1
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Chen H, Zhang Q. Native Peptide Cyclization, Sequential Chemoselective Amidation in Water. J Am Chem Soc 2023; 145:27218-27224. [PMID: 38079358 PMCID: PMC11131159 DOI: 10.1021/jacs.3c10341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Chemical synthesis offers robust tactics for structural alterations of peptides and proteins. It remains a labor-intensive and complex process due to the challenges in selectively modifying diverse amino acid side chains and termini. Direct α-peptide ligation without premodification is a significant hurdle, especially when aiming to include all proteinogenic amino acids at the ligation site. We introduce Native Peptide Cyclization (NPC), a chemoselective method enabling intramolecular peptidyl ligation without the need for premodification. NPC cyclizes unprotected linear peptides through controlled, sequential C- and N-terminal activation via pH modulation. Water-based NPC simplifies peptide ligation, easing the labor-intensive nature of peptide synthesis, aiding efficient cyclic peptide preparation and enabling cost-effective macrocycle-based therapeutics.
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Affiliation(s)
- Huan Chen
- Department of Chemistry, State University of New York, University at Albany, Albany, New York 12222, United States
| | - Qiang Zhang
- Department of Chemistry, State University of New York, University at Albany, Albany, New York 12222, United States
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2
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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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3
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Sarmiento C, Camarero JA. Biotechnological Applications of Protein Splicing. Curr Protein Pept Sci 2019; 20:408-424. [PMID: 30734675 PMCID: PMC7135711 DOI: 10.2174/1389203720666190208110416] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
Protein splicing domains, also called inteins, have become a powerful biotechnological tool for applications involving molecular biology and protein engineering. Early applications of inteins focused on self-cleaving affinity tags, generation of recombinant polypeptide α-thioesters for the production of semisynthetic proteins and backbone cyclized polypeptides. The discovery of naturallyoccurring split-inteins has allowed the development of novel approaches for the selective modification of proteins both in vitro and in vivo. This review gives a general introduction to protein splicing with a focus on their role in expanding the applications of intein-based technologies in protein engineering and chemical biology.
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Affiliation(s)
- Corina Sarmiento
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA9033 USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA9033 USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA9033 USA
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-9121, USA
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4
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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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5
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Minteer CJ, Siegart NM, Colelli KM, Liu X, Linhardt RJ, Wang C, Gomez AV, Reitter JN, Mills KV. Intein-Promoted Cyclization of Aspartic Acid Flanking the Intein Leads to Atypical N-Terminal Cleavage. Biochemistry 2017; 56:1042-1050. [PMID: 28165720 DOI: 10.1021/acs.biochem.6b00894] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein splicing is a post-translational reaction facilitated by an intein, or intervening protein, which involves the removal of the intein and the ligation of the flanking polypeptides, or exteins. A DNA polymerase II intein from Pyrococcus abyssi (Pab PolII intein) can promote protein splicing in vitro on incubation at high temperature. Mutation of active site residues Cys1, Gln185, and Cys+1 to Ala results in an inactive intein precursor, which cannot promote the steps of splicing, including cleavage of the peptide bond linking the N-extein and intein (N-terminal cleavage). Surprisingly, coupling the inactivating mutations to a change of the residue at the C-terminus of the N-extein (N-1 residue) from the native Asn to Asp reactivates N-terminal cleavage at pH 5. Similar "aspartic acid effects" have been observed in other proteins and peptides but usually only occur at lower pH values. In this case, however, the unusual N-terminal cleavage is abolished by mutations to catalytic active site residues and unfolding of the intein, indicating that this cleavage effect is mediated by the intein active site and the intein fold. We show via mass spectrometry that the reaction proceeds through cyclization of Asp resulting in anhydride formation coupled to peptide bond cleavage. Our results add to the richness of the understanding of the mechanism of protein splicing and provide insight into the stability of proteins at moderately low pH. The results also explain, and may help practitioners avoid, a side reaction that may complicate intein applications in biotechnology.
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Affiliation(s)
- Christopher J Minteer
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Nicolle M Siegart
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Kathryn M Colelli
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | | | | | | | - Alvin V Gomez
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Julie N Reitter
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
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6
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Novikova O, Jayachandran P, Kelley DS, Morton Z, Merwin S, Topilina NI, Belfort M. Intein Clustering Suggests Functional Importance in Different Domains of Life. Mol Biol Evol 2015; 33:783-99. [PMID: 26609079 PMCID: PMC4760082 DOI: 10.1093/molbev/msv271] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Inteins, also called protein introns, are self-splicing mobile elements found in all domains of life. A bioinformatic survey of genomic data highlights a biased distribution of inteins among functional categories of proteins in both bacteria and archaea, with a strong preference for a single network of functions containing replisome proteins. Many nonorthologous, functionally equivalent replicative proteins in bacteria and archaea carry inteins, suggesting a selective retention of inteins in proteins of particular functions across domains of life. Inteins cluster not only in proteins with related roles but also in specific functional units of those proteins, like ATPase domains. This peculiar bias does not fully fit the models describing inteins exclusively as parasitic elements. In such models, evolutionary dynamics of inteins is viewed primarily through their mobility with the intein homing endonuclease (HEN) as the major factor of intein acquisition and loss. Although the HEN is essential for intein invasion and spread in populations, HEN dynamics does not explain the observed biased distribution of inteins among proteins in specific functional categories. We propose that the protein splicing domain of the intein can act as an environmental sensor that adapts to a particular niche and could increase the chance of the intein becoming fixed in a population. We argue that selective retention of some inteins might be beneficial under certain environmental stresses, to act as panic buttons that reversibly inhibit specific networks, consistent with the observed intein distribution.
