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Conserved Arginines at the P-Protein Stalk Binding Site and the Active Site Are Critical for Ribosome Interactions of Shiga Toxins but Do Not Contribute to Differences in the Affinity of the A1 Subunits for the Ribosome. Infect Immun 2016; 84:3290-3301. [PMID: 27600507 DOI: 10.1128/iai.00630-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/30/2016] [Indexed: 11/20/2022] Open
Abstract
The A1 subunits of Shiga toxin 1 (Stx1A1) and Shiga toxin 2 (Stx2A1) interact with the conserved C termini of ribosomal-stalk P-proteins to remove a specific adenine from the sarcin/ricin loop. We previously showed that Stx2A1 has higher affinity for the ribosome and higher catalytic activity than Stx1A1. To determine if conserved arginines at the distal face of the active site contribute to the higher affinity of Stx2A1 for the ribosome, we mutated Arg172, Arg176, and Arg179 in both toxins. We show that Arg172 and Arg176 are more important than Arg179 for the depurination activity and toxicity of Stx1A1 and Stx2A1. Mutation of a single arginine reduced the depurination activity of Stx1A1 more than that of Stx2A1. In contrast, mutation of at least two arginines was necessary to reduce depurination by Stx2A1 to a level similar to that of Stx1A1. R176A and R172A/R176A mutations eliminated interaction of Stx1A1 and Stx2A1 with ribosomes and with the stalk, while mutation of Arg170 at the active site reduced the binding affinity of Stx1A1 and Stx2A1 for the ribosome, but not for the stalk. These results demonstrate that conserved arginines at the distal face of the active site are critical for interactions of Stx1A1 and Stx2A1 with the stalk, while a conserved arginine at the active site is critical for non-stalk-specific interactions with the ribosome. Arginine mutations at either site reduced ribosome interactions of Stx1A1 and Stx2A1 similarly, indicating that conserved arginines are critical for ribosome interactions but do not contribute to the higher affinity of Stx2A1 for the ribosome.
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2
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Di R, Tumer NE. Pokeweed antiviral protein: its cytotoxicity mechanism and applications in plant disease resistance. Toxins (Basel) 2015; 7:755-72. [PMID: 25756953 PMCID: PMC4379523 DOI: 10.3390/toxins7030755] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 02/11/2015] [Accepted: 03/02/2015] [Indexed: 11/16/2022] Open
Abstract
Pokeweed antiviral protein (PAP) is a 29 kDa type I ribosome inactivating protein (RIP) found in pokeweed plants. Pokeweed produces different forms of PAP. This review focuses on the spring form of PAP isolated from Phytolacca americana leaves. PAP exerts its cytotoxicity by removing a specific adenine from the α-sarcin/ricin loop of the large ribosomal RNA. Besides depurination of the rRNA, PAP has additional activities that contribute to its cytotoxicity. The mechanism of PAP cytotoxicity is summarized based on evidence from the analysis of transgenic plants and the yeast model system. PAP was initially found to be anti-viral when it was co-inoculated with plant viruses onto plants. Transgenic plants expressing PAP and non-toxic PAP mutants have displayed broad-spectrum resistance to both viral and fungal infection. The mechanism of PAP-induced disease resistance in transgenic plants is summarized.
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Affiliation(s)
- Rong Di
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA.
| | - Nilgun E Tumer
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA.
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3
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Yan Q, Li XP, Tumer NE. Wild type RTA and less toxic variants have distinct requirements for Png1 for their depurination activity and toxicity in Saccharomyces cerevisiae. PLoS One 2014; 9:e113719. [PMID: 25436896 PMCID: PMC4250064 DOI: 10.1371/journal.pone.0113719] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 10/30/2014] [Indexed: 01/29/2023] Open
Abstract
Ricin A chain (RTA) undergoes retrograde trafficking and is postulated to use components of the endoplasmic reticulum (ER) associated degradation (ERAD) pathway to enter the cytosol to depurinate ribosomes. However, it is not known how RTA evades degradation by the proteasome after entry into the cytosol. We observed two distinct trafficking patterns among the precursor forms of wild type RTA and nontoxic variants tagged with enhanced green fluorescent protein (EGFP) at their C-termini in yeast. One group, which included wild type RTA, underwent ER-to-vacuole transport, while another group, which included the G83D variant, formed aggregates in the ER and was not transported to the vacuole. Peptide: N-glycanase (Png1), which catalyzes degradation of unfolded glycoproteins in the ERAD pathway affected depurination activity and toxicity of wild type RTA and G83D variant differently. PreG83D variant was deglycosylated by Png1 on the ER membrane, which reduced its depurination activity and toxicity by promoting its degradation. In contrast, wild type preRTA was deglycosylated by the free pool of Png1 in the cytosol, which increased its depurination activity, possibly by preventing its degradation. These results indicate that wild type RTA has a distinct requirement for Png1 compared to the G83D variant and is deglycosylated by Png1 in the cytosol as a possible strategy to avoid degradation by the ERAD pathway to reach the ribosome.
