1
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Dutta A, Szekely Z, Guven H, Li XP, McLaughlin JE, Tumer NE. A fluorescence anisotropy-based competition assay to identify inhibitors against ricin and Shiga toxin ribosome interactions. Anal Biochem 2024; 692:115580. [PMID: 38825159 DOI: 10.1016/j.ab.2024.115580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
Ricin is one of the most toxic substances known and a type B biothreat agent. Shiga toxins (Stxs) produced by E. coli (STEC) and Shigella dysenteriae are foodborne pathogens. There is no effective therapy against ricin or STEC and there is an urgent need for inhibitors. Ricin toxin A subunit (RTA) and A1 subunit of Stx2a (Stx2A1) bind to the C-terminal domain (CTD) of the ribosomal P-stalk proteins to depurinate the sarcin/ricin loop. Modulation of toxin-ribosome interactions has not been explored as a strategy for inhibition. Therefore, development of assays that detect inhibitors targeting toxin-ribosome interactions remains a critical need. Here we describe a fluorescence anisotropy (FA)-based competitive binding assay using a BODIPY-TMR labeled 11-mer peptide (P11) derived from the P-stalk CTD to measure the binding affinity of peptides ranging from 3 to 11 amino acids for the P-stalk pocket of RTA and Stx2A1. Comparison of the affinity with the surface plasmon resonance (SPR) assay indicated that although the rank order was the same by both methods, the FA assay could differentiate better between peptides that show nonspecific interactions by SPR. The FA assay detects only interactions that compete with the labeled P11 and can validate inhibitor specificity and mechanism of action.
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Affiliation(s)
- Arkajyoti Dutta
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Zoltan Szekely
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ, 08854, USA
| | - Hakan Guven
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ, 08854, USA
| | - Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ, 08901, USA.
| | - John E McLaughlin
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Nilgun E Tumer
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ, 08854, USA.
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2
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Li XP, Rudolph MJ, Chen Y, Tumer NE. Structure-Function Analysis of the A1 Subunit of Shiga Toxin 2 with Peptides That Target the P-Stalk Binding Site and Inhibit Activity. Biochemistry 2024; 63:893-905. [PMID: 38467020 DOI: 10.1021/acs.biochem.3c00733] [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: 03/13/2024]
Abstract
Shiga toxin 2a (Stx2a) is the virulence factor of Escherichia coli (STEC), which is associated with hemolytic uremic syndrome, the leading cause of pediatric kidney failure. The A1 subunit of Stx2a (Stx2A1) binds to the conserved C-terminal domain (CTD) of the ribosomal P-stalk proteins to remove an adenine from the sarcin-ricin loop (SRL) in the 28S rRNA, inhibiting protein synthesis. There are no antidotes against Stx2a or any other ribosome-inactivating protein (RIP). The structural and functional details of the binding of Stx2A1 to the P-stalk CTD are not known. Here, we carry out a deletion analysis of the conserved P-stalk CTD and show that the last eight amino acids (P8) of the P-stalk proteins are the minimal sequence required for optimal affinity and maximal inhibitory activity against Stx2A1. We determined the first X-ray crystal structure of Stx2A1 alone and in complex with P8 and identified the exact binding site. The C-terminal aspartic acid of the P-stalk CTD serves as an anchor, forming key contacts with the conserved arginine residues at the P-stalk binding pocket of Stx2A1. Although the ricin A subunit (RTA) binds to the P-stalk CTD, the last aspartic acid is more critical for the interaction with Stx2A1, indicating that RIPs differ in their requirements for the P-stalk. These results demonstrate that the catalytic activity of Stx2A1 is inhibited by blocking its interactions with the P-stalk, providing evidence that P-stalk binding is an essential first step in the recruitment of Stx2A1 to the SRL for depurination.
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Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Michael J Rudolph
- New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, United States
| | - Yang Chen
- New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, United States
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
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3
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Rudolph MJ, Dutta A, Tsymbal AM, McLaughlin JE, Chen Y, Davis SA, Theodorous SA, Pierce M, Algava B, Zhang X, Szekely Z, Roberge JY, Li XP, Tumer NE. Structure-based design and optimization of a new class of small molecule inhibitors targeting the P-stalk binding pocket of ricin. Bioorg Med Chem 2024; 100:117614. [PMID: 38340640 DOI: 10.1016/j.bmc.2024.117614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Ricin, a category-B agent for bioterrorism, and Shiga toxins (Stxs), which cause food poisoning bind to the ribosomal P-stalk to depurinate the sarcin/ricin loop. No effective therapy exists for ricin or Stx intoxication. Ribosome binding sites of the toxins have not been targeted by small molecules. We previously identified CC10501, which inhibits toxin activity by binding the P-stalk pocket of ricin toxin A subunit (RTA) remote from the catalytic site. Here, we developed a fluorescence polarization assay and identified a new class of compounds, which bind P-stalk pocket of RTA with higher affinity and inhibit catalytic activity with submicromolar potency. A lead compound, RU-NT-206, bound P-stalk pocket of RTA with similar affinity as a five-fold larger P-stalk peptide and protected cells against ricin and Stx2 holotoxins for the first time. These results validate the P-stalk binding site of RTA as a critical target for allosteric inhibition of the active site.
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Affiliation(s)
- Michael J Rudolph
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Arkajyoti Dutta
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Anastasiia M Tsymbal
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ 08854, United States
| | - John E McLaughlin
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Yang Chen
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Simon A Davis
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Sophia A Theodorous
- New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, United States
| | - Michael Pierce
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Benjamin Algava
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Xiaoyu Zhang
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States
| | - Zoltan Szekely
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ 08854, United States
| | - Jacques Y Roberge
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Rd, Piscataway, NJ 08854, United States
| | - Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States.