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Affiliation(s)
- Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany
| | | | - Danielle S Kelley
- Department of Biomedical Sciences, School of Public Health, University at Albany
| | - Zachary Morton
- Department of Biological Sciences and RNA Institute, University at Albany
| | | | - Natalya I Topilina
- Department of Biological Sciences and RNA Institute, University at Albany
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany Department of Biomedical Sciences, School of Public Health, University at Albany
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7
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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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8
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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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9
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Novikova O, Topilina N, Belfort M. Enigmatic distribution, evolution, and function of inteins. J Biol Chem 2014; 289:14490-7. [PMID: 24695741 DOI: 10.1074/jbc.r114.548255] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inteins are mobile genetic elements capable of self-splicing post-translationally. They exist in all three domains of life including in viruses and bacteriophage, where they have a sporadic distribution even among very closely related species. In this review, we address this anomalous distribution from the point of view of the evolution of the host species as well as the intrinsic features of the inteins that contribute to their genetic mobility. We also discuss the incidence of inteins in functionally important sites of their host proteins. Finally, we describe instances of conditional protein splicing. These latter observations lead us to the hypothesis that some inteins have adapted to become sensors that play regulatory roles within their host protein, to the advantage of the organism in which they reside.
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Affiliation(s)
- Olga Novikova
- From the Department of Biological Sciences and RNA Institute, University at Albany, The State University of New York, Albany, New York 12222
| | - Natalya Topilina
- From the Department of Biological Sciences and RNA Institute, University at Albany, The State University of New York, Albany, New York 12222
| | - Marlene Belfort
- From the Department of Biological Sciences and RNA Institute, University at Albany, The State University of New York, Albany, New York 12222
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10
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Abstract
Inteins are auto-processing domains found in organisms from all domains of life. These proteins carry out a process known as protein splicing, which is a multi-step biochemical reaction comprised of both the cleavage and formation of peptide bonds. While the endogenous substrates of protein splicing are specific essential proteins found in intein-containing host organisms, inteins are also functional in exogenous contexts and can be used to chemically manipulate virtually any polypeptide backbone. Given this, protein chemists have exploited various facets of intein reactivity to modify proteins in myriad ways for both basic biological research as well as potential therapeutic applications. Here, we review the intein field, first focusing on the biological context and phylogenetic diversity of inteins, followed by a description of intein structure and biochemical function. Finally, we discuss prevalent inteinbased technologies, focusing on their applications in chemical biology, followed by persistent caveats of intein chemistry and approaches to alleviate these shortcomings. The findings summarized herein describe two and a half decades of research, leading from a biochemical curiosity to the development of powerful protein engineering tools.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, United States
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11
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Tian YF, Hudalla GA, Han H, Collier JH. Controllably degradable β-sheet nanofibers and gels from self-assembling depsipeptides. Biomater Sci 2013; 1. [PMID: 24224082 DOI: 10.1039/c3bm60161g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembled peptide materials have received considerable interest for a range of applications, including 3D cell culture, tissue engineering, and the delivery of cells and drugs. One challenge in applying such materials within these areas has been the extreme stability of β-sheet fibrillized peptides, which are resistant to proteolysis, degradation, and turnover in biological environments. In this study, we designed self-assembling depsipeptides containing ester bonds within the peptide backbone. Beta-sheet fibrillized nanofibers were formed in physiologic conditions, and two of these nanofiber-forming depsipeptides produced hydrogels that degraded controllably over the course of days-to-weeks via ester hydrolysis. With HPLC, TEM, and oscillating rheometry, we show that the rate of hydrolysis can be controlled in a straightforward manner by specifying the amino acid residues surrounding the ester bond. In 3D cell cultures, depsipeptide gels softened over the course of several days and permitted considerably more proliferation and spreading of C3H10T1/2 pluripotent stem cells than non-degradable analogs. This approach now provides a reliable and reproducible means to soften or clear β-sheet fibrillized peptide materials from biological environments.
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Affiliation(s)
- Ye F Tian
- Department of Surgery, Biological Science Division, University of Chicago, Chicago, Illinois, United States ; Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, Illinois, United States
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12
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Tadevosyan A, Vaniotis G, Allen BG, Hébert TE, Nattel S. G protein-coupled receptor signalling in the cardiac nuclear membrane: evidence and possible roles in physiological and pathophysiological function. J Physiol 2011; 590:1313-30. [PMID: 22183719 DOI: 10.1113/jphysiol.2011.222794] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G protein-coupled receptors (GPCRs) play key physiological roles in numerous tissues, including the heart, and their dysfunction influences a wide range of cardiovascular diseases. Recently, the notion of nuclear localization and action of GPCRs has become more widely accepted. Nuclear-localized receptors may regulate distinct signalling pathways, suggesting that the biological responses mediated by GPCRs are not solely initiated at the cell surface but may result from the integration of extracellular and intracellular signalling pathways. Many of the observed nuclear effects are not prevented by classical inhibitors that exclusively target cell surface receptors, presumably because of their structures, lipophilic properties, or affinity for nuclear receptors. In this topical review, we discuss specifically how angiotensin-II, endothelin, β-adrenergic and opioid receptors located on the nuclear envelope activate signalling pathways, which convert intracrine stimuli into acute responses such as generation of second messengers and direct genomic effects, and thereby participate in the development of cardiovascular disorders.
