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Panigrahi R, Kailasam S. Mapping allosteric pathway in NIa-Pro using computational approach. QUANTITATIVE BIOLOGY 2023. [DOI: 10.15302/j-qb-022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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2
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Mlinarec J, Nuskern L, Ježić M, Rigling D, Ćurković-Perica M. Molecular evolution and invasion pattern of Cryphonectria hypovirus 1 in Europe: Mutation rate, and selection pressure differ between genome domains. Virology 2018; 514:156-164. [PMID: 29179038 DOI: 10.1016/j.virol.2017.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/08/2023]
Abstract
Understanding virus evolution is a fundamental goal of virology, evolutionary biology, and disease epidemiology. We provide a detailed analysis of evolution and origin of Cryphonectria hypovirus 1 (CHV1) populations in Europe, based on the complete genome sequence of all European subtypes. Phylogenetic analyses divided European strains into two closely related clades. Strains of the subtype I belong to the first, while strains of the subtypes F1, D and E belong to the second clade suggesting that the subtypes F1, D and E are more closely related than previously thought. Strains of the subtype F2 appeared to be recombinant; subtypes F1/D/E contributed a larger fraction of sequence while subtype I contributed a smaller fraction. The p29 was the most variable domain, while the replication-associated large ORF B protein was the most conserved domain within the CHV1. Low sequence similarity, predominant negative selection and frequent recombination characterise the evolution of CHV1.
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Affiliation(s)
- Jelena Mlinarec
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia
| | - Lucija Nuskern
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia
| | - Daniel Rigling
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Mirna Ćurković-Perica
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia.
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3
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A protease-based biosensor for the detection of schistosome cercariae. Sci Rep 2016; 6:24725. [PMID: 27090566 PMCID: PMC4835807 DOI: 10.1038/srep24725] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/30/2016] [Indexed: 01/18/2023] Open
Abstract
Parasitic diseases affect millions of people worldwide, causing debilitating illnesses and death. Rapid and cost-effective approaches to detect parasites are needed, especially in resource-limited settings. A common signature of parasitic diseases is the release of specific proteases by the parasites at multiple stages during their life cycles. To this end, we engineered several modular Escherichia coli and Bacillus subtilis whole-cell-based biosensors which incorporate an interchangeable protease recognition motif into their designs. Herein, we describe how several of our engineered biosensors have been applied to detect the presence and activity of elastase, an enzyme released by the cercarial larvae stage of Schistosoma mansoni. Collectively, S. mansoni and several other schistosomes are responsible for the infection of an estimated 200 million people worldwide. Since our biosensors are maintained in lyophilised cells, they could be applied for the detection of S. mansoni and other parasites in settings without reliable cold chain access.
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4
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Pasin F, Simón-Mateo C, García JA. The hypervariable amino-terminus of P1 protease modulates potyviral replication and host defense responses. PLoS Pathog 2014; 10:e1003985. [PMID: 24603811 PMCID: PMC3946448 DOI: 10.1371/journal.ppat.1003985] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 01/23/2014] [Indexed: 12/22/2022] Open
Abstract
The replication of many RNA viruses involves the translation of polyproteins, whose processing by endopeptidases is a critical step for the release of functional subunits. P1 is the first protease encoded in plant potyvirus genomes; once activated by an as-yet-unknown host factor, it acts in cis on its own C-terminal end, hydrolyzing the P1-HCPro junction. Earlier research suggests that P1 cooperates with HCPro to inhibit host RNA silencing defenses. Using Plum pox virus as a model, we show that although P1 does not have a major direct role in RNA silencing suppression, it can indeed modulate HCPro function by its self-cleavage activity. To study P1 protease regulation, we used bioinformatic analysis and in vitro activity experiments to map the core C-terminal catalytic domain. We present evidence that the hypervariable region that precedes the protease domain is predicted as intrinsically disordered, and that it behaves as a negative regulator of P1 proteolytic activity in in vitro cleavage assays. In viral infections, removal of the P1 protease antagonistic regulator is associated with greater symptom severity, induction of salicylate-dependent pathogenesis-related proteins, and reduced viral loads. We suggest that fine modulation of a viral protease activity has evolved to keep viral amplification below host-detrimental levels, and thus to maintain higher long-term replicative capacity.
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Affiliation(s)
- Fabio Pasin
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Carmen Simón-Mateo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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5
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Mathur C, Jimsheena VK, Banerjee S, Makinen K, Gowda LR, Savithri HS. Functional regulation of PVBV Nuclear Inclusion protein-a protease activity upon interaction with Viral Protein genome-linked and phosphorylation. Virology 2011; 422:254-64. [PMID: 22099968 DOI: 10.1016/j.virol.2011.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 10/03/2011] [Accepted: 10/10/2011] [Indexed: 11/28/2022]
Abstract
Regulation of NIa-Pro is crucial for polyprotein processing and hence, for successful infection of potyviruses. We have examined two novel mechanisms that could regulate NIa-Pro activity. Firstly, the influence of VPg domain on the proteolytic activity of NIa-Pro was investigated. It was shown that the turnover number of the protease increases when these two domains interact (cis: two-fold; trans: seven-fold) with each other. Secondly, the protease activity of NIa-Pro could also be modulated by phosphorylation at Ser129. A mutation of this residue either to aspartate (phosphorylation-mimic) or alanine (phosphorylation-deficient) drastically reduces the protease activity. Based on these observations and molecular modeling studies, we propose that interaction with VPg as well as phosphorylation of Ser129 could relay a signal through Trp143 present at the protein surface to the active site pocket by subtle conformational changes, thus modulating protease activity of NIa-Pro.
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Affiliation(s)
- C Mathur
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
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6
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Kim Y, Babnigg G, Jedrzejczak R, Eschenfeldt WH, Li H, Maltseva N, Hatzos-Skintges C, Gu M, Makowska-Grzyska M, Wu R, An H, Chhor G, Joachimiak A. High-throughput protein purification and quality assessment for crystallization. Methods 2011; 55:12-28. [PMID: 21907284 DOI: 10.1016/j.ymeth.2011.07.010] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/14/2011] [Accepted: 07/14/2011] [Indexed: 12/31/2022] Open
Abstract
The ultimate goal of structural biology is to understand the structural basis of proteins in cellular processes. In structural biology, the most critical issue is the availability of high-quality samples. "Structural biology-grade" proteins must be generated in the quantity and quality suitable for structure determination using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The purification procedures must reproducibly yield homogeneous proteins or their derivatives containing marker atom(s) in milligram quantities. The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples. With structural genomics emphasizing a genome-based approach in understanding protein structure and function, a number of unique structures covering most of the protein folding space have been determined and new technologies with high efficiency have been developed. At the Midwest Center for Structural Genomics (MCSG), we have developed semi-automated protocols for high-throughput parallel protein expression and purification. A protein, expressed as a fusion with a cleavable affinity tag, is purified in two consecutive immobilized metal affinity chromatography (IMAC) steps: (i) the first step is an IMAC coupled with buffer-exchange, or size exclusion chromatography (IMAC-I), followed by the cleavage of the affinity tag using the highly specific Tobacco Etch Virus (TEV) protease; the second step is IMAC and buffer exchange (IMAC-II) to remove the cleaved tag and tagged TEV protease. These protocols have been implemented on multidimensional chromatography workstations and, as we have shown, many proteins can be successfully produced in large-scale. All methods and protocols used for purification, some developed by MCSG, others adopted and integrated into the MCSG purification pipeline and more recently the Center for Structural Genomics of Infectious Diseases (CSGID) purification pipeline, are discussed in this chapter.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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7
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Charlton A, Zachariou M. Tag removal by site-specific cleavage of recombinant fusion proteins. Methods Mol Biol 2011; 681:349-367. [PMID: 20978975 DOI: 10.1007/978-1-60761-913-0_19] [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] [Indexed: 05/30/2023]
Abstract
Where an affinity tag has served its purpose it may become desirable to remove it from the protein of interest. This chapter describes the removal of such fusion partners from the intended protein product by cleavage with site-specific endoproteases. Methods to achieve proteolytic cleavage of the fusion proteins are provided, along with techniques for optimising the yield of authentic product.