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Affiliation(s)
- Qing Yan
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Xiao-Ping Li
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nilgun E. Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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4
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Li XP, Kahn PC, Kahn JN, Grela P, Tumer NE. Arginine residues on the opposite side of the active site stimulate the catalysis of ribosome depurination by ricin A chain by interacting with the P-protein stalk. J Biol Chem 2013; 288:30270-30284. [PMID: 24003229 DOI: 10.1074/jbc.m113.510966] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Ricin inhibits protein synthesis by depurinating the α-sarcin/ricin loop (SRL). Ricin holotoxin does not inhibit translation unless the disulfide bond between the A (RTA) and B (RTB) subunits is reduced. Ricin holotoxin did not bind ribosomes or depurinate them but could depurinate free RNA. When RTA is separated from RTB, arginine residues located at the interface are exposed to the solvent. Because this positively charged region, but not the active site, is blocked by RTB, we mutated arginine residues at or near the interface of RTB to determine if they are critical for ribosome binding. These variants were structurally similar to wild type RTA but could not bind ribosomes. Their K(m) values and catalytic rates (k(cat)) for an SRL mimic RNA were similar to those of wild type, indicating that their activity was not altered. However, they showed an up to 5-fold increase in K(m) and up to 38-fold decrease in kcat toward ribosomes. These results suggest that the stalk binding stimulates the catalysis of ribosome depurination by RTA. The mutated arginines have side chains behind the active site cleft, indicating that the ribosome binding surface of RTA is on the opposite side of the surface that interacts with the SRL. We propose that stalk binding stimulates the catalysis of ribosome depurination by orienting the active site of RTA toward the SRL and thereby allows docking of the target adenine into the active site. This model may apply to the translation factors that interact with the stalk.
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Affiliation(s)
- Xiao-Ping Li
- From the Departments of Plant Biology and Pathology and
| | - Peter C Kahn
- Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey 08901-8520
| | | | | | - Nilgun E Tumer
- From the Departments of Plant Biology and Pathology and.
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5
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May KL, Yan Q, Tumer NE. Targeting ricin to the ribosome. Toxicon 2013; 69:143-51. [PMID: 23454625 DOI: 10.1016/j.toxicon.2013.02.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/01/2013] [Accepted: 02/06/2013] [Indexed: 12/15/2022]
Abstract
The plant toxin ricin is highly toxic for mammalian cells and is of concern for bioterrorism. Ricin belongs to a family of functionally related toxins, collectively referred to as ribosome inactivating proteins (RIPs), which disable ribosomes and halt protein synthesis. Currently there are no specific antidotes against ricin or related RIPs. The catalytic subunit of ricin is an N-glycosidase that depurinates a universally conserved adenine residue within the sarcin/ricin loop (SRL) of the 28S rRNA. This depurination activity inhibits translation and its biochemistry has been intensively studied. Yet, recent developments paint a more complex picture of toxicity, with ribosomal proteins and cellular signaling pathways contributing to the potency of ricin. In particular, several studies have now established the importance of the ribosomal stalk structure in facilitating the depurination activity and ribosome specificity of ricin and other RIPs. This review highlights recent developments defining toxin-ribosome interactions and examines the significance of these interactions for toxicity and therapeutic intervention.
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Affiliation(s)
- Kerrie L May
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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Kumar RB, Suresh MX. A computational perspective of molecular interactions through virtual screening, pharmacokinetic and dynamic prediction on ribosome toxin A chain and inhibitors of Ricinus communis. Pharmacognosy Res 2012; 4:2-10. [PMID: 22224054 PMCID: PMC3250034 DOI: 10.4103/0974-8490.91027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/04/2011] [Accepted: 12/22/2011] [Indexed: 11/28/2022] Open
Abstract
Background: Ricin is considered to be one of the most deadly toxins and gained its favor as a bioweapon that has a serious social and biological impact, due to its widespread nature and abundant availability. The hazardous effects of this toxin in human being are seen in almost all parts of the organ system. The severe consequences of the toxin necessitate the need for developing potential inhibitors that can effectively block its interaction with the host system. Materials and Methods: In order to identify potential inhibitors that can effectively block ricin, we employed various computational approaches. In this work, we computationally screened and analyzed 66 analogs and further tested their ADME/T profiles. From the kinetic and toxicity studies we selected six analogs that possessed appropriate pharmacokinetic and dynamic property. We have also performed a computational docking of these analogs with the target. Results: On the basis of the dock scores and hydrogen bond interactions we have identified analog 64 to be the best interacting molecule. Molecule 64 seems to have stable interaction with the residues Tyr80, Arg180, and Val81. The pharmacophore feature that describes the key functional features of a molecule was also studied and presented. Conclusion: The pharmacophore features of the drugs provided suggests the key functional groups that can aid in the design and synthesis of more potential inhibitors.
