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Wu H, Lu A, Yuan J, Yu Y, Lv C, Lu J. Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms. Cell Death Discov 2024; 10:226. [PMID: 38734665 PMCID: PMC11088682 DOI: 10.1038/s41420-024-01994-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
The functional alterations of proteins and nucleic acids mainly rely on their modifications. ADP-ribosylation is a NAD+-dependent modification of proteins and, in some cases, of nucleic acids. This modification is broadly categorized as Mono(ADP-ribosyl)ation (MARylation) or poly(ADP-ribosyl)ation (PARylation). MARylation catalyzed by mono(ADP-ribosyl) transferases (MARTs) is more common in cells and the number of MARTs is much larger than poly(ADP-ribosyl) transferases. Unlike PARylation is well-characterized, research on MARylation is at the starting stage. However, growing evidence demonstrate the cellular functions of MARylation, supporting its potential roles in human health and diseases. In this review, we outlined MARylation-associated proteins including MARTs, the ADP-ribosyl hydrolyses and ADP-ribose binding domains. We summarized up-to-date findings about MARylation onto newly identified substrates including protein, DNA and RNA, and focused on the functions of these reactions in pathophysiological conditions as well as speculated the potential mechanisms. Furthermore, new strategies of MARylation detection and the current state of MARTs inhibitors were discussed. We also provided an outlook for future study, aiming to revealing the unknown biological properties of MARylation and its relevant mechanisms, and establish a novel therapeutic perspective in human diseases.
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Affiliation(s)
- Hao Wu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Anqi Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Jiuzhi Yuan
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yang Yu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Chongning Lv
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China
| | - Jincai Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China.
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China.
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2
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Doksani Y, Lottersberger F. The risky business of ADP-ribosylating telomeric DNA. Nat Struct Mol Biol 2024; 31:737-738. [PMID: 38714888 DOI: 10.1038/s41594-024-01285-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Affiliation(s)
- Ylli Doksani
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Francisca Lottersberger
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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3
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Cihlova B, Lu Y, Mikoč A, Schuller M, Ahel I. Specificity of DNA ADP-Ribosylation Reversal by NADARs. Toxins (Basel) 2024; 16:208. [PMID: 38787060 PMCID: PMC11125620 DOI: 10.3390/toxins16050208] [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: 03/18/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Recent discoveries establish DNA and RNA as bona fide substrates for ADP-ribosylation. NADAR ("NAD- and ADP-ribose"-associated) enzymes reverse guanine ADP-ribosylation and serve as antitoxins in the DarT-NADAR operon. Although NADARs are widespread across prokaryotes, eukaryotes, and viruses, their specificity and broader physiological roles remain poorly understood. Using phylogenetic and biochemical analyses, we further explore de-ADP-ribosylation activity and antitoxin functions of NADAR domains. We demonstrate that different subfamilies of NADAR proteins from representative E. coli strains and an E. coli-infecting phage retain biochemical activity while displaying specificity in providing protection from toxic guanine ADP-ribosylation in cells. Furthermore, we identify a myxobacterial enzyme within the YbiA subfamily that functions as an antitoxin for its associated DarT-unrelated ART toxin, which we termed YarT, thus presenting a hitherto uncharacterised ART-YbiA toxin-antitoxin pair. Our studies contribute to the burgeoning field of DNA ADP-ribosylation, supporting its physiological relevance within and beyond bacterial toxin-antitoxin systems. Notably, the specificity and confinement of NADARs to non-mammals infer their potential as highly specific targets for antimicrobial drugs with minimal off-target effects.
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Affiliation(s)
- Bara Cihlova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
| | - Yang Lu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
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4
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Lye PY, Shiraki C, Fukushima Y, Takaki K, Liew MWO, Yamamoto M, Wakabayashi K, Mori H, Kotani E. Cytotoxin-mediated silk gland organ dysfunction diverts resources to enhance silkworm fecundity by potentiating nutrient-sensing IIS/TOR pathways. iScience 2024; 27:108853. [PMID: 38303707 PMCID: PMC10830876 DOI: 10.1016/j.isci.2024.108853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/16/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024] Open
Abstract
Energy reserves, primarily stored in the insect's fat body, are essential for physiological processes such as reproduction and cocoon formation. However, whether these processes are mutually constraining is unknown. Here, we showed that cocoon-free silkworms accumulate amino acid constituents of silk proteins in the hemolymph and maintain lipid and sugar reserves in the pupal fat body by repressing the expression of sericin and fibroin genes in the middle and posterior silk glands, respectively, via butterfly pierisin-1A catalytic domain expression. This, in turn, upregulates insulin/insulin-like signaling and target of rapamycin (IIS/TOR) signaling, which enhances vitellogenesis and accelerates ovarian development, thus contributing to increased fecundity. The impacts of semi-starvation on fecundity and egg hatchability were also less pronounced in cocoon-free silkworms compared with wildtype silkworms. These data uncover the resource allocation trade-off between cocoon formation and fecundity and demonstrate that nutritional signaling plays a role in regulating silkworm reproduction.