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Affiliation(s)
- Adam Charlton
- Commonwealth Serum Laboratories Ltd, Parkville, VIC, Australia
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8
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Boulware KT, Jabaiah A, Daugherty PS. Evolutionary optimization of peptide substrates for proteases that exhibit rapid hydrolysis kinetics. Biotechnol Bioeng 2010; 106:339-46. [PMID: 20148412 DOI: 10.1002/bit.22693] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protease cleavage site recognition motifs can be identified using protease substrate discovery methodologies, but typically exhibit non-optimal specificity and activity. To enable evolutionary optimization of substrate cleavage kinetics, a two-color cellular library of peptide substrates (CLiPS) methodology was developed. Two-color CLiPS was applied to identify peptide substrates for the tobacco etch virus (TEV) protease from a random pentapeptide library, which were then optimized by screening of a focused, extended substrate library. Quantitative library screening yielded seven amino acid substrates exhibiting rapid hydrolysis by TEV protease and high sequence similarity to the native seven-amino-acid substrate, with a strong consensus of EXLYPhiQG. Comparison of hydrolysis rates for a family of closely related substrates indicates that the native seven-residue TEV substrate co-evolved with TEV protease to facilitate highly efficient hydrolysis. Consensus motifs revealed by screening enabled database identification of a family of related, putative viral protease substrates. More generally, our results suggest that substrate evolution using CLiPS may be useful for optimizing substrate selectivity and activity to enable the design of more effective protease activity probes, molecular imaging agents, and prodrugs.
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Affiliation(s)
- Kevin T Boulware
- Department of Chemical Engineering, University of California-Santa Barbara, 93106, USA
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9
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Application of “Homogeneous Assay for Fluorescence Concentrated on Membrane” to the Analysis of the Substrate Specificity of Protease. Biosci Biotechnol Biochem 2010; 74:869-71. [DOI: 10.1271/bbb.90822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Nair S, Savithri H. Processing of SeMV polyproteins revisited. Virology 2010; 396:106-17. [DOI: 10.1016/j.virol.2009.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Revised: 09/01/2009] [Accepted: 09/19/2009] [Indexed: 11/29/2022]
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11
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Charlton A. Site-specific cleavage of fusion proteins. Methods Mol Biol 2008; 421:211-228. [PMID: 18826057 DOI: 10.1007/978-1-59745-582-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Where an affinity tag has served its purpose, it may become desirable to remove it from the protein of interest. This chapter describes the removal of such fusion partners from the intended protein product by cleavage with site-specific endoproteases. Methods to achieve proteolytic cleavage of the fusion proteins are provided, along with techniques for optimizing the yield of authentic product.
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Affiliation(s)
- Adam Charlton
- Industrial Biotechnology, CSIRO Molecular and Health Technology, Australia
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12
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KIM YOUNGCHANG, BIGELOW LANCE, BOROVILOS MARIA, DEMENTIEVA IRINA, DUGGAN ERIKA, HATZOS CATHERINE, JOACHIMIAK GRAZYNA, LI HUI, MULLIGAN RORY, QUARTEY PEARL, SATHER ALICIA, STOLS LUCY, VOLKART LOUR, ZHOU MIN, Volkart L, Wu R, Zhou M, Joachimiak A. Chapter 3. High-throughput protein purification for x-ray crystallography and NMR. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2008; 75:85-105. [PMID: 20731990 PMCID: PMC3366499 DOI: 10.1016/s0065-3233(07)75003-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In structural biology, the most critical issue is the availability of high-quality samples. "Structural-biology-grade" proteins must be generated in a quantity and quality suitable for structure determination using X-ray crystallography or nuclear magnetic resonance. The additional challenge for structural genomics is the need for high numbers of proteins at low cost where protein targets quite often have low sequence similarities, unknown properties and are poorly characterized. The purification procedures must reproducibly yield homogeneous proteins or their derivatives containing marker atom(s) in milligram quantities. The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples. Where the ultimate goal of structural biology is the same-to understand the structural basis of proteins in cellular processes, the structural genomics approach is different in that the functional aspects of individual protein or family are not ignored, however, emphasis here is on the number of unique structures, covering most of the protein folding space and developing new technologies with high efficiency. At the Midwest Center Structural Genomics (MCSG), we have developed semiautomated protocols for high-throughput parallel protein purification. In brief, a protein, expressed as a fusion with a cleavable affinity tag, is purified in two immobilized metal affinity chromatography (IMAC) steps: (i) first IMAC coupled with buffer-exchange step, and after tag cleavage using TEV protease, (ii) second IMAC and buffer exchange to clean up cleaved tags and tagged TEV protease. Size exclusion chromatography is also applied as needed. These protocols have been implemented on multidimensional chromatography workstations AKTAexplorer and AKTAxpress (GE Healthcare). All methods and protocols used for purification, some developed in MCSG, others adopted and integrated into the MCSG purification pipeline and more recently the Center for Structural Genomics of Infectious Disease (CSGID) purification pipeline, are discussed in this chapter.
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13
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Yogev O, Karniely S, Pines O. Translation-coupled Translocation of Yeast Fumarase into Mitochondria in Vivo. J Biol Chem 2007; 282:29222-9. [PMID: 17666392 DOI: 10.1074/jbc.m704201200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fumarase represents proteins that cannot be imported into mitochondria after the termination of translation (post-translationally). Utilizing mitochondrial and cytosolic versions of the tobacco etch virus (TEV) protease, we show that mitochondrially targeted fumarase harboring a TEV protease recognition sequence is efficiently cleaved by the mitochondrial but not by the cytosolic TEV protease. Nonetheless, fumarase was readily cleaved by cytosolic TEV when its import into mitochondria was slowed down by either (i) disrupting the activity of the TOM complex, (ii) lowering the growth temperature, or (iii) reducing the inner membrane electrochemical potential. Accessibility of the fumarase nascent chain to TEV protease under such conditions was prevented by low cycloheximide concentrations, which impede translation. In addition, depletion of the ribosome-associated nascent polypeptide-associated complex (NAC) reduced the fumarase rate of translocation into mitochondria and exposed it to TEV cleavage in the cytosol. These results indicate that cytosolic exposure of the fumarase nascent chain depends on both translocation and translation rates, allowing us to discuss the possibility that import of fumarase into mitochondria occurs while the ribosome is still attached to the nascent chain.