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Affiliation(s)
- Artavazd Tadevosyan
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada H3C 3J7
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13
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Du Z, Liu J, Albracht CD, Hsu A, Chen W, Marieni MD, Colelli KM, Williams JE, Reitter JN, Mills KV, Wang C. Structural and mutational studies of a hyperthermophilic intein from DNA polymerase II of Pyrococcus abyssi. J Biol Chem 2011; 286:38638-38648. [PMID: 21914805 PMCID: PMC3207444 DOI: 10.1074/jbc.m111.290569] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/09/2011] [Indexed: 11/06/2022] Open
Abstract
Protein splicing is a precise self-catalyzed process in which an intein excises itself from a precursor with the concomitant ligation of the flanking polypeptides (exteins). Protein splicing proceeds through a four-step reaction but the catalytic mechanism is not fully understood at the atomic level. We report the solution NMR structures of the hyperthermophilic Pyrococcus abyssi PolII intein, which has a noncanonical C-terminal glutamine instead of an asparagine. The NMR structures were determined to a backbone root mean square deviation of 0.46 Å and a heavy atom root mean square deviation of 0.93 Å. The Pab PolII intein has a common HINT (hedgehog intein) fold but contains an extra β-hairpin that is unique in the structures of thermophilic inteins. The NMR structures also show that the Pab PolII intein has a long and disordered loop in place of an endonuclease domain. The N-terminal Cys-1 amide is hydrogen bonded to the Thr-90 hydroxyl in the conserved block-B TXXH motif and the Cys-1 thiol forms a hydrogen bond with the block F Ser-166. Mutating Thr-90 to Ala dramatically slows N-terminal cleavage, supporting its pivotal role in promoting the N-S acyl shift. Mutagenesis also showed that Thr-90 and His-93 are synergistic in catalyzing the N-S acyl shift. The block F Ser-166 plays an important role in coordinating the steps of protein splicing. NMR spin relaxation indicates that the Pab PolII intein is significantly more rigid than mesophilic inteins, which may contribute to the higher optimal temperature for protein splicing.
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Affiliation(s)
- Zhenming Du
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jiajing Liu
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Clayton D Albracht
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Alice Hsu
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Wen Chen
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Michelle D Marieni
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610
| | - Kathryn M Colelli
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610
| | - Jennie E Williams
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610
| | - Julie N Reitter
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610.
| | - Chunyu Wang
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180.
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14
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Evaluation and comparison of protein splicing by exogenous inteins with foreign exteins inEscherichia coli. FEBS Lett 2011; 585:3471-7. [DOI: 10.1016/j.febslet.2011.10.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/23/2011] [Accepted: 10/04/2011] [Indexed: 11/22/2022]
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15
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Liu J, Du Z, Albracht CD, Naidu RO, Mills KV, Wang C. 1H, 13C, and 15N NMR assignments of the Pyrococcus abyssi DNA polymerase II intein. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:233-235. [PMID: 21519863 PMCID: PMC3166996 DOI: 10.1007/s12104-011-9307-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/14/2011] [Indexed: 05/30/2023]
Abstract
Protein splicing is a precise post-translational process mediated by inteins. Inteins are intervening proteins that cleave themselves from a precursor protein while joining the flanking sequences. Here we report the (15)N, (13)C, and (1)H chemical shift assignments of the intein from DNA polymerase II of Pyrococcus abyssi (Pab PolII intein), which has been recombinantly overexpressed and isotopically labeled. The NMR assignments of Pab PolII intein are essential for solution structure determination and protein dynamics study.
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Affiliation(s)
- Jiajing Liu
- Biology Department, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Zhenming Du
- Biology Department, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Clayton D. Albracht
- Biology Department, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Roshni O. Naidu
- Biology Department, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Kenneth V. Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, 01610
| | - Chunyu Wang
- Biology Department, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
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16
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Rawlings ND, Barrett AJ, Bateman A. Asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes. J Biol Chem 2011; 286:38321-38328. [PMID: 21832066 PMCID: PMC3207474 DOI: 10.1074/jbc.m111.260026] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The terms “proteolytic enzyme” and “peptidase” have been treated as synonymous, and all proteolytic enzymes have been considered to be hydrolases (EC 3.4). However, the recent discovery of proteins that cleave themselves at asparagine residues indicates that not all peptide bond cleavage occurs by hydrolysis. These self-cleaving proteins include the Tsh protein precursor of Escherichia coli, in which the large C-terminal propeptide acts as an autotransporter; certain viral coat proteins; and proteins containing inteins. Proteolysis is the action of an amidine lyase (EC 4.3.2). These proteolytic enzymes are also the first in which the nucleophile is an asparagine, defining the seventh proteolytic catalytic type and the first to be discovered since 2004. We have assembled ten families based on sequence similarity in which cleavage is thought to be catalyzed by an asparagine.