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Affiliation(s)
- R Barani Kumar
- Department of Bioinformatics, Sathyabama University, Chennai, Tamil Nadu, India
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7
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Yan Q, Li XP, Tumer NE. N-glycosylation does not affect the catalytic activity of ricin a chain but stimulates cytotoxicity by promoting its transport out of the endoplasmic reticulum. Traffic 2012; 13:1508-21. [PMID: 22882900 DOI: 10.1111/j.1600-0854.2012.01404.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 08/07/2012] [Accepted: 08/10/2012] [Indexed: 12/30/2022]
Abstract
Ricin A chain (RTA) depurinates the α-sarcin/ricin loop after it undergoes retrograde trafficking to the cytosol. The structural features of RTA involved in intracellular transport are not known. To explore this, we fused enhanced green fluorescent protein (EGFP) to precursor (preRTA-EGFP), containing a 35-residue leader, and mature RTA (matRTA-EGFP). Both were enzymatically active and toxic in Saccharomyces cerevisiae. PreRTA-EGFP was localized in the endoplasmic reticulum (ER) initially and was subsequently transported to the vacuole, whereas matRTA-EGFP remained in the cytosol, indicating that ER localization is a prerequisite for vacuole transport. When the two glycosylation sites in RTA were mutated, the mature form was fully active and toxic, suggesting that the mutations do not affect catalytic activity. However, nonglycosylated preRTA-EGFP had reduced toxicity, depurination and delayed vacuole transport, indicating that N-glycosylation affects transport of RTA out of the ER. Point mutations in the C-terminal hydrophobic region restricted RTA to the ER and eliminated toxicity and depurination, indicating that this sequence is critical for ER exit. These results demonstrate that N-glycosylation and the C-terminal hydrophobic region stimulate the toxicity of RTA by promoting ER export. The timing of depurination coincided with the timing of vacuole transport, suggesting that RTA may enter the cytosol during vacuole transport.
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Affiliation(s)
- Qing Yan
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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8
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Redmann V, Oresic K, Tortorella LL, Cook JP, Lord M, Tortorella D. Dislocation of ricin toxin A chains in human cells utilizes selective cellular factors. J Biol Chem 2011; 286:21231-8. [PMID: 21527639 DOI: 10.1074/jbc.m111.234708] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ricin is a potent A-B toxin that is transported from the cell surface to the cytosol, where it inactivates ribosomes, leading to cell death. Ricin enters cells via endocytosis, where only a minute number of ricin molecules reach the endoplasmic reticulum (ER) lumen. Subsequently, the ricin A chain traverses the ER bilayer by a process referred to as dislocation or retrograde translocation to gain access to the cytosol. To study the molecular processes of ricin A chain dislocation, we have established, for the first time, a human cell system in which enzymatically attenuated ricin toxin A chains (RTA(E177D) and RTA(Δ177-181)) are expressed in the cell and directed to the ER. Using this human cell-based system, we found that ricin A chains underwent a rapid dislocation event that was quite distinct from the dislocation of a canonical ER soluble misfolded protein, null Hong Kong variant of α(1)-antitrypsin. Remarkably, ricin A chain dislocation occurred via a membrane-integrated intermediate and utilized the ER protein SEL1L for transport across the ER bilayer to inhibit protein synthesis. The data support a model in which ricin A chain dislocation occurs via a novel strategy of utilizing the hydrophobic nature of the ER membrane and selective ER components to gain access to the cytosol.
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Affiliation(s)
- Veronika Redmann
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York 10029, USA
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9
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Di R, Kyu E, Shete V, Saidasan H, Kahn PC, Tumer NE. Identification of amino acids critical for the cytotoxicity of Shiga toxin 1 and 2 in Saccharomyces cerevisiae. Toxicon 2010; 57:525-39. [PMID: 21184769 DOI: 10.1016/j.toxicon.2010.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 12/02/2010] [Accepted: 12/06/2010] [Indexed: 10/18/2022]
Abstract
Shiga toxins (Stx1 and Stx2) are produced by E. coli O157:H7, which is a leading cause of foodborne illness. The A subunits of Stx1 (Stx1A) and Stx2 (Stx2A) are ribosome inactivating proteins (RIPs) that inhibit translation by removing an adenine from the highly conserved α-sarcin ricin loop (SRL) of the large rRNA. Here, we used mutagenesis in Saccharomyces cerevisiae to identify residues critical for cytotoxicity of Stx1A and Stx2A. The A subunits depurinated the SRL, inhibited translation and caused apoptotic-like cell death in yeast. Single mutations in Asn75, Tyr77, Glu167 and Arg176 reduced the cytotoxicity of both toxins around 10-fold. However, Asn75 and Tyr77 were more critical for the depurination activity of Stx2A, while Arg176 was more critical for the depurination activity of Stx1A. The crystal structures of the two proteins lack electron density for some surface loops, including one which is adjacent to the active site in both molecules. Modeling these loops changed neither the secondary nor the tertiary structures of the rest of the protein. Analysis of solvent accessible surface areas indicated that Asn75 and Tyr77 are more exposed in Stx2A, while Arg176 is more exposed in Stx1A, indicating that residues with higher surface exposure were more critical for enzymatic activity. Double mutations at Glu167 and Arg176 eliminated the depurination activity and cytotoxicity of both toxins. C-terminal deletions of A chains eliminated cytotoxicity of both toxins, but showed functional differences. Unlike Stx1A, cytotoxicity of Stx2A was lost before its ability to depurinate ribosomes. These results identify residues that affect enzymatic activity and cytotoxicity of Stx1A and Stx2A differently and demonstrate that the function of these residues can be differentiated in yeast. The extent of ribosome depurination and translation inhibition did not correlate with the extent of cell death, indicating that depurination of the SRL and inhibition of translation are not entirely responsible for cell death.