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Affiliation(s)
- Ping Ying Lye
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Chika Shiraki
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yuta Fukushima
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Keiko Takaki
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
- Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Mervyn Wing On Liew
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang 11800, Malaysia
| | - Masafumi Yamamoto
- ICLAS Monitoring Center, Central Institute for Experimental Animals, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Keiji Wakabayashi
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hajime Mori
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Eiji Kotani
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
- Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
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5
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Zhu K, Suskiewicz MJ, Chatrin C, Strømland Ø, Dorsey B, Aucagne V, Ahel D, Ahel I. DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on nucleic acids. Nucleic Acids Res 2024; 52:801-815. [PMID: 38000390 PMCID: PMC10810221 DOI: 10.1093/nar/gkad1119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although ubiquitylation had traditionally been considered limited to proteins, the discovery of non-proteinaceous substrates (e.g. lipopolysaccharides and adenosine diphosphate ribose (ADPr)) challenged this perspective. Our recent study showed that DTX2 E3 ligase efficiently ubiquitylates ADPr. Here, we show that the ADPr ubiquitylation activity is also present in another DELTEX family member, DTX3L, analysed both as an isolated catalytic fragment and the full-length PARP9:DTX3L complex, suggesting that it is a general feature of the DELTEX family. Since structural predictions show that DTX3L possesses single-stranded nucleic acids binding ability and given the fact that nucleic acids have recently emerged as substrates for ADP-ribosylation, we asked whether DELTEX E3s might catalyse ubiquitylation of an ADPr moiety linked to nucleic acids. Indeed, we show that DTX3L and DTX2 are capable of ubiquitylating ADP-ribosylated DNA and RNA synthesized by PARPs, including PARP14. Furthermore, we demonstrate that the Ub-ADPr-nucleic acids conjugate can be reversed by two groups of hydrolases, which remove either the whole adduct (e.g. SARS-CoV-2 Mac1 or PARP14 macrodomain 1) or just the Ub (e.g. SARS-CoV-2 PLpro). Overall, this study reveals ADPr ubiquitylation as a general function of the DELTEX family E3s and presents the evidence of reversible ubiquitylation of ADP-ribosylated nucleic acids.
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Affiliation(s)
- Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Bryan W Dorsey
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge MA 02140, USA
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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6
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Schuller M, Raggiaschi R, Mikolcevic P, Rack JGM, Ariza A, Zhang Y, Ledermann R, Tang C, Mikoc A, Ahel I. Molecular basis for the reversible ADP-ribosylation of guanosine bases. Mol Cell 2023:S1097-2765(23)00457-4. [PMID: 37390817 DOI: 10.1016/j.molcel.2023.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/13/2023] [Accepted: 06/08/2023] [Indexed: 07/02/2023]
Abstract
Modification of nucleic acids by ADP-ribosylation is catalyzed by various ADP-ribosyltransferases, including the DarT enzyme. The latter is part of the bacterial toxin-antitoxin (TA) system DarTG, which was shown to provide control of DNA replication and bacterial growth as well as protection against bacteriophages. Two subfamilies have been identified, DarTG1 and DarTG2, which are distinguished by their associated antitoxins. While DarTG2 catalyzes reversible ADP-ribosylation of thymidine bases employing a macrodomain as antitoxin, the DNA ADP-ribosylation activity of DarTG1 and the biochemical function of its antitoxin, a NADAR domain, are as yet unknown. Using structural and biochemical approaches, we show that DarT1-NADAR is a TA system for reversible ADP-ribosylation of guanosine bases. DarT1 evolved the ability to link ADP-ribose to the guanine amino group, which is specifically hydrolyzed by NADAR. We show that guanine de-ADP-ribosylation is also conserved among eukaryotic and non-DarT-associated NADAR members, indicating a wide distribution of reversible guanine modifications beyond DarTG systems.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Petra Mikolcevic
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Johannes G M Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Antonio Ariza
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - YuGeng Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Christoph Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Andreja Mikoc
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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7
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Henao L, Zade RSH, Restrepo S, Husserl J, Abeel T. Genomes of four Streptomyces strains reveal insights into putative new species and pathogenicity of scab-causing organisms. BMC Genomics 2023; 24:143. [PMID: 36959546 PMCID: PMC10037901 DOI: 10.1186/s12864-023-09190-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/15/2023] [Indexed: 03/25/2023] Open
Abstract
Genomes of four Streptomyces isolates, two putative new species (Streptomyces sp. JH14 and Streptomyces sp. JH34) and two non thaxtomin-producing pathogens (Streptomyces sp. JH002 and Streptomyces sp. JH010) isolated from potato fields in Colombia were selected to investigate their taxonomic classification, their pathogenicity, and the production of unique secondary metabolites of Streptomycetes inhabiting potato crops in this region. The average nucleotide identity (ANI) value calculated between Streptomyces sp. JH34 and its closest relatives (92.23%) classified this isolate as a new species. However, Streptomyces sp. JH14 could not be classified as a new species due to the lack of genomic data of closely related strains. Phylogenetic analysis based on 231 single-copy core genes, confirmed that the two pathogenic isolates (Streptomyces sp. JH010 and JH002) belong to Streptomyces pratensis and Streptomyces xiamenensis, respectively, are distant from the most well-known pathogenic species, and belong to two different lineages. We did not find orthogroups of protein-coding genes characteristic of scab-causing Streptomycetes shared by all known pathogenic species. Most genes involved in biosynthesis of known virulence factors are not present in the scab-causing isolates (Streptomyces sp. JH002 and Streptomyces sp. JH010). However, Tat-system substrates likely involved in pathogenicity in Streptomyces sp. JH002 and Streptomyces sp. JH010 were identified. Lastly, the presence of a putative mono-ADP-ribosyl transferase, homologous to the virulence factor scabin, was confirmed in Streptomyces sp. JH002. The described pathogenic isolates likely produce virulence factors uncommon in Streptomyces species, including a histidine phosphatase and a metalloprotease potentially produced by Streptomyces sp. JH002, and a pectinesterase, potentially produced by Streptomyces sp. JH010. Biosynthetic gene clusters (BGCs) showed the presence of clusters associated with the synthesis of medicinal compounds and BGCs potentially linked to pathogenicity in Streptomyces sp. JH010 and JH002. Interestingly, BGCs that have not been previously reported were also found. Our findings suggest that the four isolates produce novel secondary metabolites and metabolites with medicinal properties.