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, United States.
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di Leandro L, Colasante M, Pitari G, Ippoliti R. Hosts and Heterologous Expression Strategies of Recombinant Toxins for Therapeutic Purposes. Toxins (Basel) 2023; 15:699. [PMID: 38133203 PMCID: PMC10748335 DOI: 10.3390/toxins15120699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
The production of therapeutic recombinant toxins requires careful host cell selection. Bacteria, yeast, and mammalian cells are common choices, but no universal solution exists. Achieving the delicate balance in toxin production is crucial due to potential self-intoxication. Recombinant toxins from various sources find applications in antimicrobials, biotechnology, cancer drugs, and vaccines. "Toxin-based therapy" targets diseased cells using three strategies. Targeted cancer therapy, like antibody-toxin conjugates, fusion toxins, or "suicide gene therapy", can selectively eliminate cancer cells, leaving healthy cells unharmed. Notable toxins from various biological sources may be used as full-length toxins, as plant (saporin) or animal (melittin) toxins, or as isolated domains that are typical of bacterial toxins, including Pseudomonas Exotoxin A (PE) and diphtheria toxin (DT). This paper outlines toxin expression methods and system advantages and disadvantages, emphasizing host cell selection's critical role.
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Affiliation(s)
| | | | | | - Rodolfo Ippoliti
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (L.d.L.); (M.C.); (G.P.)
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5
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Cryo-EM structure of Shiga toxin 2 in complex with the native ribosomal P-stalk reveals residues involved in the binding interaction. J Biol Chem 2022; 299:102795. [PMID: 36528064 PMCID: PMC9823235 DOI: 10.1016/j.jbc.2022.102795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Shiga toxin 2a (Stx2a) is the virulence factor of enterohemorrhagic Escherichia coli. The catalytic A1 subunit of Stx2a (Stx2A1) interacts with the ribosomal P-stalk for loading onto the ribosome and depurination of the sarcin-ricin loop, which halts protein synthesis. Because of the intrinsic flexibility of the P-stalk, a structure of the Stx2a-P-stalk complex is currently unknown. We demonstrated that the native P-stalk pentamer binds to Stx2a with nanomolar affinity, and we employed cryo-EM to determine a structure of the 72 kDa Stx2a complexed with the P-stalk. The structure identifies Stx2A1 residues involved in binding and reveals that Stx2a is anchored to the P-stalk via only the last six amino acids from the C-terminal domain of a single P-protein. For the first time, the cryo-EM structure shows the loop connecting Stx2A1 and Stx2A2, which is critical for activation of the toxin. Our principal component analysis of the cryo-EM data reveals the intrinsic dynamics of the Stx2a-P-stalk interaction, including conformational changes in the P-stalk binding site occurring upon complex formation. Our computational analysis unveils the propensity for structural rearrangements within the C-terminal domain, with its C-terminal six amino acids transitioning from a random coil to an α-helix upon binding to Stx2a. In conclusion, our cryo-EM structure sheds new light into the dynamics of the Stx2a-P-stalk interaction and indicates that the binding interface between Stx2a and the P-stalk is the potential target for drug discovery.
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6
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Lu JQ, Wong KB, Shaw PC. A Sixty-Year Research and Development of Trichosanthin, a Ribosome-Inactivating Protein. Toxins (Basel) 2022; 14:toxins14030178. [PMID: 35324675 PMCID: PMC8950148 DOI: 10.3390/toxins14030178] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/04/2023] Open
Abstract
Tian Hua Fen, a herbal powder extract that contains trichosanthin (TCS), was used as an abortifacient in traditional Chinese medicine. In 1972, TCS was purified to alleviate the side effects. Because of its clinical applications, TCS became one of the most active research areas in the 1960s to the 1980s in China. These include obtaining the sequence information in the 1980s and the crystal structure in 1995. The replication block of TCS on human immunodeficiency virus in lymphocytes and macrophages was found in 1989 and started a new chapter of its development. Clinical studies were subsequently conducted. TCS was also found to have the potential for gastric and colorectal cancer treatment. Studies on its mechanism showed TCS acts as an rRNA N-glycosylase (EC 3.2.2.22) by hydrolyzing and depurinating A-4324 in α-sarcin/ricin loop on 28S rRNA of rat ribosome. Its interaction with acidic ribosomal stalk proteins was revealed in 2007, and its trafficking in mammalian cells was elucidated in the 2000s. The adverse drug reactions, such as inducing immune responses, short plasma half-life, and non-specificity, somehow became the obstacles to its usage. Immunotoxins, sequence modification, or coupling with polyethylene glycerol and dextran were developed to improve the pharmacological properties. TCS has nicely shown the scientific basis of traditional Chinese medicine and how its research and development have expanded the knowledge and applications of ribosome-inactivating proteins.
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Affiliation(s)
- Jia-Qi Lu
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (J.-Q.L.); (K.-B.W.)
| | - Kam-Bo Wong
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (J.-Q.L.); (K.-B.W.)
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (J.-Q.L.); (K.-B.W.)
