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Sharma A, Gupta S, Sharma NR, Paul K. Expanding role of ribosome-inactivating proteins: From toxins to therapeutics. IUBMB Life 2023; 75:82-96. [PMID: 36121739 DOI: 10.1002/iub.2675] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/26/2022] [Indexed: 02/02/2023]
Abstract
Ribosome-inactivating proteins (RIPs) are toxic proteins with N-glycosidase activity. RIPs exert their action by removing a specific purine from 28S rRNA, thereby, irreversibly inhibiting the process of protein synthesis. RIPs can target both prokaryotic and eukaryotic cells. In bacteria, the production of RIPs aid in the process of pathogenesis whereas, in plants, the production of these toxins has been attributed to bolster defense against insects, viral, bacterial and fungal pathogens. In recent years, RIPs have been engineered to target a particular cell type, this has fueled various experiments testing the potential role of RIPs in many biomedical applications like anti-viral and anti-tumor therapies in animals as well as anti-pest agents in engineered plants. In this review, we present a comprehensive study of various RIPs, their mode of action, their significance in various fields involving plants and animals. Their potential as treatment options for plant infections and animal diseases is also discussed.
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Affiliation(s)
- Anuj Sharma
- Department of Biochemistry, DAV University, Jalandhar, Punjab, India
| | - Shelly Gupta
- Department of Biochemistry, School of Biosciences and Bioengineering, Lovely Professional University, Phagwara, Punjab, India
| | - Neeta Raj Sharma
- School of Biosciences and Bioengineering, Lovely Professional University, Phagwara, Punjab, India
| | - Karan Paul
- Department of Biochemistry, DAV University, Jalandhar, Punjab, India
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Dougherty K, Hudak KA. Phylogeny and domain architecture of plant ribosome inactivating proteins. PHYTOCHEMISTRY 2022; 202:113337. [PMID: 35934106 DOI: 10.1016/j.phytochem.2022.113337] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/01/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Ribosome inactivating proteins (RIPs) are rRNA N-glycosylases (EC 3.2.2.22) best known for hydrolyzing an adenine base from the conserved sarcin/ricin loop of ribosomal RNA. Protein translation is inhibited by ribosome depurination; therefore, RIPs are generally considered toxic to cells. The expression of some RIPs is upregulated by biotic and abiotic stress, though the connection between RNA depurination and defense response is not well understood. Despite their prevalence in approximately one-third of flowering plant orders, our knowledge of RIPs stems primarily from biochemical analyses of individuals or genomics-scale analyses of small datasets from a limited number of species. Here, we performed an unbiased search for proteins with RIP domains and identified several-fold more RIPs than previously known - more than 800 from 120 species, many with novel associated domains and physicochemical characteristics. Based on protein domain configuration, we established 15 distinct groups, suggesting diverse functionality. Surprisingly, most of these RIPs lacked a signal peptide, indicating they may be localized to the nucleocytoplasm of cells, raising questions regarding their toxicity against conspecific ribosomes. Our phylogenetic analysis significantly extends previous models for RIP evolution in plants, predicting an original single-domain RIP that later evolved to acquire a signal peptide and different protein domains. We show that RIPs are distributed throughout 21 plant orders with many species maintaining genes for more than one RIP group. Our analyses provide the foundation for further characterization of these new RIP types, to understand how these enzymes function in plants.
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Affiliation(s)
- Kyra Dougherty
- Department of Biology, York University, Toronto, Canada.
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Iglesias R, Russo R, Landi N, Valletta M, Chambery A, Di Maro A, Bolognesi A, Ferreras JM, Citores L. Structure and Biological Properties of Ribosome-Inactivating Proteins and Lectins from Elder (Sambucus nigra L.) Leaves. Toxins (Basel) 2022; 14:toxins14090611. [PMID: 36136551 PMCID: PMC9503024 DOI: 10.3390/toxins14090611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Abstract
Ribosome-inactivating proteins (RIPs) are a group of proteins with rRNA N-glycosylase activity that catalyze the removal of a specific adenine located in the sarcin–ricin loop of the large ribosomal RNA, which leads to the irreversible inhibition of protein synthesis and, consequently, cell death. The case of elderberry (Sambucus nigra L.) is unique, since more than 20 RIPs and related lectins have been isolated and characterized from the flowers, seeds, fruits, and bark of this plant. However, these kinds of proteins have never been isolated from elderberry leaves. In this work, we have purified RIPs and lectins from the leaves of this shrub, studying their main physicochemical characteristics, sequences, and biological properties. In elderberry leaves, we found one type 2 RIP and two related lectins that are specific for galactose, four type 2 RIPs that fail to agglutinate erythrocytes, and one type 1 RIP. Several of these proteins are homologous to others found elsewhere in the plant. The diversity of RIPs and lectins in the different elderberry tissues, and the different biological activities of these proteins, which have a high degree of homology with each other, constitute an excellent source of proteins that are of great interest in diagnostics, experimental therapy, and agriculture.
