highly Efficient Protein Labeling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Thiel IV, Volkmann G, Pietrokovski S, Mootz HD. An Atypical Naturally Split Intein Engineered for Highly Efficient Protein Labeling. Angew Chem Int Ed Engl 2014; 53:1306-10. [DOI: 10.1002/anie.201307969] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 11/06/2022]
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39
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Zhulenkovs D, Jaudzems K, Zajakina A, Leonchiks A. Enzymatic activity of circular sortase A under denaturing conditions: An advanced tool for protein ligation. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Miranda E, Nordgren IK, Male AL, Lawrence CE, Hoakwie F, Cuda F, Court W, Fox KR, Townsend PA, Packham GK, Eccles SA, Tavassoli A. A cyclic peptide inhibitor of HIF-1 heterodimerization that inhibits hypoxia signaling in cancer cells. J Am Chem Soc 2013; 135:10418-25. [PMID: 23796364 PMCID: PMC3715890 DOI: 10.1021/ja402993u] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Hypoxia
inducible factor-1 (HIF-1) is a heterodimeric transcription
factor that acts as the master regulator of cellular response to reduced
oxygen levels, thus playing a key role in the adaptation, survival,
and progression of tumors. Here we report cyclo-CLLFVY,
identified from a library of 3.2 million cyclic hexapeptides using
a genetically encoded high-throughput screening platform, as an inhibitor
of the HIF-1α/HIF-1β protein–protein interaction
in vitro and in cells. The identified compound inhibits HIF-1 dimerization
and transcription activity by binding to the PAS-B domain of HIF-1α,
reducing HIF-1-mediated hypoxia response signaling in a variety of
cell lines, without affecting the function of the closely related
HIF-2 isoform. The reported cyclic peptide demonstrates the utility
of our high-throughput screening platform for the identification of
protein–protein interaction inhibitors, and forms the starting
point for the development of HIF-1 targeted cancer therapeutics.
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Affiliation(s)
- Elena Miranda
- Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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41
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Aranko AS, Oeemig JS, Iwaï H. Structural basis for proteintrans-splicing by a bacterial intein-like domain - protein ligation without nucleophilic side chains. FEBS J 2013; 280:3256-69. [DOI: 10.1111/febs.12307] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/17/2013] [Accepted: 04/22/2013] [Indexed: 12/01/2022]
Affiliation(s)
- A. Sesilja Aranko
- Research Program in Structural Biology and Biophysics; Institute of Biotechnology; University of Helsinki; Finland
| | - Jesper S. Oeemig
- Research Program in Structural Biology and Biophysics; Institute of Biotechnology; University of Helsinki; Finland
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics; Institute of Biotechnology; University of Helsinki; Finland
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42
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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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43
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Wasmuth A, Ludwig C, Mootz HD. Structure-activity studies on the upstream splice junction of a semisynthetic intein. Bioorg Med Chem 2013; 21:3495-503. [PMID: 23618706 DOI: 10.1016/j.bmc.2013.03.065] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/24/2013] [Accepted: 03/26/2013] [Indexed: 01/30/2023]
Abstract
Protein trans-splicing by split inteins holds great potential for the chemical modification and semisynthesis of proteins. However, the structural requirements of the extein sequences immediately flanking the intein are only poorly understood. This knowledge is of particular importance for protein labeling, when synthetic moieties are to be attached to the protein of interest as seamlessly as possible. Using the semisynthetic Ssp DnaB intein both in form of its wild-type sequence and its evolved M86 mutant, we systematically varied the sequence upstream of the short synthetic Int(N) fragment using both proteinogenic amino acids and unnatural building blocks. We could show for the wild-type variant that the native N-extein sequence could be reduced to the glycine residue at the (-1) position directly flanking the intein without significant loss of activity. The glycine at this position is strongly preferred over building blocks containing a phenyl group or extended alkyl chain adjacent to the scissile amide bond of the N-terminal splice junction. Despite their negative effects on the splicing yields, these unnatural substrates were well processed in the N-S acyl shift to form the respective thioesters and did not result in an increased decoupling of the asparagine cyclization step at the C-terminal splicing junction. Therefore, the transesterification step appeared to be the bottleneck of the protein splicing pathway. The fluorophore 7-hydroxycoumarinyl-4-acetic acid as a minimal N-extein was efficiently ligated to the model protein, in particular with the M86 mutant, probably because of its higher resemblance to glycine with an aliphatic c-α carbon atom at the (-1) position. This finding indicates a way for the virtually traceless labeling of proteins without inserting extra flanking residues. Due to its overall higher activity, the M86 mutant appears most promising for many protein labeling and chemical modification schemes using the split intein approach.