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Affiliation(s)
- Rong Di
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8502, USA
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10
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Odumosu O, Nicholas D, Yano H, Langridge W. AB toxins: a paradigm switch from deadly to desirable. Toxins (Basel) 2010; 2:1612-45. [PMID: 22069653 PMCID: PMC3153263 DOI: 10.3390/toxins2071612] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 06/08/2010] [Accepted: 06/23/2010] [Indexed: 11/16/2022] Open
Abstract
To ensure their survival, a number of bacterial and plant species have evolved a common strategy to capture energy from other biological systems. Being imperfect pathogens, organisms synthesizing multi-subunit AB toxins are responsible for the mortality of millions of people and animals annually. Vaccination against these organisms and their toxins has proved rather ineffective in providing long-term protection from disease. In response to the debilitating effects of AB toxins on epithelial cells of the digestive mucosa, mechanisms underlying toxin immunomodulation of immune responses have become the focus of increasing experimentation. The results of these studies reveal that AB toxins may have a beneficial application as adjuvants for the enhancement of immune protection against infection and autoimmunity. Here, we examine similarities and differences in the structure and function of bacterial and plant AB toxins that underlie their toxicity and their exceptional properties as immunomodulators for stimulating immune responses against infectious disease and for immune suppression of organ-specific autoimmunity.
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Affiliation(s)
- Oludare Odumosu
- Center for Health Disparities and Molecular Medicine, Loma Linda University, School of Medicine, Loma Linda, CA 92354, USA; (O.O.)
- Department of Biochemistry, Loma Linda University, School of Medicine, Loma Linda, CA 92354, USA; (D.N.)
| | - Dequina Nicholas
- Center for Health Disparities and Molecular Medicine, Loma Linda University, School of Medicine, Loma Linda, CA 92354, USA; (O.O.)
- Department of Biochemistry, Loma Linda University, School of Medicine, Loma Linda, CA 92354, USA; (D.N.)
| | - Hiroshi Yano
- Department of Biology, University of Redlands, 1200 East Colton Ave, P.O. Box 3080, Redlands, CA 92373, USA; (H.Y.)
| | - William Langridge
- Center for Health Disparities and Molecular Medicine, Loma Linda University, School of Medicine, Loma Linda, CA 92354, USA; (O.O.)
- Department of Biochemistry, Loma Linda University, School of Medicine, Loma Linda, CA 92354, USA; (D.N.)
- Author to whom correspondence should be addressed; ; Tel.: +1-909-558-1000 (81362); Fax: +1-909-558-0177
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Wahome PG, Bai Y, Neal LM, Robertus JD, Mantis NJ. Identification of small-molecule inhibitors of ricin and shiga toxin using a cell-based high-throughput screen. Toxicon 2010; 56:313-23. [PMID: 20350563 DOI: 10.1016/j.toxicon.2010.03.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 10/19/2022]
Abstract
The Category B agents, ricin and shiga toxin (Stx), are RNA N-glycosidases that target a highly conserved adenine residue within the sarcin-ricin loop of eukaryotic 28S ribosomal RNA. In an effort to identify small-molecule inhibitors of these toxins that could serve as lead compounds for potential therapeutics, we have developed a simple Vero cell-based high-throughput cytotoxicity assay and have used it to screen approximately 81,300 compounds in 17 commercially available chemical libraries. This initial screen identified approximately 300 compounds with weak (>or=30 to <50%), moderate (>or=50 to <80%), or strong (>or=80%) ricin inhibitory activity. Secondary analysis of 244 of these original "hits" was performed, and 20 compounds that were capable of reducing ricin cytotoxicity by >50% were chosen for further study. Four compounds demonstrated significant dose-dependent ricin inhibitory activity in the Vero cell-based assay, with 50% effective inhibitory concentration (EC(50)) values ranging from 25 to 60microM. The same 20 compounds were tested in parallel for the ability to inhibit ricin's and Stx1's enzymatic activities in an in vitro translation reaction. Three of the 20 compounds, including the most effective compound in the cell-based assay, had discernible anti-toxin activity. One compound in particular, 4-fluorophenyl methyl 2-(furan-2-yl)quinoline-4-carboxylate ("compound 8"), had 50% inhibitory concentration (IC(50)) of 30microM, a value indicating >10-fold higher potency than is the case for previously described ricin-Stx1 inhibitors. Computer modeling predicted that compound 8 is capable of docking within the ricin active site. In conclusion, we have used a simple high-throughput cell-based method to identify several new small-molecule inhibitors of ricin and Stx.