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Affiliation(s)
- Neil David Rawlings
- Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom.
| | - Alan John Barrett
- Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Alex Bateman
- Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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17
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Pereira B, Shemella PT, Amitai G, Belfort G, Nayak SK, Belfort M. Spontaneous proton transfer to a conserved intein residue determines on-pathway protein splicing. J Mol Biol 2010; 406:430-42. [PMID: 21185311 DOI: 10.1016/j.jmb.2010.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 12/16/2010] [Indexed: 02/06/2023]
Abstract
The discovery of inteins, which are protein-splicing elements, has stimulated interest for various applications in chemical biology, bioseparations, drug delivery, and sensor development. However, for inteins to effectively contribute to these applications, an increased mechanistic understanding of cleavage and splicing reactions is required. While the multistep chemical reaction that leads to splicing is often explored and utilized, it is not clear how the intein navigates through the reaction space. The sequence of reaction steps must progress in concert in order to yield efficient splicing while minimizing off-pathway cleavage reactions. In this study, we demonstrate that formation of a previously identified branched intermediate is the critical step for determining splicing over cleavage products. By combining experimental assays and quantum mechanical simulations, we identify the electrostatic interactions that are important to the dynamics of the reaction steps. We illustrate, via an animated simulation trajectory, a proton transfer from the first C-terminal extein residue to a conserved aspartate, which synchronizes the multistep enzymatic reaction that is key to splicing. This work provides new insights into the complex interplay between critical active-site residues in the protein splicing mechanism, thereby facilitating biotechnological application while shedding light on multistep enzyme activity.
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Affiliation(s)
- Brian Pereira
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
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18
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Brace LE, Southworth MW, Tori K, Cushing ML, Perler F. The Deinococcus radiodurans Snf2 intein caught in the act: detection of the Class 3 intein signature Block F branched intermediate. Protein Sci 2010; 19:1525-33. [PMID: 20521254 DOI: 10.1002/pro.431] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Inteins are the protein equivalent of introns. They are remarkable and robust single turnover enzymes that splice out of precursor proteins during post-translational maturation of the host protein (extein). The Deinococcus radiodurans Snf2 intein is the second member of the recently discovered Class 3 subfamily of inteins to be characterized. Class 3 inteins have a unique sequence signature: (a) they start with residues other than the standard Class 1 Cys, Ser or Thr, (b) have a noncontiguous, centrally located Trp/Cys/Thr triplet, and (c) all but one have Ser or Thr at the start of the C-extein instead of the more common Cys. We previously proposed that Class 3 inteins splice by a variation in the standard intein-mediated protein splicing mechanism that includes a novel initiating step leading to the formation of a previously unrecognized branched intermediate. In this mechanism defined with the Class 3 prototypic Mycobacteriophage Bethlehem DnaB intein, the triplet Cys attacks the peptide bond at the N-terminal splice junction to form the class specific branched intermediate after which the N-extein is transferred to the side chain of the Ser, Thr, or Cys at the C-terminal splice junction to form the standard intein branched intermediate. Analysis of the Deinococcus radiodurans Snf2 intein confirms this splicing mechanism. Moreover, the Class 3 specific Block F branched intermediate was isolated, providing the first direct proof of its existence.
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Affiliation(s)
- Lear E Brace
- New England BioLabs, Inc., Ipswich, Massachusetts 01938, USA
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19
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Allen MJ, Lanzén A, Bratbak G. Characterisation of the coccolithovirus intein. Mar Genomics 2010; 4:1-7. [PMID: 21429459 DOI: 10.1016/j.margen.2010.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 11/17/2022]
Abstract
The identification of inteins in viral genomes is becoming increasingly common. Inteins are selfish DNA elements found within coding regions of host proteins. Following translation, they catalyse their own excision and the formation of a peptide bond between the flanking protein regions. Many inteins also display homing endonuclease function. Here, the newly identified coccolithovirus intein is described and is predicted to have both self-splicing and homing endonuclease activity. The biochemical mechanism of its protein splicing activity is hypothesised, and the prevalence of the intein among natural coccolithovirus isolates is tested.