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Affiliation(s)
- Ohad Yogev
- Department of Molecular Biology, Hebrew University Medical School, Jerusalem 91120, Israel
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14
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Weber ANR, Gangloff M, Moncrieffe MC, Hyvert Y, Imler JL, Gay NJ. Role of the Spätzle Pro-domain in the Generation of an Active Toll Receptor Ligand. J Biol Chem 2007; 282:13522-31. [PMID: 17324925 DOI: 10.1074/jbc.m700068200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cytokine Spätzle is the ligand for Drosophila Toll, the prototype of an important family of membrane receptors that function in embryonic patterning and innate immunity. A dimeric precursor of Spätzle is processed by an endoprotease to produce a form (C-106) that cross-links Toll receptor ectodomains and establishes signaling. Here we show that before processing the pro-domain of Spätzle is required for correct biosynthesis and secretion. We mapped two loss-of-function mutations of Spätzle to a discrete site in the pro-domain and showed that the phenotype arises because of a defect in biosynthesis rather than signaling. We also report that the pro-domain and C-106 remain associated after cleavage and that this processed complex signals with the same characteristics as the C-terminal fragment. These results suggest that before activation the determinants on C-106 that bind specifically to Toll are sequestered by the pro-domain and that proteolytic processing causes conformational rearrangements that expose these determinants and enables binding to Toll. Furthermore, we show that the pro-domain is released when the Toll extracellular domain binds to the complex, a finding that has implications for the generation of a signaling-competent Toll dimer.
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Affiliation(s)
- Alexander N R Weber
- Department of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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15
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Choi HJ, Huber AH, Weis WI. Thermodynamics of beta-catenin-ligand interactions: the roles of the N- and C-terminal tails in modulating binding affinity. J Biol Chem 2005; 281:1027-38. [PMID: 16293619 DOI: 10.1074/jbc.m511338200] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
beta-Catenin is a structural component of adherens junctions, where it binds to the cytoplasmic domain of cadherin cell adhesion molecules. beta-Catenin is also a transcriptional coactivator in the Wnt signaling pathway, where it binds to Tcf/Lef family transcription factors. In the absence of a Wnt signal, nonjunctional beta-catenin is present in a multiprotein complex containing the proteins axin and adenomatous polyposis coli (APC), both of which bind directly to beta-catenin. The thermodynamics of beta-catenin binding to E-cadherin, Lef-1, APC, axin, and the transcriptional inhibitor ICAT have been determined by isothermal titration calorimetry. Most of the interactions showed large, unfavorable entropy changes, consistent with these ligands being natively unstructured in the absence of beta-catenin. Phosphorylation of serine residues present in a sequence motif common to cadherins and APC increased the affinity for beta-catenin 300-700-fold, and surface plasmon resonance measurements revealed that phosphorylation of E-cadherin both enhanced its on rate and decreased its off rate. The effects of the N- and C-terminal "tails" that flank the beta-catenin armadillo repeat domain on ligand binding have also been investigated using constructs lacking one or both tails. Contrary to earlier studies that employed less direct binding assays, the tails did not affect the affinity of beta-catenin for tight ligands such as E-cadherin, Lef-1, and phosphorylated APC. However, the beta-catenin C-terminal tail was found to decrease the affinity for the weaker ligands APC and axin, suggesting that this region may have a regulatory role in beta-catenin degradation.
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Affiliation(s)
- Hee-Jung Choi
- Department of Structural Biology, Stanford University School of Medicine, CA 94305-5126, USA
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16
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Nunn CM, Jeeves M, Cliff MJ, Urquhart GT, George RR, Chao LH, Tscuchia Y, Djordjevic S. Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site. J Mol Biol 2005; 350:145-55. [PMID: 15919091 DOI: 10.1016/j.jmb.2005.04.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 04/06/2005] [Accepted: 04/07/2005] [Indexed: 11/29/2022]
Abstract
Tobacco etch virus (TEV) protease is a cysteine protease exhibiting stringent sequence specificity. The enzyme is widely used in biotechnology for the removal of the affinity tags from recombinant fusion proteins. Crystal structures of two TEV protease mutants as complexes with a substrate and a product peptide provided the first insight into the mechanism of substrate specificity of this enzyme. We now report a 2.7A crystal structure of a full-length inactive C151A mutant protein crystallised in the absence of peptide. The structure reveals the C terminus of the protease bound to the active site. In addition, we determined dissociation constants of TEV protease substrate and product peptides using isothermal titration calorimetry for various forms of this enzyme. Data suggest that TEV protease could be inhibited by the peptide product of autolysis. Separate modes of recognition for native substrates and the site of TEV protease self-cleavage are proposed.
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Affiliation(s)
- Christine M Nunn
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
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17
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Scholle MD, Collart FR, Kay BK. In vivo biotinylated proteins as targets for phage-display selection experiments. Protein Expr Purif 2004; 37:243-52. [PMID: 15294305 DOI: 10.1016/j.pep.2004.05.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Revised: 05/07/2004] [Indexed: 10/26/2022]
Abstract
Screening phage-displayed combinatorial libraries represents an attractive method for identifying affinity reagents to target proteins. Two critical components of a successful selection experiment are having a pure target protein and its immobilization in a native conformation. To achieve both of these requirements in a single step, we have devised cytoplasmic expression vectors for expression of proteins that are tagged at the amino- or carboxy-terminus (pMCSG16 and 15) via the AviTag, which is biotinylated in vivo with concurrent expression of the BirA biotin ligase. To facilitate implementation in high-throughput applications, the engineered vectors, pMCSG15 and pMCSG16, also contain a ligase-independent cloning site (LIC), which permits up to 100% cloning efficiency. The expressed protein can be purified from bacterial cell lysates with immobilized metal affinity chromatography or streptavidin-coated magnetic beads, and the beads used directly to select phage from combinatorial libraries. From selections using the N-terminally biotinylated version of one target protein, a peptide ligand (Kd= 9 microM) was recovered that bound in a format-dependent manner. To demonstrate the utility of pMCSG16, a set of 192 open reading frames were cloned, and protein was expressed and immobilized for use in high-throughput selections of phage-display libraries.
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Affiliation(s)
- Michael D Scholle
- Combinatorial Biology, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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18
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Kim Y, Dementieva I, Zhou M, Wu R, Lezondra L, Quartey P, Joachimiak G, Korolev O, Li H, Joachimiak A. Automation of protein purification for structural genomics. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2004; 5:111-8. [PMID: 15263850 PMCID: PMC2778303 DOI: 10.1023/b:jsfg.0000029206.07778.fc] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A critical issue in structural genomics, and in structural biology in general, is the availability of high-quality samples. The additional challenge in structural genomics is the need to produce high numbers of proteins with low sequence similarities and poorly characterized or unknown properties. 'Structural-biology-grade' proteins must be generated in a quantity and quality suitable for structure determination experiments using X-ray crystallography or nuclear magnetic resonance (NMR). The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples. The purification procedure must yield a homogeneous protein and must be highly reproducible in order to supply milligram quantities of protein and/or its derivative containing marker atom(s). At the Midwest Center for Structural Genomics we have developed protocols for high-throughput protein purification. These protocols have been implemented on AKTA EXPLORER 3D and AKTA FPLC 3D workstations capable of performing multidimensional chromatography. The automated chromatography has been successfully applied to many soluble proteins of microbial origin. Various MCSG purification strategies, their implementation, and their success rates are discussed in this paper.