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Affiliation(s)
- Laura Henao
- Department of Civil and Environmental Engineering, Universidad de los Andes, 111711, Bogotá, Colombia
| | | | - Silvia Restrepo
- Laboratory of Mycology and Phytopathology - (LAMFU), Department of Chemical and Food Engineering, Universidad de los Andes, 111711, Bogotá, Colombia
| | - Johana Husserl
- Department of Civil and Environmental Engineering, Universidad de los Andes, 111711, Bogotá, Colombia
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, 2628 XE, Delft, Netherlands.
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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8
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Pangenomic analysis reveals plant NAD + manipulation as an important virulence activity of bacterial pathogen effectors. Proc Natl Acad Sci U S A 2023; 120:e2217114120. [PMID: 36753463 PMCID: PMC9963460 DOI: 10.1073/pnas.2217114120] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) has emerged as a key component in prokaryotic and eukaryotic immune systems. The recent discovery that Toll/interleukin-1 receptor (TIR) proteins function as NAD+ hydrolases (NADase) links NAD+-derived small molecules with immune signaling. We investigated pathogen manipulation of host NAD+ metabolism as a virulence strategy. Using the pangenome of the model bacterial pathogen Pseudomonas syringae, we conducted a structure-based similarity search from 35,000 orthogroups for type III effectors (T3Es) with potential NADase activity. Thirteen T3Es, including five newly identified candidates, were identified that possess domain(s) characteristic of seven NAD+-hydrolyzing enzyme families. Most Pseudomonas syringae strains that depend on the type III secretion system to cause disease, encode at least one NAD+-manipulating T3E, and many have several. We experimentally confirmed the type III-dependent secretion of a novel T3E, named HopBY, which shows structural similarity to both TIR and adenosine diphosphate ribose (ADPR) cyclase. Homologs of HopBY were predicted to be type VI effectors in diverse bacterial species, indicating potential recruitment of this activity by microbial proteins secreted during various interspecies interactions. HopBY efficiently hydrolyzes NAD+ and specifically produces 2'cADPR, which can also be produced by TIR immune receptors of plants and by other bacteria. Intriguingly, this effector promoted bacterial virulence, indicating that 2'cADPR may not be the signaling molecule that directly initiates immunity. This study highlights a host-pathogen battleground centered around NAD+ metabolism and provides insight into the NAD+-derived molecules involved in plant immunity.
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9
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Musheev MU, Schomacher L, Basu A, Han D, Krebs L, Scholz C, Niehrs C. Mammalian N1-adenosine PARylation is a reversible DNA modification. Nat Commun 2022; 13:6138. [PMID: 36253381 PMCID: PMC9576699 DOI: 10.1038/s41467-022-33731-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
Poly-ADP-ribosylation (PARylation) is regarded as a protein-specific modification. However, some PARPs were recently shown to modify DNA termini in vitro. Here, we use ultrasensitive mass spectrometry (LC-MS/MS), anti-PAR antibodies, and anti-PAR reagents to show that mammalian DNA is physiologically PARylated and to different levels in primary tissues. Inhibition of PAR glycohydrolase (PARG) increases DNA PARylation, supporting that the modification is reversible. DNA PARylation requires PARP1 and in vitro PARP1 PARylates single-stranded DNA, while PARG reverts the modification. DNA PARylation occurs at the N1-position of adenosine residues to form N1-Poly(ADP-ribosyl)-deoxyadenosine. Through partial hydrolysis of mammalian gDNA we identify PAR-DNA via the diagnostic deamination product N1-ribosyl-deoxyinosine to occur in vivo. The discovery of N1-adenosine PARylation as a DNA modification establishes the conceptual and methodological framework to elucidate its biological relevance and extends the role of PARP enzymes.