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Affiliation(s)
- Rosario Iglesias
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy
| | - Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy
| | - Andrea Bolognesi
- Department of Experimental, Diagnostic and Specialty Medicine-DIMES, Alma Mater Studiorum-University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - José M. Ferreras
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain
- Correspondence: (J.M.F.); (L.C.)
| | - Lucía Citores
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain
- Correspondence: (J.M.F.); (L.C.)
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Iglesias R, Ferreras JM, Llorente A, Citores L. Ebulin l Is Internalized in Cells by Both Clathrin-Dependent and -Independent Mechanisms and Does Not Require Clathrin or Dynamin for Intoxication. Toxins (Basel) 2021; 13:toxins13020102. [PMID: 33573355 PMCID: PMC7911328 DOI: 10.3390/toxins13020102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/27/2021] [Indexed: 11/21/2022] Open
Abstract
Ebulin l is an A-B toxin, and despite the presence of a B chain, this toxin displays much less toxicity to cells than the potent A-B toxin ricin. Here, we studied the binding, mechanisms of endocytosis, and intracellular pathway followed by ebulin l and compared it with ricin. COS-1 cells and HeLa cells with inducible synthesis of a mutant dynamin (K44A) were used in this study. The transport of these toxins was measured using radioactively or fluorescently labeled toxins. The data show that ebulin l binds to cells to a lesser extent than ricin. Moreover, the expression of mutant dynamin does not affect the endocytosis, degradation, or toxicity of ebulin l. However, the inhibition of clathrin-coated pit formation by acidification of the cytosol reduced ebulin l endocytosis but not toxicity. Remarkably, unlike ricin, ebulin l is not transported through the Golgi apparatus to intoxicate the cells and ebulin l induces apoptosis as the predominant cell death mechanism. Therefore, after binding to cells, ebulin l is taken up by clathrin-dependent and -independent endocytosis into the endosomal/lysosomal system, but there is no apparent role for clathrin and dynamin in productive intracellular routing leading to intoxication.
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Affiliation(s)
- Rosario Iglesias
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain; (R.I.); (J.M.F.)
| | - José M. Ferreras
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain; (R.I.); (J.M.F.)
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379 Oslo, Norway;
- Department of Mechanical, Electronics and Chemical Engineering Art and Design, Oslo Metropolitan University, 0130 Oslo, Norway
| | - Lucía Citores
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain; (R.I.); (J.M.F.)
- Correspondence:
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Ebulin-RP, a novel member of the Ebulin gene family with low cytotoxicity as a result of deficient sugar binding domains. Biochim Biophys Acta Gen Subj 2017; 1862:460-473. [PMID: 29154940 DOI: 10.1016/j.bbagen.2017.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/31/2017] [Accepted: 11/14/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Sambucus ebulus is a rich source of ribosome-inactivating proteins (RIPs) and RIP-related lectins generated from multiple genes. These proteins differ in their structure, enzymatic activity and sugar binding specificity. METHODS We have purified and characterized ebulin-RP from S. ebulus leaves and determined the amino acid sequence by cDNA cloning. Cytotoxicity was studied in a variety of cancer cells and a comparative study of the ability of ebulin-RP to bind sugars using "in vitro" and "in silico" approaches was performed. RESULTS Ebulin-RP is a novel heterodimeric type 2 RIP present in S. ebulus leaves together with the type 2 RIP ebulin l, which displayed rRNA N-glycosidase activity but unlike ebulin l, lacked functional sugar binding domains. As a consequence of changes in its B-chain, ebulin-RP displayed lower cytotoxicity than ebulin l towards cancer cells and induced apoptosis as the predominant pattern of cell death. CONCLUSIONS Ebulin-RP is a novel member of the ebulin gene family with low cytotoxicity as a result of deficient sugar binding domains. Type 2 RIP genes from Sambucus have evolved to render proteins with different sugar affinities that may be related to different biological activities and could result in an advantage for the plant. GENERAL SIGNIFICANCE The ebulin family of RIPs and lectins can serve as a good model for studying the evolutionary process which may have occurred in RIPs. The lack of cytotoxicity of ebulin-RP makes it a good candidate as a toxic moiety in the construction of immunotoxins and conjugates directed against specific targets.