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Affiliation(s)
- Youngchang Kim
- Biosciences Division and Structural Biology Center, Argonne National Laboratory, 9700 S. Cass Ave., Bldg 202, Argonne, IL 60439, USA
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19
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Abstract
Maturation of vaccinia virus (VV) core proteins is required for the production of infectious virions. The VV G1L and I7L gene products are the leading candidates for the viral core protein proteinase (vCPP). Using transient-expression assays, data were obtained to demonstrate that the I7L gene product and its encoded cysteine proteinase activity are responsible for vCPP activity.
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Affiliation(s)
- Chelsea M Byrd
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
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20
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Lin D, Tatham MH, Yu B, Kim S, Hay RT, Chen Y. Identification of a substrate recognition site on Ubc9. J Biol Chem 2002; 277:21740-8. [PMID: 11877416 DOI: 10.1074/jbc.m108418200] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human Ubc9 is homologous to ubiquitin-conjugating enzymes. However, instead of conjugating ubiquitin, it conjugates a ubiquitin homologue, small ubiquitin-like modifier 1 (SUMO-1), also known as UBL1, GMP1, SMTP3, PIC1, and sentrin. The SUMO-1 conjugation pathway is very similar to that of ubiquitin with regard to the primary sequences of the ubiquitin-activating enzymes (E1), the three-dimensional structures of the ubiquitin-conjugating enzymes (E2), and the chemistry of the overall conjugation pathway. The interaction of substrates with Ubc9 has been studied using NMR spectroscopy. Peptides with sequences that correspond to those of the SUMO-1 conjugation sites from p53 and c-Jun both bind to a surface adjacent to the active site Cys93 of human Ubc9, which has been previously shown to include residues that demonstrate the most significant dynamics on the microsecond to millisecond time scale. Mutations in this region, Q126A, Q130A, A131D, E132A, Y134A, and T135A, were constructed to evaluate the role of these residues in SUMO-1 conjugation. These alterations have significant effects on the conjugation of SUMO-1 with the target proteins p53, E1B, and promyelocytic leukemia protein and define a substrate binding site on Ubc9. Furthermore, the SUMO-1 conjugation site of p53 does not form any defined secondary structure when either free or bound to Ubc9. This suggests that a defined secondary structure at SUMO-1 conjugation sites in target proteins is not necessary for recognition and conjugation by the SUMO-1 pathway.
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Affiliation(s)
- Donghai Lin
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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21
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Stols L, Gu M, Dieckman L, Raffen R, Collart FR, Donnelly MI. A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. Protein Expr Purif 2002; 25:8-15. [PMID: 12071693 DOI: 10.1006/prep.2001.1603] [Citation(s) in RCA: 446] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To establish high-throughput methods for protein crystallography, all aspects of the production and analysis of protein crystals must be accelerated. Automated, plate-based methods for cloning, expression, and evaluation of target proteins will help researchers investigate the vast numbers of proteins now available from sequenced genomes. Ligation-independent cloning (LIC) is well suited to robotic cloning and expression, but few LIC vectors are available commercially. We have developed a new LIC vector, pMCSG7, that incorporates the tobacco etch virus (TEV) protease cleavage site into the leader sequence. This protease is highly specific and functions under a wide range of conditions. The new vector incorporates an N-terminal his-tag followed by the TEV protease recognition site and a SspI restriction site used for LIC. The vector functioned as expected, giving high cloning efficiencies and strong expression of proteins. Purification and cleavage of a target protein showed that the his-tag and the TEV cleavage site function properly. The protein was purified and cleaved under different conditions to simulate both plate-based screening methods and large-scale purifications for crystal production. The vector also includes a pair of adjacent, unique restriction sites that will allow insertion of additional modules between the his-tag and the cleavage site of the leader sequence to generate a family of vectors suitable for high-throughput production of proteins.
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Affiliation(s)
- Lucy Stols
- Environmental Research Division, Argonne National Laboratory, Argonne, IL 60439, USA
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22
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Kapust RB, Tözsér J, Fox JD, Anderson DE, Cherry S, Copeland TD, Waugh DS. Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng Des Sel 2001; 14:993-1000. [PMID: 11809930 DOI: 10.1093/protein/14.12.993] [Citation(s) in RCA: 670] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Because of its stringent sequence specificity, the catalytic domain of the nuclear inclusion protease from tobacco etch virus (TEV) is a useful reagent for cleaving genetically engineered fusion proteins. However, a serious drawback of TEV protease is that it readily cleaves itself at a specific site to generate a truncated enzyme with greatly diminished activity. The rate of autoinactivation is proportional to the concentration of TEV protease, implying a bimolecular reaction mechanism. Yet, a catalytically active protease was unable to convert a catalytically inactive protease into the truncated form. Adding increasing concentrations of the catalytically inactive protease to a fixed amount of the wild-type enzyme accelerated its rate of autoinactivation. Taken together, these results suggest that autoinactivation of TEV protease may be an intramolecular reaction that is facilitated by an allosteric interaction between protease molecules. In an effort to create a more stable protease, we made amino acid substitutions in the P2 and P1' positions of the internal cleavage site and assessed their impact on the enzyme's stability and catalytic activity. One of the P1' mutants, S219V, was not only far more stable than the wild-type protease (approximately 100-fold), but also a more efficient catalyst.
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Affiliation(s)
- R B Kapust
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA
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23
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Proteinases Involved in Plant Virus Genome Expression. PROTEASES OF INFECTIOUS AGENTS 1999. [PMCID: PMC7271178 DOI: 10.1016/b978-012420510-9/50037-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This chapter discusses the proteinases involved in plant virus genome expression. The chapter focuses on virus-encoded proteinases. It gives an overall view of the use of proteolytic processing by different plant virus groups for the expression of their genomes. It also discusses that the development of full-length cDNA clones from which infectious transcripts can be produced either in vitro or in vivo, has facilitated the functional analysis of the plant virus proteinases. In spite of the high specificity of the viral proteinases, cellular substrates for animal virus proteinases have been described in this chapter. The activity of the viral proteinases can interfere with important cellular processes to favor virus replication. The recent use of proteinase inhibitors in AIDS therapy has emphasized the convenience of virus-encoded proteinases as targets of antiviral action. A mutant protein able to inhibit the activity of the TEV proteinase by manipulation of the α2-macroglobulin bait region was designed by Van Rompaey.