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Affiliation(s)
- Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
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20
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Zhu X, Korlimbinis A, Truscott RJ. Age-Dependent Denaturation of Enzymes in the Human Lens: A Paradigm for Organismic Aging? Rejuvenation Res 2010; 13:553-60. [DOI: 10.1089/rej.2009.1009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Xiangjia Zhu
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
- Save Sight Institute, University of Sydney, NSW, 2001, Australia
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21
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Tori K, Dassa B, Johnson MA, Southworth MW, Brace LE, Ishino Y, Pietrokovski S, Perler FB. Splicing of the mycobacteriophage Bethlehem DnaB intein: identification of a new mechanistic class of inteins that contain an obligate block F nucleophile. J Biol Chem 2009; 285:2515-26. [PMID: 19940146 PMCID: PMC2807308 DOI: 10.1074/jbc.m109.069567] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Inteins are single turnover enzymes that splice out of protein precursors during maturation of the host protein (extein). The Cys or Ser at the N terminus of most inteins initiates a four-step protein splicing reaction by forming a (thio)ester bond at the N-terminal splice junction. Several recently identified inteins cannot perform this acyl rearrangement because they do not begin with Cys, Thr, or Ser. This study analyzes one of these, the mycobacteriophage Bethlehem DnaB intein, which we describe here as the prototype for a new class of inteins based on sequence comparisons, reactivity, and mechanism. These Class 3 inteins are characterized by a non-nucleophilic N-terminal residue that co-varies with a non-contiguous Trp, Cys, Thr triplet (WCT) and a Thr or Ser as the first C-extein residue. Several mechanistic differences were observed when compared with standard inteins or previously studied atypical KlbA Ala1 inteins: (a) cleavage at the N-terminal splice junction in the absence of all standard N- and C-terminal splice junction nucleophiles, (b) activation of the N-terminal splice junction by a variant Block B motif that includes the WCT triplet Trp, (c) decay of the branched intermediate by thiols or Cys despite an ester linkage at the C-extein branch point, and (d) an absolute requirement for the WCT triplet Block F Cys. Based on biochemical data and confirmed by molecular modeling, we propose roles for these newly identified conserved residues, a novel protein splicing mechanism that includes a second branched intermediate, and an intein classification with three mechanistic categories.
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Affiliation(s)
- Kazuo Tori
- New England Biolabs, Ipswich, Massachusetts 01938, USA
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22
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Group I introns and inteins: disparate origins but convergent parasitic strategies. J Bacteriol 2009; 191:6193-202. [PMID: 19666710 DOI: 10.1128/jb.00675-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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23
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Stepannenko VN, Esipov RS, Gurevich AI, Chupova LA, Miroshnikov AI. [Recombinant oxyntomodulin]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2007; 33:245-50. [PMID: 17476985 DOI: 10.1134/s1068162007020045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An artificial gene encoding oxyntomodulin was obtained using chemical and enzymatic methods and cloned into Escherichia coli. A recombinant plasmid was constructed containing a hybrid oxyntomodulin gene and Ssp dnaB intein from Synechocystis sp. The expression of the resulting hybrid gene in E. coli, its properties, and the conditions of its autocatalytic cleavage to oxyntomodulin were studied.
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24
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Dautin N, Barnard TJ, Anderson DE, Bernstein HD. Cleavage of a bacterial autotransporter by an evolutionarily convergent autocatalytic mechanism. EMBO J 2007; 26:1942-52. [PMID: 17347646 PMCID: PMC1847664 DOI: 10.1038/sj.emboj.7601638] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 02/06/2007] [Indexed: 11/10/2022] Open
Abstract
Bacterial autotransporters are comprised of an N-terminal 'passenger domain' and a C-terminal beta barrel ('beta domain') that facilitates transport of the passenger domain across the outer membrane. Following translocation, the passenger domains of some autotransporters are cleaved by an unknown mechanism. Here we show that the passenger domain of the Escherichia coli O157:H7 autotransporter EspP is released in a novel autoproteolytic reaction. After purification, the uncleaved EspP precursor underwent proteolytic processing in vitro. An analysis of protein topology together with mutational studies strongly suggested that the reaction occurs inside the beta barrel and revealed that two conserved residues, an aspartate within the beta domain (Asp(1120)) and an asparagine (Asn(1023)) at the P1 position of the cleavage junction, are essential for passenger domain cleavage. Interestingly, these residues were also essential for the proteolytic processing of two distantly related autotransporters. The data strongly suggest that Asp(1120) and Asn(1023) form an unusual catalytic dyad that mediates self-cleavage through the cyclization of the asparagine. Remarkably, a very similar mechanism has been proposed for the maturation of eukaryotic viral capsids.
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Affiliation(s)
- Nathalie Dautin
- Genetics and Biochemistry Branch, National Institutes of Health, Bethesda, MD, USA
| | - Travis J Barnard
- Genetics and Biochemistry Branch, National Institutes of Health, Bethesda, MD, USA
| | - D Eric Anderson
- Proteomics and Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institutes of Health, Bethesda, MD, USA
- Genetics and Biochemistry Branch, National Institutes of Health, Building 5, Room 201, Bethesda, MD 20892, USA. Tel.: +1 301 402 4770; Fax: +1 301 496 9878; E-mail:
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Shemella P, Pereira B, Zhang Y, Van Roey P, Belfort G, Garde S, Nayak SK. Mechanism for intein C-terminal cleavage: a proposal from quantum mechanical calculations. Biophys J 2006; 92:847-53. [PMID: 17085503 PMCID: PMC1779973 DOI: 10.1529/biophysj.106.092049] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inteins are autocatalytic protein cleavage and splicing elements. A cysteine to alanine mutation at the N-terminal of inteins inhibits splicing and isolates the C-terminal cleavage reaction. Experiments indicate an enhanced C-terminal cleavage reaction rate upon decreasing the solution pH for the cleavage mutant, which cannot be explained by the existing mechanistic framework. We use intein crystal structure data and the information about conserved amino acids to perform semiempirical PM3 calculations followed by high-level density functional theory calculations in both gas phase and implicit solvent environments. Based on these calculations, we propose a detailed "low pH" mechanism for intein C-terminal cleavage. Water plays an important role in the proposed reaction mechanism, acting as an acid as well as a base. The protonation of the scissile peptide bond nitrogen by a hydronium ion is an important first step in the reaction. That step is followed by the attack of the C-terminal asparagine side chain on its carbonyl carbon, causing succinimide formation and simultaneous peptide bond cleavage. The computed reaction energy barrier in the gas phase is approximately 33 kcal/mol and reduces to approximately 25 kcal/mol in solution, close to the 21 kcal/mol experimentally observed at pH 6.0. This mechanism is consistent with the observed increase in C-terminal cleavage activity at low pH for the cleavage mutant of the Mycobacterium tuberculosis RecA mini-intein.