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Affiliation(s)
- Michael U. Musheev
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Lars Schomacher
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Amitava Basu
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dandan Han
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany ,Present Address: STEMCELL Technologies Germany GmbH, 50933 Cologne, Germany
| | - Laura Krebs
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Carola Scholz
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Christof Niehrs
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany ,grid.509524.fDivision of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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10
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Weixler L, Feijs KLH, Zaja R. ADP-ribosylation of RNA in mammalian cells is mediated by TRPT1 and multiple PARPs. Nucleic Acids Res 2022; 50:9426-9441. [PMID: 36018800 PMCID: PMC9458441 DOI: 10.1093/nar/gkac711] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022] Open
Abstract
RNA function relies heavily on posttranscriptional modifications. Recently, it was shown that certain PARPs and TRPT1 can ADP-ribosylate RNA in vitro. Traditionally, intracellular ADP-ribosylation has been considered mainly as a protein posttranslational modification. To date, it is not clear whether RNA ADP-ribosylation occurs in cells. Here we present evidence that different RNA species are ADP-ribosylated in human cells. The modification of cellular RNA is mediated by several transferases such as TRPT1, PARP10, PARP11, PARP12 and PARP15 and is counteracted by different hydrolases including TARG1, PARG and ARH3. In addition, diverse cellular stressors can modulate the content of ADP-ribosylated RNA in cells. We next investigated potential consequences of ADP-ribosylation for RNA and found that ADPr-capped mRNA is protected against XRN1 mediated degradation but is not translated. T4 RNA ligase 1 can ligate ADPr-RNA in absence of ATP, resulting in the incorporation of an abasic site. We thus provide the first evidence of RNA ADP-ribosylation in mammalian cells and postulate potential functions of this novel RNA modification.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen 52074, Germany
| | - Karla L H Feijs
- Correspondence may also be addressed to Karla L.H. Feijs. Tel: +49 2418080692; Fax: +49 2418082427;
| | - Roko Zaja
- To whom correspondence should be addressed. Tel: +49 2418037944; Fax: +49 2418082427;
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11
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Li P, Lei Y, Qi J, Liu W, Yao K. Functional roles of ADP-ribosylation writers, readers and erasers. Front Cell Dev Biol 2022; 10:941356. [PMID: 36035988 PMCID: PMC9404506 DOI: 10.3389/fcell.2022.941356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
ADP-ribosylation is a reversible post-translational modification (PTM) tightly regulated by the dynamic interplay between its writers, readers and erasers. As an intricate and versatile PTM, ADP-ribosylation plays critical roles in various physiological and pathological processes. In this review, we discuss the major players involved in the ADP-ribosylation cycle, which may facilitate the investigation of the ADP-ribosylation function and contribute to the understanding and treatment of ADP-ribosylation associated disease.
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12
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Yamano M, Hirose R, Lye PY, Takaki K, Maruta R, On Liew MW, Sakurai S, Mori H, Kotani E. Bioengineered Silkworm for Producing Cocoons with High Fibroin Content for Regenerated Fibroin Biomaterial-Based Applications. Int J Mol Sci 2022; 23:ijms23137433. [PMID: 35806440 PMCID: PMC9267247 DOI: 10.3390/ijms23137433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/12/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Abstract
Silk fibroin exhibits high biocompatibility and biodegradability, making it a versatile biomaterial for medical applications. However, contaminated silkworm-derived substances in remnant sericin from the filature and degumming process can result in undesired immune reactions and silk allergy, limiting the widespread use of fibroin. Here, we established transgenic silkworms with modified middle silk glands, in which sericin expression was repressed by the ectopic expression of cabbage butterfly-derived cytotoxin pierisin-1A, to produce cocoons composed solely of fibroin. Intact, nondegraded fibroin can be prepared from the transgenic cocoons without the need for sericin removal by the filature and degumming steps that cause fibroin degradation. A wide-angle X-ray diffraction analysis revealed low crystallinity in the transgenic cocoons. However, nondegraded fibroin obtained from transgenic cocoons enabled the formation of fibroin sponges with varying densities by using 1–5% (v/v) alcohol. The effective chondrogenic differentiation of ATDC5 cells was induced following their cultivation on substrates coated with intact fibroin. Our results showed that intact, allergen-free fibroin can be obtained from transgenic cocoons without the need for sericin removal, providing a method to produce fibroin-based materials with high biocompatibility for biomedical uses.
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Affiliation(s)
- Mana Yamano
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan; (M.Y.); (R.H.); (P.Y.L.); (K.T.); (R.M.); (H.M.)
| | - Ryoko Hirose
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan; (M.Y.); (R.H.); (P.Y.L.); (K.T.); (R.M.); (H.M.)
| | - Ping Ying Lye
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan; (M.Y.); (R.H.); (P.Y.L.); (K.T.); (R.M.); (H.M.)
| | - Keiko Takaki
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan; (M.Y.); (R.H.); (P.Y.L.); (K.T.); (R.M.); (H.M.)
- Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Rina Maruta
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan; (M.Y.); (R.H.); (P.Y.L.); (K.T.); (R.M.); (H.M.)
| | - Mervyn Wing On Liew
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang 11800, Malaysia;
| | - Shinichi Sakurai
- Department of Biobased Materials Science, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan;
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Hajime Mori
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan; (M.Y.); (R.H.); (P.Y.L.); (K.T.); (R.M.); (H.M.)
| | - Eiji Kotani
- Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan; (M.Y.); (R.H.); (P.Y.L.); (K.T.); (R.M.); (H.M.)
- Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
- Correspondence: ; Tel.: +81-75-724-7774
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13
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Gan Y, Sha H, Zou R, Xu M, Zhang Y, Feng J, Wu J. Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology. Front Cell Dev Biol 2022; 10:864101. [PMID: 35652091 PMCID: PMC9149570 DOI: 10.3389/fcell.2022.864101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is a well-established post-translational modification that is inherently connected to diverse processes, including DNA repair, transcription, and cell signaling. The crucial roles of mono-ADP-ribosyltransferases (mono-ARTs) in biological processes have been identified in recent years by the comprehensive use of genetic engineering, chemical genetics, and proteomics. This review provides an update on current methodological advances in the study of these modifiers. Furthermore, the review provides details on the function of mono ADP-ribosylation. Several mono-ARTs have been implicated in the development of cancer, and this review discusses the role and therapeutic potential of some mono-ARTs in cancer.