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24
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Kim DH, Han JS, Lew J, Kim SS, Kang BH, Hwang DC, Jang DS, Kim W, Song BD, Choi KY. Effects of mutations in the C-terminal region of NIa protease on cis-cleavage between NIa and NIb. Virology 1998; 241:94-100. [PMID: 9454720 DOI: 10.1006/viro.1997.8938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mutational analyses were carried out to investigate whether the nuclear inclusion protein a (NIa) C-terminal amino acids of turnip mosaic potyvirus play any roles in the cis-cleavage between NIa and NIb. The processing rate of the NIa-NIb junction sequence was decreased significantly by either V240D or Q243A mutation while little affected by F226D, V228E, K230E, I232D, or L235D mutation. The mutation of W212S, G213S, or I217D abolishing the cleavage at the NIb-CP or 6K1-cylindrical inclusion protein junction sequence decreased the processing rate to half the level of that of the wild type. Deletion of the C-terminal one (K230), two (S229 and K230), three (S229 to L231), or six amino acids (S229 to D234) as well as the insertion of five glycines between S229 and K230 or between S220 and Q221 did not affect significantly the cleavage while the deletion of 20 amino acids (Q218 to S237) decreased the processing rate to 73% of that of the wild type. These results rule out the possibility that the C-terminal region plays a role as a spacer in right placement of the NIa-NIb junction sequence and demonstrate that the C-terminal 20 amino acids from Q218 to S237 are not crucial for the cis-cleavage of the NIa-NIb junction sequence.
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Affiliation(s)
- D H Kim
- Department of Life Sciences and Center for Biofunctional Molecules, Pohang University of Science and Technology, Pohang, 790-784, Korea
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25
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Chu M, Lopez-Moya JJ, Llave-Correas C, Pirone TP. Two separate regions in the genome of the tobacco etch virus contain determinants of the wilting response of Tabasco pepper. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1997; 10:472-480. [PMID: 9150596 DOI: 10.1094/mpmi.1997.10.4.472] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Infection of Tabasco pepper by the tobacco etch virus (TEV) typically causes wilting associated with root necrosis. However, a strain of TEV, designated TEV nonwilting (TEV NW), is able to infect Tabasco pepper plants but does not cause wilting. In order to locate the genetic determinants responsible for the wilting response, a full-length cDNA clone of TEV NW from which infectious transcripts can be derived was made. A number of chimeric constructs were prepared by substituting cDNA fragments between TEV HAT (which causes wilting) and TEV NW clones. This approach was used to identify two wilting determinants in TEV HAT: one encompasses the 3' one-third of the P3 encoding region; the other spans the 3' end of the CI, the 6-kDa protein, and the 5' end of the VPg-NIa coding regions. Substitutions of both these TEV NW fragments into TEV HAT resulted in infection but not wilting of Tabasco pepper, while the replacement of either of the fragments alone did not alter the wilting response. This indicates that both TEV NW regions contain determinants necessary but not sufficient to alter the wilting response and that both must be present in order to avoid the wilting response. There was no difference between the in vitro transcription-translation products derived from constructs containing these regions from TEV HAT and TEV NW.
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Affiliation(s)
- M Chu
- Department of Plant Pathology, University of Kentucky, Lexington 40546, USA
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26
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27
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Maia IG, Séron K, Haenni AL, Bernardi F. Gene expression from viral RNA genomes. PLANT MOLECULAR BIOLOGY 1996; 32:367-391. [PMID: 8980488 DOI: 10.1007/bf00039391] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
This review is centered on the major strategies used by plant RNA viruses to produce the proteins required for virus multiplication. The strategies at the level of transcription presented here are synthesis of mRNA or subgenomic RNAs from viral RNA templates, and 'cap-snatching'. At the level of translation, several strategies have been evolved by viruses at the steps of initiation, elongation and termination. At the initiation step, the classical scanning mode is the most frequent strategy employed by viruses; however in a vast number of cases, leaky scanning of the initiation complex allows expression of more than one protein from the same RNA sequence. During elongation, frameshift allows the formation of two proteins differing in their carboxy terminus. At the termination step, suppression of termination produces a protein with an elongated carboxy terminus. The last strategy that will be described is co- and/or post-translational cleavage of a polyprotein precursor by virally encoded proteinases. Most (+)-stranded RNA viruses utilize a combination of various strategies.
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Affiliation(s)
- I G Maia
- Institut Jacques Monod, Paris, France
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28
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Verchot J, Carrington JC. Debilitation of plant potyvirus infectivity by P1 proteinase-inactivating mutations and restoration by second-site modifications. J Virol 1995; 69:1582-90. [PMID: 7853492 PMCID: PMC188753 DOI: 10.1128/jvi.69.3.1582-1590.1995] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Tobacco etch virus (TEV) encodes three proteinases that catalyze processing of the genome-encoded polyprotein. The P1 proteinase originates from the N terminus of the polyprotein and catalyzes proteolysis between itself and the helper component proteinase (HC-Pro). Mutations resulting in substitution of a single amino acid, small insertions, or deletions were introduced into the P1 coding sequence of the TEV genome. Deletion of the N-terminal, nonproteolytic domain of P1 had only minor effects on virus infection in protoplasts and whole plants. Insertion mutations that did not impair proteolytic activity had no measurable effects regardless of whether the modification affected the N-terminal nonproteolytic or C-terminal proteolytic domain. In contrast, three mutations (termed S256A, F, and delta 304) that debilitated P1 proteolytic activity rendered the virus nonviable, whereas a fourth proteinase-debilitating mutation (termed C) resulted in a slow-infection phenotype. A strategy was devised to determine whether the defect in the P1 mutants was due to an inactive proteinase domain or due simply to a lack of proteolytic maturation between P1 and HC-Pro. Sequences coding for a surrogate cleavage site recognized by the TEV NIa proteinase were inserted into the genome of each processing-debilitated mutant at positions that resulted in NIa-mediated proteolysis between P1 and HC-Pro. The infectivity of each mutant was restored by these second-site modifications. These data indicate that P1 proteinase activity is not essential for viral infectivity but that separation of P1 and HC-Pro is required. The data also provide evidence that the proteinase domain is involved in additional, nonproteolytic functions.
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Affiliation(s)
- J Verchot
- Department of Biology, Texas A&M University, College Station 77843
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29
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GARCÍA JA, RIECHMANN JL, LAÍN S, MARTÍN MT, GUO H, SIMON L, FERNÁNDEZ A, DOMÍNGUEZ E, CERVERA MT. Molecular characterization of plum pox potyvirus. ACTA ACUST UNITED AC 1994. [DOI: 10.1111/j.1365-2338.1994.tb01067.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Marcos JF, Beachy RN. In vitro characterization of a cassette to accumulate multiple proteins through synthesis of a self-processing polypeptide. PLANT MOLECULAR BIOLOGY 1994; 24:495-503. [PMID: 8123791 DOI: 10.1007/bf00024117] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The strategy for processing the polyprotein encoded by plant potyviruses has been mimicked by constructing an expression cassette based on the nuclear inclusion (Nla) proteinase from tobacco etch virus (TEV). This cassette (pPR01), includes the TEV Nla coding region flanked on each side by its heptapeptide cleavage sequence and cloning sites for the in frame insertion of two different open reading frames. pPR01 allows the synthesis, under the control of a single transcriptional promoter, of two proteins in equimolar amounts as part of a polyprotein which is cleaved into individual mature products by the TEV protease. In in vitro reactions the cassette functioned as expected when several different protein-coding sequences were used. The potential uses of pPR01 are discussed.