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Gnanesh Kumar BS, Surolia A. Site specific N-glycan profiling of NeuAc(α2-6)-Gal/GalNAc-binding bark Sambucus nigra agglutinin using LC–MSn revealed differential glycosylation. Glycoconj J 2016; 33:907-915. [DOI: 10.1007/s10719-016-9698-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 11/30/2022]
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Schrot J, Weng A, Melzig MF. Ribosome-inactivating and related proteins. Toxins (Basel) 2015; 7:1556-615. [PMID: 26008228 PMCID: PMC4448163 DOI: 10.3390/toxins7051556] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/23/2015] [Accepted: 04/28/2015] [Indexed: 01/15/2023] Open
Abstract
Ribosome-inactivating proteins (RIPs) are toxins that act as N-glycosidases (EC 3.2.2.22). They are mainly produced by plants and classified as type 1 RIPs and type 2 RIPs. There are also RIPs and RIP related proteins that cannot be grouped into the classical type 1 and type 2 RIPs because of their different sizes, structures or functions. In addition, there is still not a uniform nomenclature or classification existing for RIPs. In this review, we give the current status of all known plant RIPs and we make a suggestion about how to unify those RIPs and RIP related proteins that cannot be classified as type 1 or type 2 RIPs.
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Affiliation(s)
- Joachim Schrot
- Institute of Pharmacy, Freie Universitaet Berlin, Koenigin-Luise-Str. 2 + 4, 14195 Berlin, Germany.
| | - Alexander Weng
- Institute of Pharmacy, Freie Universitaet Berlin, Koenigin-Luise-Str. 2 + 4, 14195 Berlin, Germany.
| | - Matthias F Melzig
- Institute of Pharmacy, Freie Universitaet Berlin, Koenigin-Luise-Str. 2 + 4, 14195 Berlin, Germany.
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Jiménez P, Tejero J, Cordoba-Diaz D, Quinto EJ, Garrosa M, Gayoso MJ, Girbés T. Ebulin from dwarf elder (Sambucus ebulus L.): a mini-review. Toxins (Basel) 2015; 7:648-58. [PMID: 25723322 PMCID: PMC4379516 DOI: 10.3390/toxins7030648] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 01/30/2015] [Accepted: 02/15/2015] [Indexed: 11/16/2022] Open
Abstract
Sambucus ebulus L. (dwarf elder) is a medicinal plant, the usefulness of which also as food is restricted due to its toxicity. In the last few years, both the chemistry and pharmacology of Sambucus ebulus L. have been investigated. Among the structural and functional proteins present in the plant, sugar-binding proteins (lectins) with or without anti-ribosomal activity and single chain ribosome-inactivating proteins (RIPs) have been isolated. RIPs are enzymes (E.C. 3.2.2.22) that display N-glycosidase activity on the 28S rRNA subunit, leading to the inhibition of protein synthesis by arresting the step of polypeptide chain elongation. The biological role of all these proteins is as yet unknown. The evidence suggests that they could be involved in the defense of the plant against predators and viruses or/and a nitrogen store, with an impact on the nutritional characteristics and food safety. In this mini-review we describe all the isoforms of ebulin that have to date been isolated from dwarf elder, as well as their functional characteristics and potential uses, whilst highlighting concern regarding ebulin toxicity.
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Affiliation(s)
- Pilar Jiménez
- Nutrition and Food Science, Faculty of Medicine, and CINAD (Center for Research in Nutrition, Food and Dietetics), University of Valladolid, Valladolid E-47005, Spain.
| | - Jesús Tejero
- Nutrition and Food Science, Faculty of Medicine, and CINAD (Center for Research in Nutrition, Food and Dietetics), University of Valladolid, Valladolid E-47005, Spain.
| | - Damián Cordoba-Diaz
- Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, and IUFI (Institute of Industrial Pharmacy), Complutense University of Madrid, Madrid E-28040, Spain.
| | - Emiliano J Quinto
- Nutrition and Food Science, Faculty of Medicine, and CINAD (Center for Research in Nutrition, Food and Dietetics), University of Valladolid, Valladolid E-47005, Spain.
| | - Manuel Garrosa
- Cell Biology, Histology and Pharmacology, Faculty of Medicine, and INCYL (Institute of Neurosciences of Castile and Leon), University of Valladolid, Valladolid E-47005, Spain.
| | - Manuel J Gayoso
- Cell Biology, Histology and Pharmacology, Faculty of Medicine, and INCYL (Institute of Neurosciences of Castile and Leon), University of Valladolid, Valladolid E-47005, Spain.
| | - Tomás Girbés
- Nutrition and Food Science, Faculty of Medicine, and CINAD (Center for Research in Nutrition, Food and Dietetics), University of Valladolid, Valladolid E-47005, Spain.