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Affiliation(s)
- Yujie Gan
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Miao Xu
- Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jifeng Feng,
| | - Jianzhong Wu
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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14
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Lüscher B, Verheirstraeten M, Krieg S, Korn P. Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cell Mol Life Sci 2022; 79:288. [PMID: 35536484 PMCID: PMC9087173 DOI: 10.1007/s00018-022-04290-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023]
Abstract
The innate immune system, the primary defense mechanism of higher organisms against pathogens including viruses, senses pathogen-associated molecular patterns (PAMPs). In response to PAMPs, interferons (IFNs) are produced, allowing the host to react swiftly to viral infection. In turn the expression of IFN-stimulated genes (ISGs) is induced. Their products disseminate the antiviral response. Among the ISGs conserved in many species are those encoding mono-ADP-ribosyltransferases (mono-ARTs). This prompts the question whether, and if so how, mono-ADP-ribosylation affects viral propagation. Emerging evidence demonstrates that some mono-ADP-ribosyltransferases function as PAMP receptors and modify both host and viral proteins relevant for viral replication. Support for mono-ADP-ribosylation in virus–host interaction stems from the findings that some viruses encode mono-ADP-ribosylhydrolases, which antagonize cellular mono-ARTs. We summarize and discuss the evidence linking mono-ADP-ribosylation and the enzymes relevant to catalyze this reversible modification with the innate immune response as part of the arms race between host and viruses.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Maud Verheirstraeten
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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15
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Schuller M, Ahel I. Beyond protein modification: the rise of non-canonical ADP-ribosylation. Biochem J 2022; 479:463-477. [PMID: 35175282 PMCID: PMC8883491 DOI: 10.1042/bcj20210280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 12/22/2022]
Abstract
ADP-ribosylation has primarily been known as post-translational modification of proteins. As signalling strategy conserved in all domains of life, it modulates substrate activity, localisation, stability or interactions, thereby regulating a variety of cellular processes and microbial pathogenicity. Yet over the last years, there is increasing evidence of non-canonical forms of ADP-ribosylation that are catalysed by certain members of the ADP-ribosyltransferase family and go beyond traditional protein ADP-ribosylation signalling. New macromolecular targets such as nucleic acids and new ADP-ribose derivatives have been established, notably extending the repertoire of ADP-ribosylation signalling. Based on the physiological relevance known so far, non-canonical ADP-ribosylation deserves its recognition next to the traditional protein ADP-ribosylation modification and which we therefore review in the following.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, U.K
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16
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Tromans-Coia C, Sanchi A, Moeller GK, Timinszky G, Lopes M, Ahel I. TARG1 protects against toxic DNA ADP-ribosylation. Nucleic Acids Res 2021; 49:10477-10492. [PMID: 34508355 PMCID: PMC8501950 DOI: 10.1093/nar/gkab771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/16/2021] [Accepted: 09/09/2021] [Indexed: 01/15/2023] Open
Abstract
ADP-ribosylation is a modification that targets a variety of macromolecules and regulates a diverse array of important cellular processes. ADP-ribosylation is catalysed by ADP-ribosyltransferases and reversed by ADP-ribosylhydrolases. Recently, an ADP-ribosyltransferase toxin termed 'DarT' from bacteria, which is distantly related to human PARPs, was shown to modify thymidine in single-stranded DNA in a sequence specific manner. The antitoxin of DarT is the macrodomain containing ADP-ribosylhydrolase DarG, which shares striking structural homology with the human ADP-ribosylhydrolase TARG1. Here, we show that TARG1, like DarG, can reverse thymidine-linked DNA ADP-ribosylation. We find that TARG1-deficient human cells are extremely sensitive to DNA ADP-ribosylation. Furthermore, we also demonstrate the first detection of reversible ADP-ribosylation on genomic DNA in vivo from human cells. Collectively, our results elucidate the impact of DNA ADP-ribosylation in human cells and provides a molecular toolkit for future studies into this largely unknown facet of ADP-ribosylation.
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Affiliation(s)
- Callum Tromans-Coia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Giuliana K Moeller
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6276 Szeged, Hungary
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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17
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Groslambert J, Prokhorova E, Ahel I. ADP-ribosylation of DNA and RNA. DNA Repair (Amst) 2021; 105:103144. [PMID: 34116477 PMCID: PMC8385414 DOI: 10.1016/j.dnarep.2021.103144] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022]
Abstract
ADP-ribosylation is a chemical modification of macromolecules found across all domains of life and known to regulate a variety of cellular processes. Notably, it has a well-established role in the DNA damage response. While it was historically known as a post-translational modification of proteins, recent studies have shown that nucleic acids can also serve as substrates of reversible ADP-ribosylation. More precisely, ADP-ribosylation of DNA bases, phosphorylated DNA ends and phosphorylated RNA ends have been reported. We will discuss these three types of modification in details. In a variety of bacterial species, including Mycobacterium tuberculosis, ADP-ribosylation of thymidine has emerged as the mode of action of a toxin-antitoxin system named DarTG, with the resultant products perceived as DNA damage by the cell. On the other hand, mammalian DNA damage sensors PARP1, PARP2 and PARP3 were shown to ADP-ribosylate phosphorylated ends of double-stranded DNA in vitro. Additionally, TRPT1 and several PARP enzymes, including PARP10, can add ADP-ribose to the 5'-phosphorylated end of single-stranded RNA in vitro, representing a novel RNA capping mechanism. Together, these discoveries have led to the emergence of a new and exciting research area, namely DNA and RNA ADP-ribosylation, that is likely to have far-reaching implications for the fields of DNA repair, replication and epigenetics.