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Affiliation(s)
- J F Marcos
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037
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31
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Carrington JC, Haldeman R, Dolja VV, Restrepo-Hartwig MA. Internal cleavage and trans-proteolytic activities of the VPg-proteinase (NIa) of tobacco etch potyvirus in vivo. J Virol 1993; 67:6995-7000. [PMID: 8230423 PMCID: PMC238159 DOI: 10.1128/jvi.67.12.6995-7000.1993] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The NIa protein of plant potyviruses is a bifunctional protein containing an N-terminal VPg domain and a C-terminal proteinase region. The majority of tobacco etch potyvirus (TEV) NIa molecules are localized to the nucleus of infected cells, although a proportion of NIa is attached covalently as VPg to viral RNA in the cytoplasm. A suboptimal cleavage site that is recognized by the NIa proteinase is located between the two domains. This site was found to be utilized in the VPg-associated, but not the nuclear, pool of NIa. A mutation converting Glu-189 to Leu at the P1 position of the processing site inhibited internal cleavage. Introduction of this mutation into TEV-GUS, an engineered variant of TEV that expresses a reporter protein (beta-glucuronidase [GUS]) fused to the N terminus of the helper component-proteinase (HC-Pro), rendered the virus replication defective in tobacco protoplasts. Site-specific reversion of the mutant internal processing site to the wild-type sequence restored virus viability. In addition, the trans-processing activity of NIa proteinase was tested in vivo after introduction of an artificial cleavage site between the GUS and HC-Pro sequences in the cytoplasmic GUS/HC-Pro polyprotein encoded by TEV-GUS. The novel site was recognized and processed in plants infected by the engineered virus, indicating the presence of excess NIa processing capacity in the cytoplasm. The potential roles of internal NIa processing in TEV-infected cells are discussed.
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Affiliation(s)
- J C Carrington
- Department of Biology, Texas A & M University, College Station 77843
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32
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Palkovics L, Burgyán J, Balázs E. Comparative sequence analysis of four complete primary structures of plum pox virus strains. Virus Genes 1993; 7:339-47. [PMID: 8122394 DOI: 10.1007/bf01703390] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The complete nucleotide sequence of plum pox virus (PPV) strain SK 68 was determined from a series of overlapping cDNA clones. The exact 5' terminus was determined by direct RNA sequencing. The RNA sequence was 9786 nucleotides in length, excluding a 3' terminal poly(A) sequence. The large open reading frame starts at nucleotide position 147 and is terminated at position 9568. Comparison of cistrons from other plum pox virus strains with those predicted for the SK 68 strain indicated the same genomic organizations. Comparison of sequences leads to the following conclusions: (1) The genetic organization of all four PPV strains is identical, containing one large polyprotein gene and two noncoding regions at the 5' and 3' ends; (2) pairwise comparison of the genomic sequence of PPV SK 68 with other PPV strains shows 11% alteration. Sequence differences among strains are spread in a uniform manner upon the genome, except for the P1, HC-pro, and two noncoding regions, which are more conserved (with a 4% and 6.6% change). The stability of the noncoding regions is probably linked to their role in replication. The sequence variation has little effect on the amino acid sequence of the corresponding polypeptides, as changes occur preferentially in the third position of the reading frame triplets, except in the case of the 5' end of the coat protein gene (2.7% average difference in amino acid level, while in the case of coat protein it is 7.7%).(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- L Palkovics
- Institute for Plant Sciences, Agricultural Biotechnology Center, Gödöllö, Hungary
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33
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Dougherty WG, Semler BL. Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes. Microbiol Rev 1993; 57:781-822. [PMID: 8302216 PMCID: PMC372939 DOI: 10.1128/mr.57.4.781-822.1993] [Citation(s) in RCA: 198] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Many viruses express their genome, or part of their genome, initially as a polyprotein precursor that undergoes proteolytic processing. Molecular genetic analyses of viral gene expression have revealed that many of these processing events are mediated by virus-encoded proteinases. Biochemical activity studies and structural analyses of these viral enzymes reveal that they have remarkable similarities to cellular proteinases. However, the viral proteinases have evolved unique features that permit them to function in a cellular environment. In this article, the current status of plant and animal virus proteinases is described along with their role in the viral replication cycle. The reactions catalyzed by viral proteinases are not simple enzyme-substrate interactions; rather, the processing steps are highly regulated, are coordinated with other viral processes, and frequently involve the participation of other factors.
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Affiliation(s)
- W G Dougherty
- Department of Microbiology, Oregon State University, Corvallis 97331-3804
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34
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Welch AR, McNally LM, Hall MR, Gibson W. Herpesvirus proteinase: site-directed mutagenesis used to study maturational, release, and inactivation cleavage sites of precursor and to identify a possible catalytic site serine and histidine. J Virol 1993; 67:7360-72. [PMID: 8230459 PMCID: PMC238200 DOI: 10.1128/jvi.67.12.7360-7372.1993] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The cytomegalovirus maturational proteinase is synthesized as a precursor that undergoes at least three processing cleavages. Two of these were predicted to be at highly conserved consensus sequences--one near the carboxyl end of the precursor, called the maturational (M) site, and the other near the middle of the precursor, called the release (R) site. A third less-well-conserved cleavage site, called the inactivation (I) site, was also identified near the middle of the human cytomegalovirus 28-kDa assemblin homolog. We have used site-directed mutagenesis to verify all three predicted sequences in the simian cytomegalovirus proteinase, and have shown that the proteinase precursor is active without cleavage at these sites. We have also shown that the P4 tyrosine and the P2 lysine of the R site were more sensitive to substitution than the other R- and M-site residues tested: substitution of alanine for P4 tyrosine at the R site severely reduced cleavage at that site but not at the M site, and substitution of asparagine for lysine at P2 of the R site reduced M-site cleavage and nearly eliminated I-site cleavage but had little effect on R-site cleavage. With the exception of P1' serine, all R-site mutations hindered I-site cleavage, suggesting a role for the carboxyl end of assemblin in I-site cleavage. Pulse-chase radiolabeling and site-directed mutagenesis indicated that assemblin is metabolically unstable and is degraded by cleavage at its I site. Fourteen amino acid substitutions were also made in assemblin, the enzymatic amino half of the proteinase precursor. Among those tested, only 2 amino acids were identified as essential for activity: the single absolutely conserved serine and one of the two absolutely conserved histidines. When the highly conserved glutamic acid (Glu22) was substituted, the proteinase was able to cleave at the M and I sites but not at the R site, suggesting either a direct (e.g., substrate recognition) or indirect (e.g., protein conformation) role for this residue in determining substrate specificity.