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Affiliation(s)
- Paul G Wahome
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, USA
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12
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McHugh CA, Tammariello RF, Millard CB, Carra JH. Improved stability of a protein vaccine through elimination of a partially unfolded state. Protein Sci 2004; 13:2736-43. [PMID: 15340172 PMCID: PMC2286567 DOI: 10.1110/ps.04897904] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Revised: 06/29/2004] [Accepted: 07/02/2004] [Indexed: 10/26/2022]
Abstract
Ricin is a potent toxin presenting a threat as a biological weapon. The holotoxin consists of two disulfide-linked polypeptides: an enzymatically active A chain (RTA) and a galactose/N-acetylgalactosamine-binding B chain. Efforts to develop an inactivated version of the A chain as a vaccine have been hampered by limitations of stability and solubility. Previously, recombinant truncated versions of the 267-amino-acid A chain consisting of residues 1-33/44-198 or 1-198 were designed by protein engineering to overcome these limits and were shown to be effective and nontoxic as vaccines in mice. Herein we used CD, dynamic light scattering, fluorescence, and Fourier-transform infrared spectroscopy to examine the biophysical properties of these proteins. Although others have found that recombinant RTA (rRTA) adopts a partially unfolded, molten globule-like state at 45 degrees C, rRTA 1-33/44-198 and 1-198 are significantly more thermostable, remaining completely folded at temperatures up to 53 degrees C and 51 degrees C, respectively. Deleting both an exposed loop region (amino acids 34-43) and the C-terminal domain (199-267) contributed to increased thermostability. We found that chemically induced denaturation of rRTA, but not the truncated variants, proceeds through at least a three-state mechanism. The intermediate state in rRTA unfolding has a hydrophobic core accessible to ANS and an unfolded C-terminal domain. Removing the C-terminal domain changed the mechanism of rRTA unfolding, eliminating a tendency to adopt a partially unfolded state. Our results support the conclusion that these derivatives are superior candidates for development as vaccines against ricin and suggest an approach of reduction to minimum essential domains for design of more thermostable recombinant antigens.
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Affiliation(s)
- Colleen A McHugh
- United States Army Medical Research Institute of Infectious Diseases, Department of Cell Biology and Biochemistry, 1425 Porter Street, Frederick, MD 21702, USA
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13
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Hudak KA, Parikh BA, Di R, Baricevic M, Santana M, Seskar M, Tumer NE. Generation of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: evidence that ribosome depurination is not sufficient for cytotoxicity. Nucleic Acids Res 2004; 32:4244-56. [PMID: 15304562 PMCID: PMC514378 DOI: 10.1093/nar/gkh757] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein that depurinates the highly conserved alpha-sarcin/ricin loop in the large rRNA. Here, using site-directed mutagenesis and systematic deletion analysis from the 5' and the 3' ends of the PAP cDNA, we identified the amino acids important for ribosome depurination and cytotoxicity of PAP. Truncating the first 16 amino acids of PAP eliminated its cytotoxicity and the ability to depurinate ribosomes. Ribosome depurination gradually decreased upon the sequential deletion of C-terminal amino acids and was abolished when a stop codon was introduced at Glu-244. Cytotoxicity of the C-terminal deletion mutants was lost before their ability to depurinate ribosomes. Mutations in Tyr-123 at the active site affected cytotoxicity without altering the ribosome depurination ability. Total translation was not inhibited in yeast expressing the non-toxic Tyr-123 mutants, although ribosomes were depurinated. These mutants depurinated ribosomes only during their translation and could not depurinate ribosomes in trans in a translation-independent manner. A mutation in Leu-71 in the central domain affected cytotoxicity without altering the ability to depurinate ribosomes in trans and inhibit translation. These results demonstrate that the ability to depurinate ribosomes in trans in a catalytic manner is required for the inhibition of translation, but is not sufficient for cytotoxicity.
