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Toxins
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ADP-Ribosylation and Beyond
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ADP-Ribosylation and Beyond

A special issue of Toxins (ISSN 2072-6651). This special issue belongs to the section "Bacterial Toxins".

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 6555

Special Issue Editor

Prof. Dr. Hideaki Tsuge

E-Mail Website
Guest Editor
Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
Interests: ADP-ribosylating toxin; binary toxin; protein translocation; clostridium perfringens toxin; clostridioides difficile toxin; toxin-host interaction

Special Issue Information

Dear Colleagues,

ADP-ribosylation is a reversible post-translational modification defined by adding ADP-ribose moieties from NAD+ to the target. ADP-ribosylaton is widely used post-trans-modifications in all kingdoms of life. The system likely originated in bacteria, which functions in inter- and intra-species signalling, and stress response. At first, as bacterial toxins, it was found that cholera toxin ADP-ribosylates a specific arginine in the Gsa of heteromeric G-proteins, and the diphtheria toxin ADP-ribosdylates the eukaryotic elongation factor 2 (eEF2). Later, the ARTC and ARTD families were named because they are characterized by a catalytic domain fold related to cholera toxin or diphtheria toxin, respectively. For understanding mammalian ADP-ribosylation systems, these classifications were used. Later, other toxins such as C3 exoenzyme and C2 toxin were found to ADP-ribosylate RhoA and actin, respectively. These canonical bacterial toxins studies could give us basic knowledge of ADP-ribosylation.

On the other hand, recent studies opened the non-canonical ADP-ribosylation system. (1) DNA ADP-ribosylation: The target of ADP-ribosylation is not only protein but also nucleic acids, DNA. For example, pierisin found in cabbage butterflies was shown to modify DNA. Its related enzyme Streptomyces coelicolor　ScARP ADP-ribosylates GDP. Following, reversible ADP-ribosylation of DNA on thymidine bases occurs through the DarT-DarG toxin-antitoxin system, which is found in a variety of bacteria, including such as Mycobacterium tuberculosis, enteropathogenic Escherichia coli and Pseudomonas aeruginosa. (2) Ubiquitination via ADP-ribosylations: Legionella pneumophila SidE effector ubiquitylates serine residues in substrate via an ADP-ribosylated ubiquitin intermediate without E1 and E2 enzymes. (3) ADP-riboxanation: The type III secretion system effector of Shigella flexneri, OspC3, ADP-ribosylates the caspase and then followed by non-enzymatic deamidation.

In addition to a basic understanding of canonical ADP-ribosylation, studies of non-canonical ADP-ribosylation would benefit an understanding of deep ADP ribosylation systems. Therefore, we are calling for the community to submit original research articles or reviews on elucidating the role of ADP-ribosylation, including both canonical and non-canonical ADP-ribosylation systems. The target includes not only bacterial enzymes but also plant, insect and virus enzymes.

Prof. Dr. Hideaki Tsuge
Guest Editor

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Keywords

  • canonical ADP-ribosylation
  • non-canonical ADP-ribosylation
  • ubiquitination
  • DNA ADP-ribosylation
  • ADP-riboxanation

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Published Papers (5 papers)