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Affiliation(s)
- Philip Shemella
- Department of Physics, Applied Physics and Astronomy, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
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Goodwin TJD, Butler MI, Poulter RTM. Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes. BMC Biol 2006; 4:38. [PMID: 17069655 PMCID: PMC1635734 DOI: 10.1186/1741-7007-4-38] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 10/27/2006] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Inteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi. RESULTS We identified seven intein coding sequences within nuclear genes coding for the second largest subunits of RNA polymerase. These sequences were found in diverse eukaryotes: one is in the second largest subunit of RNA polymerase I (RPA2) from the ascomycete fungus Phaeosphaeria nodorum, one is in the RNA polymerase III (RPC2) of the slime mould Dictyostelium discoideum and four intein coding sequences are in RNA polymerase II genes (RPB2), one each from the green alga Chlamydomonas reinhardtii, the zygomycete fungus Spiromyces aspiralis and the chytrid fungi Batrachochytrium dendrobatidis and Coelomomyces stegomyiae. The remaining intein coding sequence is in a viral relic embedded within the genome of the oomycete Phytophthora ramorum. The Chlamydomonas and Dictyostelium inteins are the first nuclear-encoded inteins found outside of the fungi. These new inteins represent a unique dataset: they are found in homologous proteins that form a paralogous group. Although these paralogues diverged early in eukaryotic evolution, their sequences can be aligned over most of their length. The inteins are inserted at multiple distinct sites, each of which corresponds to a highly conserved region of RNA polymerase. This dataset supports earlier work suggesting that inteins preferentially occur in highly conserved regions of their host proteins. CONCLUSION The identification of these new inteins increases the known host range of intein sequences in eukaryotes, and provides fresh insights into their origins and evolution. We conclude that inteins are ancient eukaryote elements once found widely among microbial eukaryotes. They persist as rarities in the genomes of a sporadic array of microorganisms, occupying highly conserved sites in diverse proteins.
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Affiliation(s)
- Timothy JD Goodwin
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Margaret I Butler
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Russell TM Poulter
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
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Fitzgerald LA, Graves MV, Li X, Feldblyum T, Nierman WC, Van Etten JL. Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A. Virology 2006; 358:472-84. [PMID: 17027058 PMCID: PMC1904511 DOI: 10.1016/j.virol.2006.08.033] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 08/17/2006] [Accepted: 08/23/2006] [Indexed: 10/24/2022]
Abstract
Viruses NY-2A and AR158, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella NC64A. The 368,683-bp genome of NY-2A and the 344,690-bp genome of AR158 are the two largest chlorella virus genomes sequenced to date; NY-2A contains 404 putative protein-encoding and 7 tRNA-encoding genes and AR158 contains 360 putative protein-encoding and 6 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Two of the NY-2A genes encode inteins, the large subunit of ribonucleotide reductase and a superfamily II helicase. These are the first inteins to be detected in the chlorella viruses. Approximately 40% of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. These include GDP-d-mannose dehydratase, fucose synthase, aspartate transcarbamylase, Ca(++) transporting ATPase and ubiquitin. Comparison of NY-2A and AR158 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that 85% of the genes are present in all three viruses.
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Affiliation(s)
- Lisa A. Fitzgerald
- Deparment of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Michael V. Graves
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, MA 01854
| | - Xiao Li
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, MA 01854
| | - Tamara Feldblyum
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850
| | - William C. Nierman
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850
- The George Washington University School of Medicine, Department of Biochemistry and Molecular Biology, Washington, DC 20037
| | - James L. Van Etten
- Deparment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722 and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68588-0666
- *Corresponding author. Mailing address: Department of Plant Pathology, University of Nebraska-Lincoln, NE 68383-0722. Phone: (402) 472-3168. Fax: (402) 472-2853. E-mail:
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Xu MQ, Evans TC. Recent advances in protein splicing: manipulating proteins in vitro and in vivo. Curr Opin Biotechnol 2005; 16:440-6. [PMID: 16026977 DOI: 10.1016/j.copbio.2005.06.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 06/10/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
Protein splicing is an intricate self-catalyzed protein rearrangement that converts an inactive protein precursor to biologically active proteins. In the past decade, mechanistic studies and extensive engineering of the naturally occurring protein splicing elements, termed inteins, has led to the development of numerous novel technologies. These intein-based methodologies permit in vitro and in vivo protein processing in ways previously not possible using traditional biochemical and genetic approaches. Inteins have been utilized in the production of protein and peptide arrays, as molecular switches and in the reconstitution of functional proteins by split-gene techniques.