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Affiliation(s)
- Alexandra Wasmuth
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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44
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Volkmann G, Mootz HD. Recent progress in intein research: from mechanism to directed evolution and applications. Cell Mol Life Sci 2013; 70:1185-206. [PMID: 22926412 PMCID: PMC11113529 DOI: 10.1007/s00018-012-1120-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 07/23/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
Abstract
Inteins catalyze a post-translational modification known as protein splicing, where the intein removes itself from a precursor protein and concomitantly ligates the flanking protein sequences with a peptide bond. Over the past two decades, inteins have risen from a peculiarity to a rich source of applications in biotechnology, biomedicine, and protein chemistry. In this review, we focus on developments of intein-related research spanning the last 5 years, including the three different splicing mechanisms and their molecular underpinnings, the directed evolution of inteins towards improved splicing in exogenous protein contexts, as well as novel applications of inteins for cell biology and protein engineering, which were made possible by a clearer understanding of the protein splicing mechanism.
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Affiliation(s)
- Gerrit Volkmann
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Henning D. Mootz
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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45
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Binschik J, Mootz HD. Chemical bypass of intein-catalyzed N-S acyl shift in protein splicing. Angew Chem Int Ed Engl 2013; 52:4260-4. [PMID: 23468274 DOI: 10.1002/anie.201208863] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/13/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Jens Binschik
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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46
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Binschik J, Mootz HD. Chemischer “Bypass” des Intein-katalysierten N-S-Acyltransfers im Proteinspleißen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Sakamoto S, Terauchi M, Hugo A, Kim T, Araki Y, Wada T. Creation of a caspase-3 sensing system using a combination of split-GFP and split-intein. Chem Commun (Camb) 2013; 49:10323-5. [DOI: 10.1039/c3cc43389g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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48
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Ramirez M, Valdes N, Guan D, Chen Z. Engineering split intein DnaE from Nostoc punctiforme for rapid protein purification. Protein Eng Des Sel 2012; 26:215-23. [PMID: 23223807 DOI: 10.1093/protein/gzs097] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the engineering of a DnaE intein able to catalyze rapid C-terminal cleavage in the absence of N-terminal cleavage. A single mutation in DnaE intein from Nostoc punctiforme PCC73102 (NpuDnaE), Asp118Gly, was introduced based on sequence alignment with a previously engineered C-terminal cleaving intein mini-MtuRecA. This mutation was able to both suppress N-terminal cleavage and significantly elevate C-terminal cleavage efficiency. Molecular modeling suggests that in NpuDnaE Asp118 forms a hydrogen bond with the penultimate Asn, preventing its spontaneous cyclization prior to N-terminal cleavage. Mutation of Asp118 to Gly essentially abolishes this restriction leading to subsequent C-terminal cleavage in the absence of N-terminal cleavage. The Gly118 NpuDnaE mutant exhibits rapid thio-dependent C-terminal cleavage kinetics with 80% completion within 3 h at room temperature. We used this newly engineered intein to develop both column-free and chromatography-based protein purification methods utilizing the elastin-like-polypeptide and chitin-binding protein as removable purification tags, respectively. We demonstrate rapid target protein purification to electrophoretic purity at yields up to 84 mg per liter of Escherichia coli culture.
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Affiliation(s)
- Miguel Ramirez
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
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49
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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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50
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Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. PLoS One 2012; 7:e43820. [PMID: 22937103 PMCID: PMC3427171 DOI: 10.1371/journal.pone.0043820] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/26/2012] [Indexed: 01/30/2023] Open
Abstract
Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods for identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP) sites in proteins have the potential to act as split sites and that CP prediction can be used to search for internal permissive sites for creating new split proteins. Using a protein ligase, intein, as a model, CP predictor facilitated the creation of circular permutants in which backbone opening imposes the least detrimental effects on intein folding. We screened a series of predicted intein CPs and identified stable and native-fold CPs. When the valid CP sites were introduced as split sites, there was a reduction in folding enthalpy caused by the new backbone opening; however, the coincident loss in entropy was sufficient to be compensated, yielding a favorable free energy for self-association. Since split intein is exploited in protein semi-synthesis, we tested the related protein trans-splicing (PTS) activities of the corresponding split inteins. Notably, a novel functional split intein composed of the N-terminal 36 residues combined with the remaining C-terminal fragment was identified. Its PTS activity was shown to be better than current reported two-piece intein with a short N-terminal segment. Thus, the incorporation of in silico CP prediction facilitated the design of split intein as well as circular permutants.
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