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Affiliation(s)
- Joséphine Groslambert
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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18
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Weixler L, Schäringer K, Momoh J, Lüscher B, Feijs KLH, Žaja R. ADP-ribosylation of RNA and DNA: from in vitro characterization to in vivo function. Nucleic Acids Res 2021; 49:3634-3650. [PMID: 33693930 PMCID: PMC8053099 DOI: 10.1093/nar/gkab136] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The functionality of DNA, RNA and proteins is altered dynamically in response to physiological and pathological cues, partly achieved by their modification. While the modification of proteins with ADP-ribose has been well studied, nucleic acids were only recently identified as substrates for ADP-ribosylation by mammalian enzymes. RNA and DNA can be ADP-ribosylated by specific ADP-ribosyltransferases such as PARP1-3, PARP10 and tRNA 2'-phosphotransferase (TRPT1). Evidence suggests that these enzymes display different preferences towards different oligonucleotides. These reactions are reversed by ADP-ribosylhydrolases of the macrodomain and ARH families, such as MACROD1, TARG1, PARG, ARH1 and ARH3. Most findings derive from in vitro experiments using recombinant components, leaving the relevance of this modification in cells unclear. In this Survey and Summary, we provide an overview of the enzymes that ADP-ribosylate nucleic acids, the reversing hydrolases, and the substrates' requirements. Drawing on data available for other organisms, such as pierisin1 from cabbage butterflies and the bacterial toxin-antitoxin system DarT-DarG, we discuss possible functions for nucleic acid ADP-ribosylation in mammals. Hypothesized roles for nucleic acid ADP-ribosylation include functions in DNA damage repair, in antiviral immunity or as non-conventional RNA cap. Lastly, we assess various methods potentially suitable for future studies of nucleic acid ADP-ribosylation.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Katja Schäringer
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
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19
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The Buzz about ADP-Ribosylation Toxins from Paenibacillus larvae, the Causative Agent of American Foulbrood in Honey Bees. Toxins (Basel) 2021; 13:toxins13020151. [PMID: 33669183 PMCID: PMC7919650 DOI: 10.3390/toxins13020151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/02/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Abstract
The Gram-positive, spore-forming bacterium Paenibacillus larvae is the etiological agent of American Foulbrood, a highly contagious and often fatal honey bee brood disease. The species P. larvae comprises five so-called ERIC-genotypes which differ in virulence and pathogenesis strategies. In the past two decades, the identification and characterization of several P. larvae virulence factors have led to considerable progress in understanding the molecular basis of pathogen-host-interactions during P. larvae infections. Among these virulence factors are three ADP-ribosylating AB-toxins, Plx1, Plx2, and C3larvin. Plx1 is a phage-born toxin highly homologous to the pierisin-like AB-toxins expressed by the whites-and-yellows family Pieridae (Lepidoptera, Insecta) and to scabin expressed by the plant pathogen Streptomyces scabiei. These toxins ADP-ribosylate DNA and thus induce apoptosis. While the presumed cellular target of Plx1 still awaits final experimental proof, the classification of the A subunits of the binary AB-toxins Plx2 and C3larvin as typical C3-like toxins, which ADP-ribosylate Rho-proteins, has been confirmed experimentally. Normally, C3-exoenzymes do not occur together with a B subunit partner, but as single domain toxins. Interestingly, the B subunits of the two P. larvae C3-like toxins are homologous to the B-subunits of C2-like toxins with striking structural similarity to the PA-63 protomer of Bacillus anthracis.
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20
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Masutani M, Nakagama H. Takashi Sugimura (1926-2020). DNA Repair (Amst) 2021. [DOI: 10.1016/j.dnarep.2020.103033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites. Commun Biol 2021; 4:123. [PMID: 33504944 PMCID: PMC7840908 DOI: 10.1038/s42003-020-01633-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
The macro domain is an ADP-ribose (ADPR) binding module, which is considered to act as a sensor to recognize nicotinamide adenine dinucleotide (NAD) metabolites, including poly ADPR (PAR) and other small molecules. The recognition of macro domains with various ligands is important for a variety of biological functions involved in NAD metabolism, including DNA repair, chromatin remodeling, maintenance of genomic stability, and response to viral infection. Nevertheless, how the macro domain binds to moieties with such structural obstacles using a simple cleft remains a puzzle. We systematically investigated the Middle East respiratory syndrome-coronavirus (MERS-CoV) macro domain for its ligand selectivity and binding properties by structural and biophysical approaches. Of interest, NAD, which is considered not to interact with macro domains, was co-crystallized with the MERS-CoV macro domain. Further studies at physiological temperature revealed that NAD has similar binding ability with ADPR because of the accommodation of the thermal-tunable binding pocket. This study provides the biochemical and structural bases of the detailed ligand-binding mode of the MERS-CoV macro domain. In addition, our observation of enhanced binding affinity of the MERS-CoV macro domain to NAD at physiological temperature highlights the need for further study to reveal the biological functions. Meng-Hsuan Lin et al. investigate MERS-CoV macro domain binding selectivity with NAD and NAD metabolites under various conditions. At physiological temperature, NAD is observed to have enhanced binding affinity to the MERS-CoV macro domain, shedding light on a new possible role of the MERS-CoV macro domain in viral replication.