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Tejero J, Jiménez P, Quinto EJ, Cordoba-Diaz D, Garrosa M, Cordoba-Diaz M, Gayoso MJ, Girbés T. Elderberries: a source of ribosome-inactivating proteins with lectin activity. Molecules 2015; 20:2364-87. [PMID: 25647575 PMCID: PMC6272206 DOI: 10.3390/molecules20022364] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 11/16/2022] Open
Abstract
Sambucus (Adoxaceae) species have been used for both food and medicine purposes. Among these, Sambucus nigra L. (black elder), Sambucus ebulus L. (dwarf elder), and Sambucus sieboldiana L. are the most relevant species studied. Their use has been somewhat restricted due to the presence of bioactive proteins or/and low molecular weight compounds whose ingestion could trigger deleterious effects. Over the last few years, the chemical and pharmacological characteristics of Sambucus species have been investigated. Among the proteins present in Sambucus species both type 1, and type 2 ribosome-inactivating proteins (RIPs), and hololectins have been reported. The biological role played by these proteins remains unknown, although they are conjectured to be involved in defending plants against insect predators and viruses. These proteins might have an important impact on the nutritional characteristics and food safety of elderberries. Type 2 RIPs are able to interact with gut cells of insects and mammals triggering a number of specific and mostly unknown cell signals in the gut mucosa that could significantly affect animal physiology. In this paper, we describe all known RIPs that have been isolated to date from Sambucus species, and comment on their antiviral and entomotoxic effects, as well as their potential uses.
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Affiliation(s)
- Jesús Tejero
- Nutrición y Bromatología, Facultad de Medicina and Centro de Investigación en Nutrición, Alimentación y Dietética (CINAD), Universidad de Valladolid, Valladolid 47005, Spain.
| | - Pilar Jiménez
- Nutrición y Bromatología, Facultad de Medicina and Centro de Investigación en Nutrición, Alimentación y Dietética (CINAD), Universidad de Valladolid, Valladolid 47005, Spain.
| | - Emiliano J Quinto
- Nutrición y Bromatología, Facultad de Medicina and Centro de Investigación en Nutrición, Alimentación y Dietética (CINAD), Universidad de Valladolid, Valladolid 47005, Spain.
| | - Damián Cordoba-Diaz
- Farmacia y Tecnología Farmacéutica, Facultad de Farmacia and Instituto Universitario de Farmacia Industrial (IUFI), Universidad Complutense de Madrid, Madrid 28040, Spain.
| | - Manuel Garrosa
- Biología Celular, Histología y Farmacología, Facultad de Medicina and Instituto de Neurociencias de Castilla y León (INCYL), Universidad de Valladolid, Valladolid 47005, Spain.
| | - Manuel Cordoba-Diaz
- Farmacia y Tecnología Farmacéutica, Facultad de Farmacia and Instituto Universitario de Farmacia Industrial (IUFI), Universidad Complutense de Madrid, Madrid 28040, Spain.
| | - Manuel J Gayoso
- Biología Celular, Histología y Farmacología, Facultad de Medicina and Instituto de Neurociencias de Castilla y León (INCYL), Universidad de Valladolid, Valladolid 47005, Spain.
| | - Tomás Girbés
- Nutrición y Bromatología, Facultad de Medicina and Centro de Investigación en Nutrición, Alimentación y Dietética (CINAD), Universidad de Valladolid, Valladolid 47005, Spain.
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Ferreras JM, Citores L, Iglesias R, Jiménez P, Girbés T. Use of ribosome-inactivating proteins from Sambucus for the construction of immunotoxins and conjugates for cancer therapy. Toxins (Basel) 2011; 3:420-41. [PMID: 22069717 PMCID: PMC3202832 DOI: 10.3390/toxins3050420] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/02/2011] [Accepted: 04/25/2011] [Indexed: 01/28/2023] Open
Abstract
The type 2 ribosome-inactivating proteins (RIPs) isolated from some species belonging to the Sambucus genus, have the characteristic that although being even more active than ricin inhibiting protein synthesis in cell-free extracts, they lack the high toxicity of ricin and related type 2 RIPs to intact cells and animals. This is due to the fact that after internalization, they follow a different intracellular pathway that does not allow them to reach the cytosolic ribosomes. The lack of toxicity of type 2 RIPs from Sambucus make them good candidates as toxic moieties in the construction of immunotoxins and conjugates directed against specific targets. Up to now they have been conjugated with either transferrin or anti-CD105 to target either transferrin receptor- or endoglin-overexpressing cells, respectively.
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Affiliation(s)
- José M. Ferreras
- Department of Biochemistry, Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47005 Valladolid, Spain; (L.C.); (R.I.)
| | - Lucía Citores
- Department of Biochemistry, Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47005 Valladolid, Spain; (L.C.); (R.I.)
| | - Rosario Iglesias
- Department of Biochemistry, Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47005 Valladolid, Spain; (L.C.); (R.I.)
| | - Pilar Jiménez
- Nutrition and Bromatology, Faculty of Medicine, E-47005 Valladolid, Spain; (P.J.); (T.G.)
| | - Tomás Girbés
- Nutrition and Bromatology, Faculty of Medicine, E-47005 Valladolid, Spain; (P.J.); (T.G.)
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