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Affiliation(s)
- A R Welch
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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35
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García JA, Cervera MT, Riechmann JL, López-Otín C. Inhibitory effects of human cystatin C on plum pox potyvirus proteases. PLANT MOLECULAR BIOLOGY 1993; 22:697-701. [PMID: 8343605 PMCID: PMC7089253 DOI: 10.1007/bf00047410] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/1992] [Accepted: 03/24/1993] [Indexed: 05/22/2023]
Abstract
The effect of different protease inhibitors on the proteolytic processing of the plum pox potyvirus (PPV) polyprotein has been analyzed. Human cystatin C, an inhibitor of cysteine proteases, interfered with the autoprocessing of the viral papain-like cysteine protease HCPro. Unexpectedly, it also had an inhibitory effect on the autocatalytic cleavage of the Nla protease which, although it has a Cys residue in its active center, has been described as structurally related to serine proteases. Other protease inhibitors tested had no effect on any of the cleavage events analyzed.
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Affiliation(s)
- J A García
- Centro de Biología Molecular (CSIC-UAM)-Centro Nacional de Biotecnología, Campus de la Universidad Autónoma de Madrid, Spain
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36
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Restrepo-Hartwig MA, Carrington JC. Regulation of nuclear transport of a plant potyvirus protein by autoproteolysis. J Virol 1992; 66:5662-6. [PMID: 1501298 PMCID: PMC289134 DOI: 10.1128/jvi.66.9.5662-5666.1992] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The NIa proteinase encoded by tobacco etch potyvirus catalyzes six processing events, three of which occur by an autoproteolytic mechanism. Autoproteolysis is necessary to cleave the boundaries of both NIa and the 6-kDa protein, which is located adjacent to the N terminus of NIa in the viral polyprotein. As a consequence, NIa may exist in a free form or in a transient polyprotein form containing the 6-kDa protein. While the majority of NIa molecules localize to the nuclei of infected cells, a fraction of the NIa pool is attached covalently to the 5' terminus of genomic RNA in the cytoplasm. To determine whether the presence of the 6-kDa protein affects the nuclear transport properties of NIa, we have generated transgenic plants that express genes encoding a reporter enzyme, beta-glucuronidase (GUS), fused to NIa or NIa-containing polyproteins. The NIa/GUS fusion protein was detected by histochemical analysis in the nucleus. Similarly, an NIa/GUS fusion protein that arose by autoproteolysis of a 6-kDa/NIa/GUS polyprotein was found in the nucleus. In contrast, fusion protein consisting of 6-kDa/NIa/GUS, which failed to undergo proteolysis because of the presence of a Cys-to-Ala substitution in the proteolytic domain of NIa, was detected in the cytoplasm. The inhibition of NIa-mediated nuclear transport was not due to the Cys-to-Ala substitution, since this alteration had no effect on translocation in the absence of the 6-kDa protein. These results indicate that the 6-kDa protein impedes nuclear localization of NIa and suggest that subcellular transport of NIa may be regulated by autoproteolysis.
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37
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García JA, Martín MT, Cervera MT, Riechmann JL. Proteolytic processing of the plum pox potyvirus polyprotein by the NIa protease at a novel cleavage site. Virology 1992; 188:697-703. [PMID: 1585641 DOI: 10.1016/0042-6822(92)90524-s] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The expression of potyvirus genomic RNA takes place through translation of its unique long and functional open reading frame into a large polyprotein that undergoes extensive proteolytic processing. Most of the cleavages are performed by the virus-encoded NIa protease, which cuts the polyprotein at defined sites that are characterized by conserved heptapeptide sequences. We have demonstrated in vitro cleavage activity by the plum pox potyvirus (PPV) NIa protease at a novel site, previously identified by sequence analysis, thus allowing a further refinement of the potyviral genetic map. This novel site is located 52 amino acids upstream from the site corresponding to the N-terminus of the CI protein (the NIa cleavage site previously considered the closest to the beginning of the polyprotein). The specificity of the processing was demonstrated by its abolishment when the Gln at position -1 of the cleavage site was changed to His. This novel NIa cleavage site was only partially processed, a characteristic that was not altered when its heptapeptide sequence was modified to become that of the efficiently cleaved NIb-CP junction. On the contrary, substitutions at the nonconserved position +3 had notable effects, positive or negative, on the efficiency of processing. These results show the relevance of sequence and/or conformational context outside the conserved heptapeptide for modulating the cleavage reaction catalyzed by the NIa protease.
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Affiliation(s)
- J A García
- Centro de Biología Molecular (CSIC-UAM), Madrid, Spain
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38
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Abstract
The helper component-proteinase (HC-Pro) encoded by potyviruses functions to cleave the viral polyprotein by an autoproteolytic mechanism at the HC-Pro C-terminus. This protein belongs to a group of viral cysteine-type proteinases and has been shown previously to catalyze proteolysis between a Gly-Gly dipeptide. The amino acid sequence requirements surrounding the HC-Pro C-terminal cleavage site of the tobacco etch virus polyprotein have been investigated using site-directed mutagenesis and in vitro expression systems. A total of 51 polyprotein derivatives, each differing by the substitution of a single amino acid between the P5 and P2' positions, were tested for autoproteolytic activity. Substitutions of Tyr (P4), Val (P2), Gly (P1), and Gly (P1') were found to eliminate or nearly eliminate proteolysis. Substitutions of Thr (P5), Asn (P3), and Met (P2'), on the other hand, were permissive for proteolysis, although the apparent processing rates of some polyproteins containing these alterations were reduced. These results suggest that auto-recognition by HC-Pro involves the interaction of the enzymatic binding site with four amino acids surrounding the cleavage site. Comparison of the homologous sequences of five potyviral polyproteins revealed that the residues essential for processing are strictly conserved, whereas the nonessential residues are divergent. The relationship between HC-Pro and other viral and cellular cysteine-type proteinases is discussed.
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Affiliation(s)
- J C Carrington
- Department of Biology, Texas A&M University, College Station 77843
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39
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Hellen CU, Wimmer E. The role of proteolytic processing in the morphogenesis of virus particles. EXPERIENTIA 1992; 48:201-15. [PMID: 1740191 PMCID: PMC7087542 DOI: 10.1007/bf01923512] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proteinases are encoded by many RNA viruses, all retroviruses and several DNA viruses. They play essential roles at various stages in viral replication, including the coordinated assembly and maturation of virions. Most of these enzymes belong to one of three (Ser, Cys or Asp) of the four major classes of proteinases, and have highly substrate-selective and cleavage specific activities. They can be thought of as playing one of two general roles in viral morphogenesis. Structural proteins are encoded by retroviruses and many RNA viruses as part of large polyproteins. Their proteolytic release is a prerequisite to particle assembly; consequent structural rearrangement of the capsid domains serves to regulate and direct association and assembly of capsid subunits. The second general role of proteolysis is in assembly-dependent maturation of virus particles, which is accompanied by the acquisition of infectivity.