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22
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Vatta M, Lyons B, Heney KA, Lidster T, Merrill AR. Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies. Toxins (Basel) 2021; 13:toxins13010055. [PMID: 33450958 PMCID: PMC7828395 DOI: 10.3390/toxins13010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 11/16/2022] Open
Abstract
Scabin is a mono-ADP-ribosyltransferase toxin/enzyme and possible virulence factor produced by the agriculture pathogen, Streptomyces scabies. Recently, molecular dynamic approaches and MD simulations revealed its interaction with both NAD+ and DNA substrates. An Essential Dynamics Analysis identified a crab-claw-like mechanism, including coupled changes in the exposed motifs, and the Rβ1-RLa-NLc-STTβ2-WPN-WARTT-(QxE)ARTT sequence motif was proposed as a catalytic signature of the Pierisin family of DNA-acting toxins. A new fluorescence assay was devised to measure the kinetics for both RNA and DNA substrates. Several protein variants were prepared to probe the Scabin-NAD-DNA molecular model and to reveal the reaction mechanism for the transfer of ADP-ribose to the guanine base in the DNA substrate. The results revealed that there are several lysine and arginine residues in Scabin that are important for binding the DNA substrate; also, key residues such as Asn110 in the mechanism of ADP-ribose transfer to the guanine base were identified. The DNA-binding residues are shared with ScARP from Streptomyces coelicolor but are not conserved with Pierisin-1, suggesting that the modification of guanine bases by ADP-ribosyltransferases is divergent even in the Pierisin family.
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Affiliation(s)
- Maritza Vatta
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Bronwyn Lyons
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada;
| | - Kayla A. Heney
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada;
| | - Taylor Lidster
- Department of Biological Sciences, Brock University, St. Catherines, ON L2S 3A1, Canada;
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: ; Fax: +1-519-837-1802
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23
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Yoshida T, Tsuge H. Common Mechanism for Target Specificity of Protein- and DNA-Targeting ADP-Ribosyltransferases. Toxins (Basel) 2021; 13:toxins13010040. [PMID: 33430384 PMCID: PMC7827354 DOI: 10.3390/toxins13010040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/14/2022] Open
Abstract
Many bacterial pathogens utilize ADP-ribosyltransferases (ARTs) as virulence factors. The critical aspect of ARTs is their target specificity. Each individual ART modifies a specific residue of its substrates, which could be proteins, DNA, or antibiotics. However, the mechanism underlying this specificity is poorly understood. Here, we review the substrate recognition mechanism and target residue specificity based on the available complex structures of ARTs and their substrates. We show that there are common mechanisms of target residue specificity among protein- and DNA-targeting ARTs.
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Affiliation(s)
- Toru Yoshida
- Faculty of Science, Japan Women’s University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan;
| | - Hideaki Tsuge
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Correspondence: ; Tel.: +81-75-705-3117
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24
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The N-terminus of Paenibacillus larvae C3larvinA modulates catalytic efficiency. Biosci Rep 2021; 41:227200. [PMID: 33289829 PMCID: PMC7789906 DOI: 10.1042/bsr20203727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/21/2023] Open
Abstract
C3larvinA was recently described as a mono-ADP-ribosyltransferase (mART) toxin from the enterobacterial repetitive intergenic consensus (ERIC) III genotype of the agricultural pathogen, Paenibacillus larvae. It was shown to be the full-length, functional version of the previously described C3larvintrunc toxin, due to a 33-residue extension of the N-terminus of the protein. In the present study, a series of deletions and substitutions were made to the N-terminus of C3larvinA to assess the contribution of the α1-helix to toxin structure and function. Catalytic characterization of these variants identified Asp23 and Ala31 residues as supportive to enzymatic function. A third residue, Lys36, was also found to contribute to the catalytic activity of the enzyme. Analysis of the C3larvinA homology model revealed that these three residues were participating in a series of interactions to properly orient both the Q-X-E and S-T-S motifs. Ala31 and Lys36 were found to associate with a structural network of residues previously identified in silico, whereas Asp23 forms novel interactions not previously described. At last, the membrane translocation activity into host target cells of each variant was assessed, highlighting a possible relationship between protein dipole and target cell entry.
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25
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Munnur D, Ahel I. Detecting ADP-Ribosylation in RNA. Methods Mol Biol 2021; 2298:231-243. [PMID: 34085249 DOI: 10.1007/978-1-0716-1374-0_15] [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] [Indexed: 02/11/2024]
Abstract
ADP-ribosylation is a widespread reversible chemical modification of macromolecular targets. Protein ADP-ribosylation has been widely studied and plays a vital role in the regulation of several biological processes. In recent years there has been increasing interest in alternative ADP-ribosylation targets such as nucleic acids-DNA and RNA. Here we report different methods to detect ADP-ribosylation of RNA substrates.
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Affiliation(s)
- Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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26
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Nishimura S, Nakagama H. Takashi Sugimura: In Memoriam (1926–2020)–A Personal Perspective. Cancer Res 2021. [DOI: 10.1158/0008-5472.can-20-3998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Hitoshi Nakagama
- 2National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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27
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Housh K, Jha JS, Haldar T, Amin SBM, Islam T, Wallace A, Gomina A, Guo X, Nel C, Wyatt JW, Gates KS. Formation and repair of unavoidable, endogenous interstrand cross-links in cellular DNA. DNA Repair (Amst) 2020; 98:103029. [PMID: 33385969 DOI: 10.1016/j.dnarep.2020.103029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
Genome integrity is essential for life and, as a result, DNA repair systems evolved to remove unavoidable DNA lesions from cellular DNA. Many forms of life possess the capacity to remove interstrand DNA cross-links (ICLs) from their genome but the identity of the naturally-occurring, endogenous substrates that drove the evolution and retention of these DNA repair systems across a wide range of life forms remains uncertain. In this review, we describe more than a dozen chemical processes by which endogenous ICLs plausibly can be introduced into cellular DNA. The majority involve DNA degradation processes that introduce aldehyde residues into the double helix or reactions of DNA with endogenous low molecular weight aldehyde metabolites. A smaller number of the cross-linking processes involve reactions of DNA radicals generated by oxidation.