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Affiliation(s)
- Ming-Qun Xu
- New England Biolabs, Inc., 32 Tozer Road, Beverly, Massachusetts 01915, USA.
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29
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Abstract
Inteins are protein splicing elements that employ standard enzyme strategies to excise themselves from precursor proteins and ligate the surrounding sequences (exteins). The protein splicing pathway consists of four nucleophilic displacements directed by the intein plus the first C-extein residue. The intein active site(s) are formed by folding of the intein within the precursor, which brings together the splice junctions and internal intein residues that assist catalysis. Inteins with non-canonical catalytic residues splice by modified pathways. Understanding intein proteolytic cleavage and ligation activities has led to the development of many novel applications in the fields of protein engineering, enzymology, microarray production, target detection and activation of transgenes in plants. Recent advances include intein-mediated attachment of proteins to solid supports for microarray or western blot analysis, linking nucleic acids to proteins and controllable splicing, which converts inteins into molecular switches.
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30
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Nagasaki K, Shirai Y, Tomaru Y, Nishida K, Pietrokovski S. Algal viruses with distinct intraspecies host specificities include identical intein elements. Appl Environ Microbiol 2005; 71:3599-607. [PMID: 16000767 PMCID: PMC1169056 DOI: 10.1128/aem.71.7.3599-3607.2005] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Accepted: 01/20/2005] [Indexed: 11/20/2022] Open
Abstract
Heterosigma akashiwo virus (HaV) is a large double-stranded DNA virus infecting the single-cell bloom-forming raphidophyte (golden brown alga) H. akashiwo. A molecular phylogenetic sequence analysis of HaV DNA polymerase showed that it forms a sister group with Phycodnaviridae algal viruses. All 10 examined HaV strains, which had distinct intraspecies host specificities, included an intein (protein intron) in their DNA polymerase genes. The 232-amino-acid inteins differed from each other by no more than a single nucleotide change. All inteins were present at the same conserved position, coding for an active-site motif, which also includes inteins in mimivirus (a very large double-stranded DNA virus of amoebae) and in several archaeal DNA polymerase genes. The HaV intein is closely related to the mimivirus intein, and both are apparently monophyletic to the archaeal inteins. These observations suggest the occurrence of horizontal transfers of inteins between viruses of different families and between archaea and viruses and reveal that viruses might be reservoirs and intermediates in horizontal transmissions of inteins. The homing endonuclease domain of the HaV intein alleles is mostly deleted. The mechanism keeping their sequences basically identical in HaV strains specific for different hosts is yet unknown. One possibility is that rapid and local changes in the HaV genome change its host specificity. This is the first report of inteins found in viruses infecting eukaryotic algae.
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Affiliation(s)
- Keizo Nagasaki
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Hiroshima, Japan
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31
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Ogata H, Raoult D, Claverie JM. A new example of viral intein in Mimivirus. Virol J 2005; 2:8. [PMID: 15707490 PMCID: PMC549080 DOI: 10.1186/1743-422x-2-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Accepted: 02/11/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inteins are "protein introns" that remove themselves from their host proteins through an autocatalytic protein-splicing. After their discovery, inteins have been quickly identified in all domains of life, but only once to date in the genome of a eukaryote-infecting virus. RESULTS Here we report the identification and bioinformatics characterization of an intein in the DNA polymerase PolB gene of amoeba infecting Mimivirus, the largest known double-stranded DNA virus, the origin of which has been proposed to predate the emergence of eukaryotes. Mimivirus intein exhibits canonical sequence motifs and clearly belongs to a subclass of archaeal inteins always found in the same location of PolB genes. On the other hand, the Mimivirus PolB is most similar to eukaryotic Poldelta sequences. CONCLUSIONS The intriguing association of an extremophilic archaeal-type intein with a mesophilic eukaryotic-like PolB in Mimivirus is consistent with the hypothesis that DNA viruses might have been the central reservoir of inteins throughout the course of evolution.
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Affiliation(s)
- Hiroyuki Ogata
- Information Génomique et Structurale, UPR2589 CNRS, IBSM, IFR88, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Didier Raoult
- Unité des Rickettsies, CNRS UPRESA 6020, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Jean-Michel Claverie
- Information Génomique et Structurale, UPR2589 CNRS, IBSM, IFR88, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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32
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Mills KV, Dorval DM, Lewandowski KT. Kinetic Analysis of the Individual Steps of Protein Splicing for the Pyrococcus abyssi PolII Intein. J Biol Chem 2005; 280:2714-20. [PMID: 15557319 DOI: 10.1074/jbc.m412313200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein splicing involves the excision of an intervening polypeptide, the intein, from flanking polypeptides, the exteins, concomitant with the specific ligation of the exteins. The intein that interrupts the DNA polymerase II DP2 subunit in Pyrococcus abyssi can be overexpressed and purified as an unspliced precursor, which allows for a detailed in vitro kinetic analysis of the individual steps of protein splicing. The first order rate constant for splicing of this intein, which has a non-canonical Gln at its C terminus, is 9.3 x 10(-6) s(-1) at 60 degrees C. The rate constant for splicing increases 3-fold with substitution of Asn for the C-terminal Gln. The pseudo first order rate constant of dithiothreitol-dependent N-terminal cleavage is 1 x 10(-4) s(-1). The first order rate constant of C-terminal cleavage is 1.2 x 10(-5) s(-1) with Gln at the C-terminal position, 2.8 x 10(-4) s(-1) with Asn, and decreases significantly with mutation of the penultimate His of the intein to Ala. N-terminal cleavage is most efficient between pH 7 and 7.5 and decreases at both more acidic and alkaline pH values, whereas C-terminal cleavage and splicing are both efficient over a broader range of pH values.