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Affiliation(s)
- Katalin A Hudak
- Biotechnology Center for Agriculture and the Environment and the Department of Plant Biology and Pathology, Cook College, Rutgers University, New Brunswick, NJ 08901-8520, USA
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14
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Word JM, Bateman RC, Presley BK, Lovell SC, Richardson DC. Exploring steric constraints on protein mutations using MAGE/PROBE. Protein Sci 2000; 9:2251-9. [PMID: 11152136 PMCID: PMC2144501 DOI: 10.1110/ps.9.11.2251] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
When planning a mutation to test some hypothesis, one crucial question is whether the new side chain is compatible with the existing structure; only if it is compatible can the interpretation of mutational results be straightforward. This paper presents a simple way of using the sensitive geometry of all-atom contacts (including hydrogens) to answer that question. The interactive MAGE/PROBE system lets the biologist explore conformational space for the mutant side chain, with an interactively updated kinemage display of its all-atom contacts to the original structure. The Autobondrot function in PROBE systematically explores that same conformational space, outputting contact scores at each point, which are then contoured and displayed. These procedures are applied here in two types of test cases, with known mutant structures. In ricin A chain, the ability of a neighboring glutamate to rescue activity of an active-site mutant is modeled successfully. In T4 lysozyme, six mutations to Leu are analyzed within the wild-type background structure, and their Autobondrot score maps correctly predict whether or not their surroundings must shift significantly in the actual mutant structures; interactive examination of contacts for the conformations involved explains which clashes are relieved by the motions. These programs are easy to use, are available free for UNIX or Microsoft Windows operating systems, and should be of significant help in choosing good mutation experiments or in understanding puzzling results.
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Affiliation(s)
- J M Word
- Department of Biochemistry, Duke University, Durham, North Carolina 27710-3711, USA
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15
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Skinner LM, Jackson MP. Investigation of ribosome binding by the Shiga toxin A1 subunit, using competition and site-directed mutagenesis. J Bacteriol 1997; 179:1368-74. [PMID: 9023224 PMCID: PMC178838 DOI: 10.1128/jb.179.4.1368-1374.1997] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The enzymatic subunit of Shiga toxin (StxA1) is a member of the ribosome-inactivating protein (RIP) family, which includes the ricin A chain as well as other examples of plant toxins. StxA1 catalytically depurinates a well-conserved GAGA tetra-loop of 28S rRNA which lies in the acceptor site of eukaryotic ribosomes. The specific activities of native StxA1, as well as mutated forms of the enzyme with substitutions in catalytic site residues, were measured by an in vitro translation assay. Electroporation was developed as an alternative method for the delivery of purified A1 polypeptides into Vero cells. Site-directed mutagenesis coupled with N-bromosuccinimide modification indicated that the sole tryptophan residue of StxA1 is required for binding it to the 28S rRNA backbone. Northern analysis established that the catalytic site substitutions reduced enzymatic activity by specifically interfering with the capacity of StxA1 to depurinate 28S rRNA. Ribosomes were protected from StxA1 by molar excesses of tRNA and free adenine, indicating that RIPs have the capacity to enter the acceptor site groove prior to binding and depurinating the GAGA tetra-loop.
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Affiliation(s)
- L M Skinner
- Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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16
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Chen RS, Leung HW, Dong YC, Wong RN. Modeling of the three-dimensional structure of luffin-alpha and its simulated reaction with the substrate oligoribonucleotide GAGA. JOURNAL OF PROTEIN CHEMISTRY 1996; 15:649-57. [PMID: 8968956 DOI: 10.1007/bf01886747] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A fundamental problem in biochemistry and molecular biology is understanding the spatial structure of macromolecules and then analyzing their functions. In this study, the three-dimensional structure of a ribosome-inactivating protein luffin-alpha was predicted using a neural network method and molecular dynamics simulation. A feedforward neural network with the backpropagation learning algorithm were trained on model class of homologous proteins including trichosanthin and alpha-momorcharin. The distance constraints for the C alpha atoms in the protein backbone were utilized to generate a folded crude conformation of luffin-alpha by model building and the steepest descent minimization approach. The crude conformation was refined by molecular dynamics techniques and a simulated annealing procedure. The interaction between luffin-alpha and its analogous substrate GAGA was also simulated to understand its action mechanism.
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Affiliation(s)
- R S Chen
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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17
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Hur Y, Hwang DJ, Zoubenko O, Coetzer C, Uckun FM, Tumer NE. Isolation and characterization of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: identification of residues important for toxicity. Proc Natl Acad Sci U S A 1995; 92:8448-52. [PMID: 7667309 PMCID: PMC41174 DOI: 10.1073/pnas.92.18.8448] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Pokeweed antiviral protein (PAP), a 29-kDa protein isolated from Phytolacca americana inhibits translation by catalytically removing a specific adenine residue from the 28S rRNA of eukaryotic ribosomes. PAP has potent antiviral activity against many plant and animal viruses, including human immunodeficiency virus. We describe here development of a positive selection system to isolate PAP mutants with reduced toxicity. In vitro translation in the presence or absence of microsomal membranes shows that PAP is synthesized as a precursor and undergoes at least two different proteolytic processing steps to generate mature PAP. The PAP cDNA was placed under control of the galactose-inducible GAL1 promoter and transformed into Saccharomyces cerevisiae. Induction of PAP expression was lethal to yeast. The PAP expression plasmid was mutagenized and plasmids encoding mutant PAP genes were identified by their failure to kill S. cerevisiae. A number of mutant alleles were sequenced. In one mutant, a point mutation at Glu-177 inactivated enzymatic function in vitro, suggesting that this glutamic acid residue is located at or near the catalytic site. Mutants with either point mutations near the N terminus or a nonsense mutation at residue 237 produced protein that was enzymatically active in vitro, suggesting that the toxicity of PAP is not due solely to enzymatic activity. Toxicity of PAP appears to be a multistep process that involves possibly different domains of the protein.