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Review

9 pages, 1979 KiB  
Review
An Emerging Way for Bacteria to Engage with Host Cells via Protein ADP-riboxanation
by Wei Xian, Zhiheng Tang, Qinxin Zhang, Ying Wang and Xiaoyun Liu
Toxins 2024, 16(11), 467; https://doi.org/10.3390/toxins16110467 - 1 Nov 2024
Viewed by 530
Abstract
Post-translational modifications (PTMs) are increasingly recognized as important strategies used by bacterial pathogens to modulate host cellular functions. Protein ADP-riboxanation, a derivative of ADP-ribosylation, has recently emerged as a new biochemical way by which bacterial pathogens interact with host cells. Recent studies have [...] Read more.
Post-translational modifications (PTMs) are increasingly recognized as important strategies used by bacterial pathogens to modulate host cellular functions. Protein ADP-riboxanation, a derivative of ADP-ribosylation, has recently emerged as a new biochemical way by which bacterial pathogens interact with host cells. Recent studies have revealed that this modification has broad regulatory roles in host processes including cell death, protein translation, and stress granule formation. Given that the vast majority of bacterial ADP-riboxanases are still uncharacterized, in this review we also highlight the utility of advanced proteomic tools in the functional dissection of ADP-riboxanation events during bacterial infections. Full article
(This article belongs to the Special Issue ADP-Ribosylation and Beyond)
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9 pages, 1159 KiB  
Review
DNA Repair and Mutagenesis of ADP-Ribosylated DNA by Pierisin
by Masanobu Kawanishi, Takashi Yagi, Yukari Totsuka and Keiji Wakabayashi
Toxins 2024, 16(8), 331; https://doi.org/10.3390/toxins16080331 - 26 Jul 2024
Viewed by 865
Abstract
Pierisin is a DNA-targeting ADP-ribosyltransferase found in cabbage white butterfly (Pieris rapae). Pierisin transfers an ADP-ribosyl moiety to the 2-amino group of the guanine residue in DNA, yielding N2-(ADP-ribos-1-yl)-2′-deoxyguanosine (N2-ADPR-dG). Generally, such chemically modified DNA is [...] Read more.
Pierisin is a DNA-targeting ADP-ribosyltransferase found in cabbage white butterfly (Pieris rapae). Pierisin transfers an ADP-ribosyl moiety to the 2-amino group of the guanine residue in DNA, yielding N2-(ADP-ribos-1-yl)-2′-deoxyguanosine (N2-ADPR-dG). Generally, such chemically modified DNA is recognized as DNA damage and elicits cellular responses, including DNA repair pathways. In Escherichia coli and human cells, it has been experimentally demonstrated that N2-ADPR-dG is a substrate of the nucleotide excision repair system. Although DNA repair machineries can remove most lesions, some unrepaired damages frequently lead to mutagenesis through DNA replication. Replication past the damaged DNA template is called translesion DNA synthesis (TLS). In vitro primer extension experiments have shown that eukaryotic DNA polymerase κ is involved in TLS across N2-ADPR-dG. In many cases, TLS is error-prone and thus a mutagenic process. Indeed, the induction of G:C to T:A and G:C to C:G mutations by N2-ADPR-dG in the hypoxanthine phosphoribosyltransferase gene mutation assay with Chinese hamster cells and supF shuttle vector plasmids assay using human fibroblasts has been reported. This review provides a detailed overview of DNA repair, TLS and mutagenesis of N2-ADPR-dG induced by cabbage butterfly pierisin-1. Full article
(This article belongs to the Special Issue ADP-Ribosylation and Beyond)
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14 pages, 2717 KiB  
Review
General ADP-Ribosylation Mechanism Based on the Structure of ADP-Ribosyltransferase–Substrate Complexes
by Hideaki Tsuge, Noriyuki Habuka and Toru Yoshida
Toxins 2024, 16(7), 313; https://doi.org/10.3390/toxins16070313 - 11 Jul 2024
Viewed by 972
Abstract
ADP-ribosylation is a ubiquitous modification of proteins and other targets, such as nucleic acids, that regulates various cellular functions in all kingdoms of life. Furthermore, these ADP-ribosyltransferases (ARTs) modify a variety of substrates and atoms. It has been almost 60 years since ADP-ribosylation [...] Read more.
ADP-ribosylation is a ubiquitous modification of proteins and other targets, such as nucleic acids, that regulates various cellular functions in all kingdoms of life. Furthermore, these ADP-ribosyltransferases (ARTs) modify a variety of substrates and atoms. It has been almost 60 years since ADP-ribosylation was discovered. Various ART structures have been revealed with cofactors (NAD+ or NAD+ analog). However, we still do not know the molecular mechanisms of ART. It needs to be better understood how ART specifies the target amino acids or bases. For this purpose, more information is needed about the tripartite complex structures of ART, the cofactors, and the substrates. The tripartite complex is essential to understand the mechanism of ADP-ribosyltransferase. This review updates the general ADP-ribosylation mechanism based on ART tripartite complex structures. Full article