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Correspondence:
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7
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Czajka TF, Vance DJ, Davis S, Rudolph MJ, Mantis NJ. Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins. J Biol Chem 2022; 298:101742. [PMID: 35182523 PMCID: PMC8941211 DOI: 10.1016/j.jbc.2022.101742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 12/27/2022] Open
Abstract
During ricin intoxication in mammalian cells, ricin's enzymatic (RTA) and binding (RTB) subunits disassociate in the endoplasmic reticulum. RTA is then translocated into the cytoplasm where, by virtue of its ability to depurinate a conserved residue within the sarcin-ricin loop (SRL) of 28S rRNA, it functions as a ribosome-inactivating protein. It has been proposed that recruitment of RTA to the SRL is facilitated by ribosomal P-stalk proteins, whose C-terminal domains interact with a cavity on RTA normally masked by RTB; however, evidence that this interaction is critical for RTA activity within cells is lacking. Here, we characterized a collection of single-domain antibodies (VHHs) whose epitopes overlap with the P-stalk binding pocket on RTA. The crystal structures of three such VHHs (V9E1, V9F9, and V9B2) in complex with RTA revealed not only occlusion of the ribosomal P-stalk binding pocket but also structural mimicry of C-terminal domain peptides by complementarity-determining region 3. In vitro assays confirmed that these VHHs block RTA-P-stalk peptide interactions and protect ribosomes from depurination. Moreover, when expressed as "intrabodies," these VHHs rendered cells resistant to ricin intoxication. One VHH (V9F6), whose epitope was structurally determined to be immediately adjacent to the P-stalk binding pocket, was unable to neutralize ricin within cells or protect ribosomes from RTA in vitro. These findings are consistent with the recruitment of RTA to the SRL by ribosomal P-stalk proteins as a requisite event in ricin-induced ribosome inactivation.
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Affiliation(s)
- Timothy F Czajka
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - David J Vance
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA; Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Simon Davis
- New York Structural Biology Center, New York, New York, USA
| | | | - Nicholas J Mantis
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA; Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
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8
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Abstract
Ricin is a plant-derived toxin with a history as a biothreat agent. The toxin's enzymatic subunit, ricin toxin A chain (RTA), is a ribosome-inactivating protein that, when delivered into the cytoplasm of mammalian cells, arrests protein synthesis with extraordinary efficiency. Once within the cytoplasm, RTA is shielded from circulating toxin-neutralizing antibodies. Here, we describe methods we developed to neutralize RTA within the cytoplasm of Vero cells using DNA-based delivery of alpaca-derived single-domain antibodies (VHHs) targeting RTA's active site. We describe the design of the VHH expression vectors, assessment of transient expression of VHHs in Vero cells by enzyme-linked immunosorbent assay and western blotting, and cytotoxicity studies. While the protocols here are specific to ricin, they are easily modified for other toxins or even intracellular pathogens such as viruses.
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Affiliation(s)
- Timothy F Czajka
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, USA
| | - Nicholas J Mantis
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, USA.
- Division of Infectious Diseases, New York State Department of Health, Wadsworth Center, Albany, NY, USA.
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9
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Li XP, Harijan RK, Cao B, Kahn JN, Pierce M, Tsymbal AM, Roberge JY, Augeri D, Tumer NE. Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design. J Med Chem 2021; 64:15334-15348. [PMID: 34648707 PMCID: PMC10704857 DOI: 10.1021/acs.jmedchem.1c01370] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ricin toxin A subunit (RTA) is the catalytic subunit of ricin, which depurinates an adenine from the sarcin/ricin loop in eukaryotic ribosomes. There are no approved inhibitors against ricin. We used a new strategy to disrupt RTA-ribosome interactions by fragment screening using surface plasmon resonance. Here, using a structure-guided approach, we improved the affinity and inhibitory activity of small-molecular-weight lead compounds and obtained improved compounds with over an order of magnitude higher efficiency. Four advanced compounds were characterized by X-ray crystallography. They bind at the RTA-ribosome binding site as the original compound but in a distinctive manner. These inhibitors bind remotely from the catalytic site and cause local conformational changes with no alteration of the catalytic site geometry. Yet they inhibit depurination by ricin holotoxin and inhibit the cytotoxicity of ricin in mammalian cells. They are the first agents that protect against ricin holotoxin by acting directly on RTA.
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Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Bin Cao
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jennifer N Kahn
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Michael Pierce
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Anastasiia M Tsymbal
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jacques Y Roberge
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - David Augeri
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
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10
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Horbowicz-Drożdżal P, Kamel K, Kmiecik S, Borkiewicz L, Tumer NE, Shaw PC, Tchórzewski M, Grela P. Phosphorylation of the conserved C-terminal domain of ribosomal P-proteins impairs the mode of interaction with plant toxins. FEBS Lett 2021; 595:2221-2236. [PMID: 34328639 DOI: 10.1002/1873-3468.14170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 11/12/2022]
Abstract
The ribosome is subjected to post-translational modifications, including phosphorylation, that affect its biological activity. Among ribosomal elements, the P-proteins undergo phosphorylation within the C terminus, the element which interacts with trGTPases or ribosome-inactivating proteins (RIPs); however, the role of phosphorylation has never been elucidated. Here, we probed the function of phosphorylation on the interaction of P-proteins with RIPs using the ribosomal P1-P2 dimer. We determined the kinetic parameters of the interaction with the toxins using biolayer interferometry and microscale thermophoresis. The results present the first mechanistic insight into the function of P-protein phosphorylation, showing that introduction of a negative charge into the C terminus of P1-P2 proteins promotes α-helix formation and decreases the affinity of the P-proteins for the RIPs.