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Affiliation(s)
- Y Hur
- Center for Agricultural Molecular Biology, Rutgers University, Cook College, New Brunswick, NJ 08903-0231, USA
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18
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Morris KN, Wool IG. Analysis of the contribution of an amphiphilic alpha-helix to the structure and to the function of ricin A chain. Proc Natl Acad Sci U S A 1994; 91:7530-3. [PMID: 8052614 PMCID: PMC44435 DOI: 10.1073/pnas.91.16.7530] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The A chain of ricin is a cytotoxic RNA N-glycosidase that inactivates eukaryotic ribosomes. The contribution of the amphiphilic helix D, which is distant from the active site, to the catalysis of the depurination of the adenosine at position 4324 in 28S rRNA has been examined by systematic deletion of amino acids. Two sets of consecutive two- or three-amino acid deletions of the 12 residues in helix D, a total of 20 mutants, were constructed. All 12 of the amino acids could be deleted in one mutant or another without loss of activity; however, mutations that disrupted the amphiphilicity of the helix led to inactivation of the enzyme. Thus, the minimum contribution of helix D to the structure of the ricin A chain is to provide hydrophobic and hydrophilic surfaces to shield helix E, which has the active-site residues; moreover, no amino acid side chain in helix D makes a specific contribution to the recognition of the RNA substrate or to catalysis; and, finally, phasing of the amino acid deletions can be important to the phenotype of mutants.
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Affiliation(s)
- K N Morris
- Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637
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19
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Haddad JE, al-Jaufy AY, Jackson MP. Minimum domain of the Shiga toxin A subunit required for enzymatic activity. J Bacteriol 1993; 175:4970-8. [PMID: 8349540 PMCID: PMC204961 DOI: 10.1128/jb.175.16.4970-4978.1993] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The minimum sequence of the enzymatic (A) subunit of Shiga toxin (STX) required for activity was investigated by introducing N-terminal and C-terminal deletions in the molecule. Enzymatic activity was assessed by using an in vitro translation system. A 253-amino-acid STX A polypeptide, which is recognized as the enzymatically active portion of the 293-amino-acid A subunit, expressed less than wild-type levels of activity. In addition, alteration of the proposed nicking site between Ala-253 and Ser-254 by site-directed mutagenesis apparently prevented proteolytic processing but had no effect on the enzymatic activity of the molecule. Therefore, deletion analysis was used to identify amino acid residue 271 as the C terminus of the enzymatically active portion of the STX A subunit. STX A polypeptides with N-terminal and C-terminal deletions were released into the periplasmic space of Escherichia coli by fusion to the signal peptide and the first 22 amino acids of Shiga-like toxin type II, a member of the STX family. Although these fusion proteins expressed less than wild-type levels of enzymatic activity, they confirmed the previous finding that Tyr-77 is an active-site residue. Therefore, the minimum domain of the A polypeptide which was required for the expression of enzymatic activity was defined as StxA residues 75 to 268.
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Affiliation(s)
- J E Haddad
- Department of Immunology and Microbiology, Wayne State University School of Medicine, Detroit, Michigan 48201
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20
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Morris KN, Wool IG. Determination by systematic deletion of the amino acids essential for catalysis by ricin A chain. Proc Natl Acad Sci U S A 1992; 89:4869-73. [PMID: 1594586 PMCID: PMC49189 DOI: 10.1073/pnas.89.11.4869] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The A chain of ricin is a RNA N-glycosidase that inactivates ribosomes by depurination of a single adenosine in 28S rRNA. Of the 267 amino acids in the protein, 222 (83%) could be deleted from one or another of 74 mutants without loss of the capacity of the protein to recognize a single nucleotide from among the 7000 in ribosomes or to catalyze hydrolysis.