(This article belongs to the Special Issue ADP-Ribosylation and Beyond)
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12 pages, 1462 KiB  
Review
Pierisin, Cytotoxic and Apoptosis-Inducing DNA ADP-Ribosylating Protein in Cabbage Butterfly
by Azusa Takahashi-Nakaguchi, Yu Horiuchi, Masafumi Yamamoto, Yukari Totsuka and Keiji Wakabayashi
Toxins 2024, 16(6), 270; https://doi.org/10.3390/toxins16060270 - 14 Jun 2024
Cited by 1 | Viewed by 1081
Abstract
Pierisin-1 was serendipitously discovered as a strong cytotoxic and apoptosis-inducing protein from pupae of the cabbage butterfly Pieris rapae against cancer cell lines. This 98-kDa protein consists of the N-terminal region (27 kDa) and C-terminal region (71 kDa), and analysis of their biological [...] Read more.
Pierisin-1 was serendipitously discovered as a strong cytotoxic and apoptosis-inducing protein from pupae of the cabbage butterfly Pieris rapae against cancer cell lines. This 98-kDa protein consists of the N-terminal region (27 kDa) and C-terminal region (71 kDa), and analysis of their biological function revealed that pierisin-1 binds to cell surface glycosphingolipids on the C-terminal side, is taken up into the cell, and is cleaved to N- and C-terminal portions, where the N-terminal portion mono-ADP-ribosylates the guanine base of DNA in the presence of NAD to induce cellular genetic mutation and apoptosis. Unlike other ADP-ribosyltransferases, pieisin-1 was first found to exhibit DNA mono-ADP-ribosylating activity and show anti-cancer activity in vitro and in vivo against various cancer cell lines. Pierisin-1 was most abundantly produced during the transition from the final larval stage to the pupal stage of the cabbage butterfly, and this production was regulated by ecdysteroid hormones. This suggests that pierisn-1 might play a pivotal role in the process of metamorphosis. Moreover, pierisin-1 could contribute as a defense factor against parasitization and microbial infections in the cabbage butterfly. Pierisin-like proteins in butterflies were shown to be present not only among the subtribe Pierina but also among the subtribes Aporiina and Appiadina, and pierisin-2, -3, and -4 were identified in these butterflies. Furthermore, DNA ADP-ribosylating activities were found in six different edible clams. Understanding of the biological nature of pierisin-1 with DNA mono-ADP-ribosylating activity could open up exciting avenues for research and potential therapeutic applications, making it a subject of great interest in the field of molecular biology and biotechnology. Full article
(This article belongs to the Special Issue ADP-Ribosylation and Beyond)
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11 pages, 670 KiB  
Review
Cellular Uptake and Cytotoxicity of Clostridium perfringens Iota-Toxin
by Masahiro Nagahama, Masaya Takehara, Soshi Seike and Yoshihiko Sakaguchi
Toxins 2023, 15(12), 695; https://doi.org/10.3390/toxins15120695 - 11 Dec 2023
Cited by 3 | Viewed by 2176
Abstract
Clostridium perfringens iota-toxin is composed of two separate proteins: a binding protein (Ib) that recognizes a host cell receptor and promotes the cellular uptake of a catalytic protein and (Ia) possessing ADP-ribosyltransferase activity that induces actin cytoskeleton disorganization. Ib exhibits the overall structure [...] Read more.
Clostridium perfringens iota-toxin is composed of two separate proteins: a binding protein (Ib) that recognizes a host cell receptor and promotes the cellular uptake of a catalytic protein and (Ia) possessing ADP-ribosyltransferase activity that induces actin cytoskeleton disorganization. Ib exhibits the overall structure of bacterial pore-forming toxins (PFTs). Lipolysis-stimulated lipoprotein receptor (LSR) is defined as a host cell receptor for Ib. The binding of Ib to LSR causes an oligomer formation of Ib in lipid rafts of plasma membranes, mediating the entry of Ia into the cytoplasm. Ia induces actin cytoskeleton disruption via the ADP-ribosylation of G-actin and causes cell rounding and death. The binding protein alone disrupts the cell membrane and induces cytotoxicity in sensitive cells. Host cells permeabilized by the pore formation of Ib are repaired by a Ca2+-dependent plasma repair pathway. This review shows that the cellular uptake of iota-toxin utilizes a pathway of plasma membrane repair and that Ib alone induces cytotoxicity. Full article
(This article belongs to the Special Issue ADP-Ribosylation and Beyond)
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