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Affiliation(s)
- Patrycja Horbowicz-Drożdżal
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Karol Kamel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Poland
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Poland
| | - Nilgun E Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Pang-Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, China
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Grela
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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11
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Rudolph MJ, Davis SA, Tumer NE, Li XP. Structural basis for the interaction of Shiga toxin 2a with a C-terminal peptide of ribosomal P stalk proteins. J Biol Chem 2020; 295:15588-15596. [PMID: 32878986 PMCID: PMC7667979 DOI: 10.1074/jbc.ac120.015070] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
The principal virulence factor of human pathogenic enterohemorrhagic Escherichia coli is Shiga toxin (Stx). Shiga toxin 2a (Stx2a) is the subtype most commonly associated with severe disease outcomes such as hemorrhagic colitis and hemolytic uremic syndrome. The catalytic A1 subunit (Stx2A1) binds to the conserved elongation factor binding C-terminal domain (CTD) of ribosomal P stalk proteins to inhibit translation. Stx2a holotoxin also binds to the CTD of P stalk proteins because the ribosome-binding site is exposed. We show here that Stx2a binds to an 11-mer peptide (P11) mimicking the CTD of P stalk proteins with low micromolar affinity. We cocrystallized Stx2a with P11 and defined their interactions by X-ray crystallography. We found that the last six residues of P11 inserted into a shallow pocket on Stx2A1 and interacted with Arg-172, Arg-176, and Arg-179, which were previously shown to be critical for binding of Stx2A1 to the ribosome. Stx2a formed a distinct P11-binding mode within a different surface pocket relative to ricin toxin A subunit and trichosanthin, suggesting different ribosome recognition mechanisms for each ribosome inactivating protein (RIP). The binding mode of Stx2a to P11 is also conserved among the different Stx subtypes. Furthermore, the P stalk protein CTD is flexible and adopts distinct orientations and interaction modes depending on the structural differences between the RIPs. Structural characterization of the Stx2a-ribosome complex is important for understanding the role of the stalk in toxin recruitment to the sarcin/ricin loop and may provide a new target for inhibitor discovery.
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Affiliation(s)
| | - Simon A. Davis
- New York Structural Biology Center, New York, New York, USA
| | - Nilgun E. Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA,For correspondence: Xiao-Ping Li, ; Nilgun E. Tumer,
| | - Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA,For correspondence: Xiao-Ping Li, ; Nilgun E. Tumer,
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12
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Leucine 232 and hydrophobic residues at the ribosomal P stalk binding site are critical for biological activity of ricin. Biosci Rep 2020; 39:BSR20192022. [PMID: 31548364 PMCID: PMC6822507 DOI: 10.1042/bsr20192022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 01/16/2023] Open
Abstract
Ricin interacts with the ribosomal P stalk to cleave a conserved adenine from the α-sarcin/ricin loop (SRL) of the rRNA. Ricin toxin A chain (RTA) uses Arg235 as the most critical arginine for binding to the P stalk through electrostatic interactions to facilitate depurination. Structural analysis showed that a P2 peptide binds to a hydrophobic pocket on RTA and the last two residues form hydrogen bonds with Arg235. The importance of hydrophobic residues relative to Arg235 in the interaction with the P stalk in vivo and on the toxicity of RTA is not known. Here, we mutated residues in the hydrophobic pocket to analyze their contribution to toxicity and depurination activity in yeast and in mammalian cells. We found that Leu232, Tyr183 and Phe240 contribute cumulatively to toxicity, with Leu232 being the most significant. A quadruple mutant, Y183A/L232A/R235A/F240A, which combined mutations in critical hydrophobic residues with R235A completely abolished the activity of RTA, indicating that Arg235 and hydrophobic residues are required for full biological activity. Y183A and F240A mutants had reduced activity on RNA, but higher activity on ribosomes compared with R235A in vitro, suggesting that they could partially regain activity upon interaction with ribosomes. These results expand the region of interaction between RTA and the P stalk critical for cellular activity to include the hydrophobic pocket and provide the first evidence that interaction of P stalk with the hydrophobic pocket promotes a conformational rearrangement of RTA to correctly position the active site residues for catalytic attack on the SRL.
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Li XP, Harijan RK, Kahn JN, Schramm VL, Tumer NE. Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes. ACS Infect Dis 2020; 6:1894-1905. [PMID: 32428396 DOI: 10.1021/acsinfecdis.0c00127] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Ricin toxin A subunit (RTA) removes an adenine from the universally conserved sarcin/ricin loop (SRL) on eukaryotic ribosomes, thereby inhibiting protein synthesis. No high affinity and selective small molecule therapeutic antidotes have been reported against ricin toxicity. RTA binds to the ribosomal P stalk to access the SRL. The interaction anchors RTA to the P protein C-termini at a well-defined hydrophobic pocket, which is on the opposite face relative to the active site. The RTA ribosome binding site has not been previously targeted by small molecule inhibitors. We used fragment screening with surface plasmon resonance to identify small molecular weight lead compounds that bind RTA and defined their interactions by crystallography. We identified five fragments, which bound RTA with mid-micromolar affinity. Three chemically distinct binding fragments were cocrystallized with RTA, and crystal structures were solved. Two fragments bound at the P stalk binding site, and the third bound to helix D, a motif distinct from the P stalk binding site. All fragments bound RTA remote from the catalytic site and caused little change in catalytic site geometry. Two fragments uniquely bound at the hydrophobic pocket with affinity sufficient to inhibit the catalytic activity on eukaryotic ribosomes in the low micromolar range. The binding mode of these inhibitors mimicked the interaction of the P stalk peptide, establishing that small molecule inhibitors can inhibit RTA binding to the ribosome with the potential for therapeutic intervention.