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Affiliation(s)
- K N Morris
- Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637
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21
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Gordon VM, Whipp SC, Moon HW, O'Brien AD, Samuel JE. An enzymatic mutant of Shiga-like toxin II variant is a vaccine candidate for edema disease of swine. Infect Immun 1992; 60:485-90. [PMID: 1730480 PMCID: PMC257653 DOI: 10.1128/iai.60.2.485-490.1992] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Edema disease (ED) of weanling pigs is caused by an infection with Escherichia coli that produces Shiga-like toxin II variant (SLT-IIv). Pathology identical to that caused by ED can be duplicated in pigs that are injected with less than 10 ng of purified SLT-IIv per kg of body weight. Therefore, SLT-IIv was mutated to create an immunoreactive form of the toxin that was significantly reduced in enzymatic activity. Initially, purified SLT-IIv was treated with formaldehyde which abrogated cytotoxic activity. Pigs were vaccinated with the toxoid (100 micrograms) to determine whether a toxoid was a viable vaccine candidate and whether young pigs were capable of mounting an immune response. Although the pigs developed a neutralizing antibody titer (1:128 to 1:512) 28 days postinjection, they also lost weight and developed ED lesions. The deleterious effect of the toxoid appeared to result from residual enzymatic activity or a reversion to a toxic form. An alternative method, site-directed mutagenesis, was employed to consistently reduce the enzymatic activity of SLT-IIv. Glutamate at position 167 of the mature A subunit was replaced by aspartate (E167D), and arginine at position 170 was replaced by lysine (R170K). These mutations reduced cytotoxic activity 10(4)-fold and 10-fold, respectively, while the enzymatic activities were decreased 400-fold and 5-fold, respectively. The activity of a toxin that contained both mutations (SLT-IIvE167D/R170K) closely resembled that of SLT-IIvE167D. When position 167 was replaced by glutamine (E167Q), the cytotoxic activity decreased 10(6)-fold and the enzymatic activity decreased approximately 1,500-fold. Pigs that were vaccinated with purified, mutant toxin designated SLT-IIvE167Q developed a neutralizing antibody titer of 1:512 21 days postinjection, and their tissues were free of ED lesions. These data suggest that SLT-IIvE167Q may represent an effective vaccine against ED.
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Affiliation(s)
- V M Gordon
- Department of Microbiology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 22908
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22
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Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes. Mol Cell Biol 1991. [PMID: 1978925 DOI: 10.1128/mcb.10.12.6257] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene for ricin toxin A chain was modified by site-specific mutagenesis to change arginine 180 to alanine, glutamine, methionine, lysine, or histidine. Separately, glutamic acid 177 was changed to alanine and glutamic acid 208 was changed to aspartic acid. Both the wild-type and mutant proteins were expressed in Escherichia coli and, when soluble, purified and tested quantitatively for enzyme activity. A positive charge at position 180 was found necessary for solubility of the protein and for enzyme activity. Similarly, a negative charge with a proper geometry in the vicinity of position 177 was critical for ricin toxin A chain catalysis. When glutamic acid 177 was converted to alanine, nearby glutamic acid 208 could largely substitute for it. This observation provided valuable structural information concerning the nature of second-site mutations.
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23
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Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes. Mol Cell Biol 1990; 10:6257-63. [PMID: 1978925 PMCID: PMC362900 DOI: 10.1128/mcb.10.12.6257-6263.1990] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The gene for ricin toxin A chain was modified by site-specific mutagenesis to change arginine 180 to alanine, glutamine, methionine, lysine, or histidine. Separately, glutamic acid 177 was changed to alanine and glutamic acid 208 was changed to aspartic acid. Both the wild-type and mutant proteins were expressed in Escherichia coli and, when soluble, purified and tested quantitatively for enzyme activity. A positive charge at position 180 was found necessary for solubility of the protein and for enzyme activity. Similarly, a negative charge with a proper geometry in the vicinity of position 177 was critical for ricin toxin A chain catalysis. When glutamic acid 177 was converted to alanine, nearby glutamic acid 208 could largely substitute for it. This observation provided valuable structural information concerning the nature of second-site mutations.
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24
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Jackson MP, Deresiewicz RL, Calderwood SB. Mutational analysis of the Shiga toxin and Shiga-like toxin II enzymatic subunits. J Bacteriol 1990; 172:3346-50. [PMID: 2345150 PMCID: PMC209145 DOI: 10.1128/jb.172.6.3346-3350.1990] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The A-subunit polypeptides of Shiga toxin, the Shiga-like toxins (SLTs), and the plant lectin ricin inactivate eucaryotic ribosomes by enzymatically depurinating 28S rRNA. Comparison of the amino acid sequences of the members of the Shiga toxin family and ricin revealed two regions of significant homology that lie within a proposed active-site cleft of the ricin A chain. In previous studies, these conserved sequences of the SLT-I and ricin A subunits have been implicated as active sites. To establish the importance of these regions of homology, we used site-directed mutagenesis to alter the A-subunit sequences of two members of the Shiga toxin family. Substitution of an aspartic acid for glutamic acid 166 of the Slt-IIA subunit decreased the capacity of the polypeptides to inhibit protein synthesis at least 100-fold in a cell-free translation system. However, this mutation did not prevent the expression of immunoreactive, full-length Slt-IIA. In addition, SLT-II holotoxin containing the mutated A subunit was 1,000-fold less toxic to Vero cells. Finally, site-directed mutagenesis was used to delete sequences encoding amino acids 202 through 213 of the Shiga toxin A subunit. Although this deletion did not prevent holotoxin assembly, it abolished cytotoxic activity.
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Affiliation(s)
- M P Jackson
- Department of Microbiology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
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