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Affiliation(s)
- Kenneth V Mills
- College of the Holy Cross, Department of Chemistry, Worcester, Massachusetts 01610, USA.
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Sun W, Yang J, Liu XQ. Synthetic Two-piece and Three-piece Split Inteins for Protein trans-Splicing. J Biol Chem 2004; 279:35281-6. [PMID: 15194682 DOI: 10.1074/jbc.m405491200] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inteins are protein-intervening sequences that can self-excise and concomitantly splice together the flanking polypeptides. Two-piece split inteins capable of protein trans-splicing have been found in nature and engineered in laboratories, but they all have a similar split site corresponding to the endonuclease domain of the intein. Can inteins be split at other sites and do trans-splicing? After testing 13 split sites engineered into a Ssp DnaB mini-intein, we report the finding of three new split sites that each produced a two-piece split intein capable of protein trans-splicing. These three functional split sites are located in different loop regions between beta-strands of the intein structure, and one of them is just 11 amino acids from the beginning of the intein. Because different inteins have similar structures and similar beta-strands, these new split sites may be generalized to other inteins. We have also demonstrated for the first time that a three-piece split intein could function in protein trans-splicing. These findings have implications for intein structure-function, evolution, and uses in biotechnology.
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Affiliation(s)
- Wenchang Sun
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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Dassa B, Haviv H, Amitai G, Pietrokovski S. Protein splicing and auto-cleavage of bacterial intein-like domains lacking a C'-flanking nucleophilic residue. J Biol Chem 2004; 279:32001-7. [PMID: 15150275 DOI: 10.1074/jbc.m404562200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial intein-like (BIL) domains are newly identified homologs of intein protein-splicing domains. The two known types of BIL domains together with inteins and hedgehog (Hog) auto-processing domains form the Hog/intein (HINT) superfamily. BIL domains are distinct from inteins and Hogs in sequence, phylogenetic distribution, and host protein type, but little is known about their biochemical activity. Here we experimentally study the auto-processing activity of four BIL domains. An A-type BIL domain from Clostridium thermocellum showed both protein-splicing and auto-cleavage activities. The splicing is notable, because this domain has a native Ala C'-flanking residue rather than a nucleophilic residue, which is absolutely necessary for intein protein splicing. B-type BIL domains from Rhodobacter sphaeroides and Rhodobacter capsulatus cleaved their N' or C' ends. We propose an alternative protein-splicing mechanism for the A-type BIL domains. After an initial N-S acyl shift, creating a thioester bond at the N' end of the domain, the C' end of the domain is cleaved by Asn cyclization. The resulting amino end of the C'-flank attacks the thioester bond next at the N' end of the domain. This aminolysis step splices the two flanks of the domain. The B-type BIL domain cleavage activity is explained in the context of the canonical intein protein-splicing mechanism. Our results suggest that the different HINT domains have related biochemical activities of proteolytic cleavages, ligation and splicing. Yet the predominant reactions diverged in each HINT type according to their specific biological roles. We suggest that the BIL domain cleavage and splicing reactions are mechanisms for post-translationally generating protein variability, particularly in extracellular bacterial proteins.
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Affiliation(s)
- Bareket Dassa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 76100
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Mills KV, Manning JS, Garcia AM, Wuerdeman LA. Protein splicing of a Pyrococcus abyssi intein with a C-terminal glutamine. J Biol Chem 2004; 279:20685-91. [PMID: 15024006 DOI: 10.1074/jbc.m400887200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein splicing involves the excision of an intervening polypeptide sequence, the intein, from a precursor protein and the concomitant ligation of the flanking polypeptides, the exteins, by a peptide bond. Most reported inteins have a C-terminal asparagine residue, and it has been shown that cyclization of this residue is coupled to peptide bond cleavage between the intein and C-extein. We show that the intein interrupting the DNA polymerase II DP2 subunit in Pyrococcus abyssi, which has a C-terminal glutamine, is capable of facilitating protein splicing. Substitution of an asparagine for the C-terminal glutamine moderately improves the rate and extent of protein splicing. However, substitution of an alanine for the penultimate histidine residue, with either asparagine or glutamine in the C-terminal position, prevents protein splicing and facilitates cleavage at the intein N terminus. The intein facilitates in vitro protein splicing only at temperatures above 30 degrees C and can be purified as a nonspliced precursor. This temperature dependence has enabled us to characterize the optimal in vitro splicing conditions and determine the rate constants for splicing as a function of temperature.
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Affiliation(s)
- Kenneth V Mills
- College of the Holy Cross, Department of Chemistry, 1 College Street, Worcester, MA 01610, USA.
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