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Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Rajesh K. Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus,1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Jennifer N. Kahn
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus,1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Nilgun E. Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
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Fan X, Wang Y, Guo F, Zhang Y, Jin T. Atomic-resolution structures of type I ribosome inactivating protein alpha-momorcharin with different substrate analogs. Int J Biol Macromol 2020; 164:265-276. [PMID: 32653369 DOI: 10.1016/j.ijbiomac.2020.07.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/26/2020] [Accepted: 07/03/2020] [Indexed: 10/23/2022]
Abstract
Alpha-momorcharin (Alpha-MMC) from the seed of bitter melon is a type I ribosome inactivating protein (RIP) that removes a specific adenine from 28S rRNA and inhibits protein biosynthesis. Here, we report seven crystal complex structures of alpha-MMC with different substrate analogs (adenine, AMP, cAMP, dAMP, ADP, GMP, and xanthosine) at 1.08 Å to 1.52 Å resolution. These structures reveal that not only adenine, but also guanine and their analogs can effectively bind to alpha-MMC. The side chain of Tyr93 adopts two conformations, serving as a switch to open and close the substrate binding pocket of alpha-MMC. Although adenine, AMP, GMP, and guanine are located in a similar active site in different RIPs, residues involved in the interaction between RIPs and substrate analogs are slightly different. Complex structures of alpha-MMC with different substrate analogs solved in this study provide useful information on its enzymatic mechanisms and may enable the development of new inhibitors to treat the poisoning of alpha-MMC.
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Affiliation(s)
- Xiaojiao Fan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Yang Wang
- Department of Biology, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA
| | - Feng Guo
- Department of Biology, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA
| | - Yuzhu Zhang
- Department of Biology, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA; Processed Foods Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China; Department of Biology, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA.
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15
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Jiao Z, Ke Y, Li S, Su D, Gan C, Hu L, Zhao X, Gao B, Song Y, Zhou D, Qiu Y, Yang H. Pretreatment with Retro-2 protects cells from death caused by ricin toxin by retaining the capacity of protein synthesis. J Appl Toxicol 2020; 40:1440-1450. [PMID: 32474962 DOI: 10.1002/jat.3997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/14/2020] [Accepted: 04/19/2020] [Indexed: 12/21/2022]
Abstract
The current study explores the detoxification effect of Retro-2 on ricin toxin (RT) cytotoxicity, as well as the mechanisms underlying such effects, to provide a basis for follow-up clinical applications of Retro-2. The mouse-derived mononuclear/macrophage cell line, RAW264.7, was used to evaluate the detoxification effect of Retro-2 on RT by detecting cell viability, capacity for protein synthesis and the expression of cytokines, as well as endoplasmic reticulum stress (ERS)-related mRNA. The results indicated that many cells died when challenged with concentrations of RT ≥50ng/mL. The protein synthesis capacity of cells decreased when challenged with 200ng/mL RT for 2hours. Furthermore, the synthesis and release of many cytokines decreased, while the expression of cytokines or ERS-related mRNA increased when challenged with 200ng/mL of RT for 12 or more hours. However, cell viability, capacity for protein synthesis and release levels of many cytokines were higher, while the expression levels of cytokine, or ERS-related mRNA, were lower in cells pretreated with 20μm Retro-2 and challenged with RT, compared with those that had not been pretreated with Retro-2. In conclusion, Retro-2 retained the capacity for protein synthesis inhibited by RT, alleviated ERS induced by RT and increased the viability of cells challenged with RT. Retro-2 shows the potential for clinical applications.
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Affiliation(s)
- Zhouguang Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuehua Ke
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Sha Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Duo Su
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Changjiao Gan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaodong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yefeng Qiu
- Laboratory Animal Center, Academy of Military Medical Science, Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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16
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Szajwaj M, Wawiórka L, Molestak E, Michalec-Wawiórka B, Mołoń M, Wojda I, Tchórzewski M. The influence of ricin-mediated rRNA depurination on the translational machinery in vivo - New insight into ricin toxicity. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118554. [DOI: 10.1016/j.bbamcr.2019.118554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/10/2019] [Accepted: 09/04/2019] [Indexed: 11/29/2022]
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17
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Choi KHA, Yang L, Lee KM, Yu CWH, Banfield DK, Ito K, Uchiumi T, Wong KB. Structural and Mutagenesis Studies Evince the Role of the Extended Protuberant Domain of Ribosomal Protein uL10 in Protein Translation. Biochemistry 2019; 58:3744-3754. [PMID: 31419120 DOI: 10.1021/acs.biochem.9b00528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lateral stalk of ribosomes constitutes the GTPase-associated center and is responsible for recruiting translation factors to the ribosomes. The eukaryotic stalk contains a P-complex, in which one molecule of uL10 (formerly known as P0) protein binds two copies of P1/P2 heterodimers. Unlike bacterial uL10, eukaryotic uL10 has an extended protuberant (uL10ext) domain inserted into the N-terminal RNA-binding domain. Here, we determined the solution structure of the extended protuberant domain of Bombyx mori uL10 by nuclear magnetic resonance spectroscopy. Comparison of the structures of the B. mori uL10ext domain with eRF1-bound and eEF2-bound ribosomes revealed significant structural rearrangement in a "hinge" region surrounding Phe183, a residue conserved in eukaryotic but not in archaeal uL10. 15N relaxation analyses showed that residues in the hinge region have significantly large values of transverse relaxation rates. To test the role of the conserved phenylalanine residue, we created a yeast mutant strain expressing an F181A variant of uL10. An in vitro translation assay showed that the alanine substitution increased the level of polyphenylalanine synthesis by ∼33%. Taken together, our results suggest that the hinge motion of the uL10ext domain facilitates the binding of different translation factors to the GTPase-associated center during protein synthesis.