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Affiliation(s)
- C U Hellen
- Department of Microbiology, State University of New York, Stony Brook 11794-8631
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40
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Rodríguez-Cerezo E, Shaw JG. Two newly detected nonstructural viral proteins in potyvirus-infected cells. Virology 1991; 185:572-9. [PMID: 1962438 DOI: 10.1016/0042-6822(91)90527-i] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The existence of two viral RNA-encoded proteins in cells infected with tobacco vein mottling potyvirus (TVMV) has been demonstrated. One of the proteins (named 34K) maps at the N-terminus of the TVMV polyprotein and the other (42K) between the helper component and cylindrical inclusion proteins; both had previously been predicted in the consensus potyviral genetic map. The 34K and 42K coding regions of TVMV were cloned separately in a bacterial expression vector and the proteins were isolated from transformed Escherichia coli. These were used to raise polyclonal antibodies which reacted specifically with proteins of the expected size in immunoblots of extracts of TVMV-infected tobacco leaves and protoplasts. In addition to 42K, the anti-42K serum detected similar amounts of a second protein of apparent size 37 kDa that was absent in 42K-expressing bacteria. Both 34K and 42K were present predominantly in membrane-enriched fractions of extracts of TVMV-infected tobacco leaves. Computer analysis of the deduced amino acid sequence of 42K suggests that this viral protein may be an integral transmembrane protein.
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41
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Verchot J, Koonin EV, Carrington JC. The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase. Virology 1991; 185:527-35. [PMID: 1962435 DOI: 10.1016/0042-6822(91)90522-d] [Citation(s) in RCA: 140] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The polyprotein encoded by plant potyviruses is proteolytically processed to at least eight mature products by viral-encoded proteinases. While the proteinases that catalyze processing at most of the cleavage sites have been identified, the enzyme responsible for cleavage between the 35-kDa protein and helper component-proteinase (HC-Pro), near the N-terminus of the viral polyprotein, has not been mapped or characterized previously. Polyproteins containing the 35-kDa protein and HC-Pro were synthesized in the wheat germ system using defined RNA transcripts and were demonstrated to undergo proteolysis to generate products that resemble fully processed proteins. The C-terminal half of the 35-kDa protein was found to be required for proteolysis, whereas most of the HC-Pro sequence was dispensable. Amino acid substitutions affecting three positions, each of which are conserved in the 35-kDa protein encoded by five potyviruses, were shown to inhibit protein processing. These data suggest that the 35-kDa protein functions as a proteinase to cleave at its C-terminus. A model that accounts for all proteolytic processing events in the potyviral polyprotein is presented.
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Affiliation(s)
- J Verchot
- Department of Biology, Texas A&M University, College Station 77843
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42
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Dougherty WG, Parks TD. Post-translational processing of the tobacco etch virus 49-kDa small nuclear inclusion polyprotein: identification of an internal cleavage site and delimitation of VPg and proteinase domains. Virology 1991; 183:449-56. [PMID: 1853555 DOI: 10.1016/0042-6822(91)90974-g] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The 49,000-dalton (49-kDa) small nuclear inclusion (NI) protein of tobacco etch virus (TEV) has two distinct functions associated with it. An N-terminal segment is covalently attached to the genomic length RNA and likely involved in RNA replication, while the C-terminal half is associated with a proteolytic activity critical for genome expression. The junction delineating these two proteins has not been identified. We have analyzed naturally occurring cleavage products of TEV NI proteins and have identified a possible internal cleavage site between Glu and Gly residues at TEV 49-kDa NI protein amino acids 189-190. Similar 49-kDa-derived products are formed in cell-free translation studies in minor amounts upon the addition of excess amounts of NI protein. Cleavage of the 49-kDa (430 amino acids) protein is predicted to result in the formation of two products, 21-kDa (189 amino acids) and 27 kDa (241 amino acids) in size. Complementary DNA encoding the 27-kDa C-terminal portion of the 49-kDa protein gene was cloned into various DNA sequences. This allowed us to express the 27-kDa protein alone or as part of higher molecular weight polyproteins containing flanking TEV or foreign protein sequences. This 27-kDa amino acid sequence had a proteolytic activity similar to the 49-kDa-associated activity.
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Affiliation(s)
- W G Dougherty
- Department of Microbiology, Oregon State University, Corvallis 97331-3804
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43
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Parks TD, Dougherty WG. Substrate recognition by the NIa proteinase of two potyviruses involves multiple domains: characterization using genetically engineered hybrid proteinase molecules. Virology 1991; 182:17-27. [PMID: 2024462 DOI: 10.1016/0042-6822(91)90643-p] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The proteolytic activity associated with the small nuclear inclusion protein (NIa proteinase) of tobacco etch virus (TEV), a potyvirus, catalyzes several cleavages at sites within the polyprotein derived from the TEV RNA genome. The homologous proteinase of tobacco vein mottling virus (TVMV), a closely related potyvirus, cleaves at similar, yet distinct, recognition sites. We examined these proteinases, in a cell-free cleavage system, in an attempt to define the biochemical basis of substrate specificity. Each proteinase was specific for its own cleavage site sequence in cell-free trans processing reactions, and no processing of the heterologous cleavage site was evident. Domains of the proteinase which were important in determining this substrate specificity were identified by generating hybrid proteinase genes containing both TEV and TVMV NIa proteinase coding sequences. Using site-directed mutagenesis and standard recombinant DNA techniques, plasmids were constructed which contained coding sequences for hybrid TEV-TVMV proteinases. These plasmids were expressed and tested in a cell-free environment for their ability to cleave both TEV and TVMV substrates. The data suggest that the carboxy-terminal 150 amino acids of the NIa protein contain the necessary information to specifically recognize a particular cleavage site sequence, and that specificity determinants are contained in at least three interactive subdomains within this region.
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Affiliation(s)
- T D Parks
- Department of Microbiology, Oregon State University, Corvallis 97331-3804
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44
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Abstract
Plasmids encoding chimeric NIa-type proteases made of sequences from the potyviruses plum pox virus (PPV) and tobacco etch virus (TEV) have been constructed. Their proteolytic activity on the large nuclear inclusion protein (NIb)-capsid protein (CP) junction of each virus was assayed in Escherichia coli cells. The amino half of the protease seemed to be involved neither in the enzymatic catalysis nor in substrate recognition. In spite of the large homology among the PPV and TEV NIa-type proteases, the exchange of fragments from the carboxyl halves of the molecules usually caused a drastic decrease in the enzymatic activity. Inactive chimeric proteases did not interfere with cleavage by PPV wild type protease expressed from a second plasmid. The results suggest that the recognition and catalytic sites of the NIa proteases are closely interlinked and, although residues relevant for the correct interaction with the substrate could be present in other parts of the protein, a main determinant for substrate specificity should lie in a region situated, approximately, between positions 30 and 90 from the carboxyl end. This region includes the conserved His at position 360 of PPV or 355 of TEV, which has been postulated to interact with the Gln at position -1 of the cleavage sites.
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Affiliation(s)
- J A García
- Centro de Biología Molecular (CSIC-UAM), Universidad Autónoma de Madrid, Spain
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45
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Hellen CU, Kräusslich HG, Wimmer E. Proteolytic processing of polyproteins in the replication of RNA viruses. Biochemistry 1989; 28:9881-90. [PMID: 2695162 DOI: 10.1021/bi00452a001] [Citation(s) in RCA: 133] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C U Hellen
- Department of Microbiology, School of Medicine, State University of New York, Stony Brook 11794
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