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Affiliation(s)
- Kwok-Ho Andrew Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - Lei Yang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - Conny Wing-Heng Yu
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - David K Banfield
- Division of Life Science , Hong Kong University of Science and Technology , Clear Water Bay , Hong Kong , China
| | - Kosuke Ito
- Department of Biology, Faculty of Science , Niigata University , Ikarashi 2-8050 , Nishi-ku, Niigata 950-2191 , Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science , Niigata University , Ikarashi 2-8050 , Nishi-ku, Niigata 950-2191 , Japan
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
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Intracellular Transport and Cytotoxicity of the Protein Toxin Ricin. Toxins (Basel) 2019; 11:toxins11060350. [PMID: 31216687 PMCID: PMC6628406 DOI: 10.3390/toxins11060350] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022] Open
Abstract
Ricin can be isolated from the seeds of the castor bean plant (Ricinus communis). It belongs to the ribosome-inactivating protein (RIP) family of toxins classified as a bio-threat agent due to its high toxicity, stability and availability. Ricin is a typical A-B toxin consisting of a single enzymatic A subunit (RTA) and a binding B subunit (RTB) joined by a single disulfide bond. RTA possesses an RNA N-glycosidase activity; it cleaves ribosomal RNA leading to the inhibition of protein synthesis. However, the mechanism of ricin-mediated cell death is quite complex, as a growing number of studies demonstrate that the inhibition of protein synthesis is not always correlated with long term ricin toxicity. To exert its cytotoxic effect, ricin A-chain has to be transported to the cytosol of the host cell. This translocation is preceded by endocytic uptake of the toxin and retrograde traffic through the trans-Golgi network (TGN) and the endoplasmic reticulum (ER). In this article, we describe intracellular trafficking of ricin with particular emphasis on host cell factors that facilitate this transport and contribute to ricin cytotoxicity in mammalian and yeast cells. The current understanding of the mechanisms of ricin-mediated cell death is discussed as well. We also comment on recent reports presenting medical applications for ricin and progress associated with the development of vaccines against this toxin.
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Integrative transcriptomics, proteomics, and metabolomics data analysis exploring the injury mechanism of ricin on human lung epithelial cells. Toxicol In Vitro 2019; 60:160-172. [PMID: 31103672 DOI: 10.1016/j.tiv.2019.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/05/2019] [Accepted: 05/15/2019] [Indexed: 11/24/2022]
Abstract
Ricin (RT) is a plant toxin belonging to the family of type II ribosome-inactivating protein with high bioterrorism potential. Aerosol RT exposure is the most lethal route, but its mechanism of injury needs further investigation. In the present study, we performed a comprehensive transcriptomics, proteomics and metabolomics analysis on the potential mechanism of injury caused by RT on human lung epithelial cells. In total, 5872 genes, 187 proteins, and 143 metabolites were shown to be significantly changed in human lung epithelial cells after RT treatment. Molecular function, pathway, and network analyses, the genes and proteins regulated in RT-treated cells were mainly attributed to fatty acid metabolism, arginine and proline metabolism and ubiquitin-mediated proteolysis pathway. Furthermore, a comprehensive analysis of transcripts, proteins, and metabolites was performed. The results revealed the correlated genes, proteins, and metabolic pathways regulated in metabolic pathways, amino acid metabolism, transcription and energy metabolism. These genes, proteins, and metabolites involved in these dis-regulated pathways may provide a more targeted and credible direction to study the mechanism of RT injury on human lung epithelial cells. This study provides large-scale omics data that can be used to develop a new strategy for the prevention, rapid diagnosis, and treatment of RT poisoning, especially of RT aerosol.
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20
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How Ricin Damages the Ribosome. Toxins (Basel) 2019; 11:toxins11050241. [PMID: 31035546 PMCID: PMC6562825 DOI: 10.3390/toxins11050241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022] Open
Abstract
Ricin belongs to the group of ribosome-inactivating proteins (RIPs), i.e., toxins that have evolved to provide particular species with an advantage over other competitors in nature. Ricin possesses RNA N-glycosidase activity enabling the toxin to eliminate a single adenine base from the sarcin-ricin RNA loop (SRL), which is a highly conserved structure present on the large ribosomal subunit in all species from the three domains of life. The SRL belongs to the GTPase associated center (GAC), i.e., a ribosomal element involved in conferring unidirectional trajectory for the translational apparatus at the expense of GTP hydrolysis by translational GTPases (trGTPases). The SRL represents a critical element in the GAC, being the main triggering factor of GTP hydrolysis by trGTPases. Enzymatic removal of a single adenine base at the tip of SRL by ricin blocks GTP hydrolysis and, at the same time, impedes functioning of the translational machinery. Here, we discuss the consequences of SRL depurination by ricin for ribosomal performance, with emphasis on the mechanistic model overview of the SRL modus operandi.
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Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
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Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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22
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Li XP, Kahn JN, Tumer NE. Peptide Mimics of the Ribosomal P Stalk Inhibit the Activity of Ricin A Chain by Preventing Ribosome Binding. Toxins (Basel) 2018; 10:E371. [PMID: 30217009 PMCID: PMC6162817 DOI: 10.3390/toxins10090371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 11/27/2022] Open
Abstract
Ricin A chain (RTA) depurinates the sarcin/ricin loop (SRL) by interacting with the C-termini of the ribosomal P stalk. The ribosome interaction site and the active site are located on opposite faces of RTA. The interaction with P proteins allows RTA to depurinate the SRL on the ribosome at physiological pH with an extremely high activity by orienting the active site towards the SRL. Therefore, if an inhibitor disrupts RTA⁻ribosome interaction by binding to the ribosome binding site of RTA, it should inhibit the depurination activity. To test this model, we synthesized peptides mimicking the last 3 to 11 amino acids of P proteins and examined their interaction with wild-type RTA and ribosome binding mutants by Biacore. We measured the inhibitory activity of these peptides on RTA-mediated depurination of yeast and rat liver ribosomes. We found that the peptides interacted with the ribosome binding site of RTA and inhibited depurination activity by disrupting RTA⁻ribosome interactions. The shortest peptide that could interact with RTA and inhibit its activity was four amino acids in length. RTA activity was inhibited by disrupting its interaction with the P stalk without targeting the active site, establishing the ribosome binding site as a new target for inhibitor discovery.
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Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, USA.
| | - Jennifer N Kahn
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, USA.
| | - Nilgun E Tumer
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, USA.
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Zhou Y, Li XP, Kahn JN, Tumer NE. Functional Assays for Measuring the Catalytic Activity of Ribosome Inactivating Proteins. Toxins (Basel) 2018; 10:toxins10060240. [PMID: 29899209 PMCID: PMC6024586 DOI: 10.3390/toxins10060240] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 12/11/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) are potent toxins that inactivate ribosomes by catalytically removing a specific adenine from the α-sarcin/ricin loop (SRL) of the large rRNA. Direct assays for measuring depurination activity and indirect assays for measuring the resulting translation inhibition have been employed to determine the enzyme activity of RIPs. Rapid and sensitive methods to measure the depurination activity of RIPs are critical for assessing their reaction mechanism, enzymatic properties, interaction with ribosomal proteins, ribotoxic stress signaling, in the search for inhibitors and in the detection and diagnosis of enteric infections. Here, we review the major assays developed for measuring the catalytic activity of RIPs, discuss their advantages and disadvantages and explain how they are used in understanding the catalytic mechanism, ribosome specificity, and dynamic enzymatic features of RIPs.
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Affiliation(s)
- Yijun Zhou
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, USA.
| | - Xiao-Ping Li
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, USA.
| | - Jennifer N Kahn
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, USA.
| | - Nilgun E Tumer
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, USA.
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24
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Barbier J, Gillet D. Ribosome Inactivating Proteins: From Plant Defense to Treatments against Human Misuse or Diseases. Toxins (Basel) 2018; 10:toxins10040160. [PMID: 29669991 PMCID: PMC5923326 DOI: 10.3390/toxins10040160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022] Open
Abstract
Ribosome inactivating proteins (RIPs) form a vast family of hundreds of toxins from plants, fungi, algae, and bacteria. RIP activities have also been detected in animal tissues. They exert an N-glycosydase catalytic activity that is targeted to a single adenine of a ribosomal RNA, thereby blocking protein synthesis and leading intoxicated cells to apoptosis. In many cases, they have additional depurinating activities that act against other nucleic acids, such as viral RNA and DNA, or genomic DNA. Although their role remains only partially understood, their functions may be related to plant defense against predators and viruses, plant senescence, or bacterial pathogenesis.
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Affiliation(s)
- Julien Barbier
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France.
| | - Daniel Gillet
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France.
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Human ribosomal P1-P2 heterodimer represents an optimal docking site for ricin A chain with a prominent role for P1 C-terminus. Sci Rep 2017; 7:5608. [PMID: 28717148 PMCID: PMC5514047 DOI: 10.1038/s41598-017-05675-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/15/2017] [Indexed: 12/26/2022] Open
Abstract
The eukaryotic P-stalk contains two P1-P2 protein dimers with a conserved C- terminal domain (CTD) critical for the interaction with external factors. To understand the role of the individual CTD of human P1/P2 proteins, we examined the interaction of reconstituted human P-protein complexes and C-terminally truncated forms with ricin A chain (RTA), which binds to the stalk to depurinate the sarcin/ricin loop (SRL). The interaction between P-protein complexes and RTA was examined by surface plasmon resonance, isothermal titration calorimetry, microscale thermophoresis and bio-layer interferometry. The P1-P2 heterodimer missing a CTD on P2 was able to bind RTA. In contrast, the P1-P2 heterodimer missing the CTD of P1 protein displayed almost no binding toward RTA. Very low interaction was detected between RTA and the non-truncated P2-P2 homodimer, suggesting that the structural architecture of the P1-P2 heterodimer is critical for binding RTA. The reconstituted pentameric human stalk complex had higher affinity for RTA than the P1-P2 dimer. Deletion of P1 CTD, but not P2 CTD reduced the affinity of the pentamer for RTA. These results highlight the importance of the heterodimeric organization of P1-P2 in the human stalk pentamer and functional non-equivalence of the individual P-protein CTDs in the interaction with RTA.
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Li XP, Tumer NE. Differences in Ribosome Binding and Sarcin/Ricin Loop Depurination by Shiga and Ricin Holotoxins. Toxins (Basel) 2017; 9:toxins9040133. [PMID: 28398250 PMCID: PMC5408207 DOI: 10.3390/toxins9040133] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/28/2017] [Accepted: 04/05/2017] [Indexed: 11/16/2022] Open
Abstract
Both ricin and Shiga holotoxins display no ribosomal activity in their native forms and need to be activated to inhibit translation in a cell-free translation inhibition assay. This is because the ribosome binding site of the ricin A chain (RTA) is blocked by the B subunit in ricin holotoxin. However, it is not clear why Shiga toxin 1 (Stx1) or Shiga toxin 2 (Stx2) holotoxin is not active in a cell-free system. Here, we compare the ribosome binding and depurination activity of Stx1 and Stx2 holotoxins with the A1 subunits of Stx1 and Stx2 using either the ribosome or a 10-mer RNA mimic of the sarcin/ricin loop as substrates. Our results demonstrate that the active sites of Stx1 and Stx2 holotoxins are blocked by the A2 chain and the B subunit, while the ribosome binding sites are exposed to the solvent. Unlike ricin, which is enzymatically active, but cannot interact with the ribosome, Stx1 and Stx2 holotoxins are enzymatically inactive but can interact with the ribosome.
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Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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De Zaeytijd J, Van Damme EJM. Extensive Evolution of Cereal Ribosome-Inactivating Proteins Translates into Unique Structural Features, Activation Mechanisms, and Physiological Roles. Toxins (Basel) 2017; 9:E123. [PMID: 28353660 PMCID: PMC5408197 DOI: 10.3390/toxins9040123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/21/2017] [Accepted: 03/25/2017] [Indexed: 11/16/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) are a class of cytotoxic enzymes that can depurinate rRNAs thereby inhibiting protein translation. Although these proteins have also been detected in bacteria, fungi, and even some insects, they are especially prevalent in the plant kingdom. This review focuses on the RIPs from cereals. Studies on the taxonomical distribution and evolution of plant RIPs suggest that cereal RIPs have evolved at an enhanced rate giving rise to a large and heterogeneous RIP gene family. Furthermore, several cereal RIP genes are characterized by a unique domain architecture and the lack of a signal peptide. This advanced evolution of cereal RIPs translates into distinct structures, activation mechanisms, and physiological roles. Several cereal RIPs are characterized by activation mechanisms that include the proteolytic removal of internal peptides from the N-glycosidase domain, a feature not documented for non-cereal RIPs. Besides their role in defense against pathogenic fungi or herbivorous insects, cereal RIPs are also involved in endogenous functions such as adaptation to abiotic stress, storage, induction of senescence, and reprogramming of the translational machinery. The unique properties of cereal RIPs are discussed in this review paper.
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Affiliation(s)
- Jeroen De Zaeytijd
- Lab Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium.
| | - Els J M Van Damme
- Lab Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium.
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Zhou Y, Li XP, Chen BY, Tumer NE. Ricin uses arginine 235 as an anchor residue to bind to P-proteins of the ribosomal stalk. Sci Rep 2017; 7:42912. [PMID: 28230053 PMCID: PMC5322317 DOI: 10.1038/srep42912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/17/2017] [Indexed: 01/24/2023] Open
Abstract
Ricin toxin A chain (RTA) binds to stalk P-proteins to reach the α-sarcin/ricin loop (SRL) where it cleaves a conserved adenine. Arginine residues at the RTA/RTB interface are involved in this interaction. To investigate the individual contribution of each arginine, we generated single, double and triple arginine mutations in RTA. The R235A mutation reduced toxicity and depurination activity more than any other single arginine mutation in yeast. Further reduction in toxicity, depurination activity and ribosome binding was observed when R235A was combined with a mutation in a nearby arginine. RTA interacts with the ribosome via a two-step process, which involves slow and fast interactions. Single arginine mutations eliminated the fast interactions with the ribosome, indicating that they increase the binding rate of RTA. Arginine residues form a positively charged patch to bind to negatively charged residues at the C-termini of P-proteins. When electrostatic interactions conferred by the arginines are lost, hydrophobic interactions are also abolished, suggesting that the hydrophobic interactions alone are insufficient to allow binding. We propose that Arg235 serves as an anchor residue and cooperates with nearby arginines and the hydrophobic interactions to provide the binding specificity and strength in ribosome targeting of RTA.
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Affiliation(s)
- Yijun Zhou
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
| | - Xiao-Ping Li
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
| | - Brian Y Chen
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015-3084, USA
| | - Nilgun E Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey 08901-8520, USA
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Structures and Ribosomal Interaction of Ribosome-Inactivating Proteins. Molecules 2016; 21:molecules21111588. [PMID: 27879643 PMCID: PMC6273143 DOI: 10.3390/molecules21111588] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/09/2016] [Accepted: 11/15/2016] [Indexed: 11/27/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) including ricin, Shiga toxin, and trichosanthin, are RNA N-glycosidases that depurinate a specific adenine residue (A-4324 in rat 28S ribosomal RNA, rRNA) in the conserved α-sarcin/ricin loop (α-SRL) of rRNA. RIPs are grouped into three types according to the number of subunits and the organization of the precursor sequences. RIPs are two-domain proteins, with the active site located in the cleft between the N- and C-terminal domains. It has been found that the basic surface residues of the RIPs promote rapid and specific targeting to the ribosome and a number of RIPs have been shown to interact with the C-terminal regions of the P proteins of the ribosome. At present, the structural basis for the interaction of trichosanthin and ricin-A chain toward P2 peptide is known. This review surveys the structural features of the representative RIPs and discusses how they approach and interact with the ribosome.
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