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Affiliation(s)
- Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jay S Jha
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tuhin Haldar
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Saosan Binth Md Amin
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tanhaul Islam
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Amanda Wallace
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Anuoluwapo Gomina
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Xu Guo
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Christopher Nel
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jesse W Wyatt
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States; University of Missouri, Department of Biochemistry, Columbia, MO 65211, United States.
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Nakagama H. Takashi Sugimura 1926‐2020. Cancer Sci 2020. [DOI: 10.1111/cas.14736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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29
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Tremblay O, Thow Z, Merrill AR. Several New Putative Bacterial ADP-Ribosyltransferase Toxins Are Revealed from In Silico Data Mining, Including the Novel Toxin Vorin, Encoded by the Fire Blight Pathogen Erwinia amylovora. Toxins (Basel) 2020; 12:E792. [PMID: 33322547 PMCID: PMC7764402 DOI: 10.3390/toxins12120792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/28/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
Mono-ADP-ribosyltransferase (mART) toxins are secreted by several pathogenic bacteria that disrupt vital host cell processes in deadly diseases like cholera and whooping cough. In the last two decades, the discovery of mART toxins has helped uncover the mechanisms of disease employed by pathogens impacting agriculture, aquaculture, and human health. Due to the current abundance of mARTs in bacterial genomes, and an unprecedented availability of genomic sequence data, mART toxins are amenable to discovery using an in silico strategy involving a series of sequence pattern filters and structural predictions. In this work, a bioinformatics approach was used to discover six bacterial mART sequences, one of which was a functional mART toxin encoded by the plant pathogen, Erwinia amylovora, called Vorin. Using a yeast growth-deficiency assay, we show that wild-type Vorin inhibited yeast cell growth, while catalytic variants reversed the growth-defective phenotype. Quantitative mass spectrometry analysis revealed that Vorin may cause eukaryotic host cell death by suppressing the initiation of autophagic processes. The genomic neighbourhood of Vorin indicated that it is a Type-VI-secreted effector, and co-expression experiments showed that Vorin is neutralized by binding of a cognate immunity protein, VorinI. We demonstrate that Vorin may also act as an antibacterial effector, since bacterial expression of Vorin was not achieved in the absence of VorinI. Vorin is the newest member of the mART family; further characterization of the Vorin/VorinI complex may help refine inhibitor design for mART toxins from other deadly pathogens.
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Affiliation(s)
| | | | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (O.T.); (Z.T.)
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30
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Sanderson DJ, Cohen MS. Mechanisms governing PARP expression, localization, and activity in cells. Crit Rev Biochem Mol Biol 2020; 55:541-554. [PMID: 32962438 DOI: 10.1080/10409238.2020.1818686] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Poly-(ADP)-ribose polymerases (PARPs) are a family of 17 enzymes in humans that have diverse roles in cell physiology including DNA damage repair, transcription, innate immunity, and regulation of signaling pathways. The modular domain architecture of PARPs gives rise to this functional diversity. PARPs catalyze the transfer of ADP-ribose from nicotinamide adenine dinucleotide (NAD+) to targets-proteins and poly-nucleic acids. This enigmatic post-translational modification comes in two varieties: the transfer of a single unit of ADP-ribose, known as mono-ADP-ribosylation (MARylation) or the transfer of multiple units of ADP-ribose, known as poly-ADP-ribosylation (PARylation). Emerging data shows that PARPs are regulated at multiple levels to control when and where PARP-mediated M/PARylation occurs in cells. In this review, we will discuss the latest knowledge regarding the regulation of PARPs in cells: from transcription and protein stability to subcellular localization and modulation of catalytic activity.
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Affiliation(s)
- Daniel J Sanderson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
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31
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Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
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Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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32
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Kim DS, Challa S, Jones A, Kraus WL. PARPs and ADP-ribosylation in RNA biology: from RNA expression and processing to protein translation and proteostasis. Genes Dev 2020; 34:302-320. [PMID: 32029452 PMCID: PMC7050490 DOI: 10.1101/gad.334433.119] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Kim et al. discuss the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. ADP-ribosylation (ADPRylation) is a posttranslational modification of proteins discovered nearly six decades ago, but many important questions remain regarding its molecular functions and biological roles, as well as the activity of the ADP-ribose (ADPR) transferase enzymes (PARP family members) that catalyze it. Growing evidence indicates that PARP-mediated ADPRylation events are key regulators of the protein biosynthetic pathway, leading from rDNA transcription and ribosome biogenesis to mRNA synthesis, processing, and translation. In this review we describe the role of PARP proteins and ADPRylation in all facets of this pathway. PARP-1 and its enzymatic activity are key regulators of rDNA transcription, which is a critical step in ribosome biogenesis. An emerging role of PARPs in alternative splicing of mRNAs, as well as direct ADPRylation of mRNAs, highlight the role of PARP members in RNA processing. Furthermore, PARP activity, stimulated by cellular stresses, such as viral infections and ER stress, leads to the regulation of mRNA stability and protein synthesis through posttranscriptional mechanisms. Dysregulation of PARP activity in these processes can promote disease states. Collectively, these results highlight the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. Future studies in these areas will yield new insights into the fundamental mechanisms and a broader utility for PARP-targeted therapeutic agents.
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Affiliation(s)
- Dae-Seok Kim
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Aarin Jones
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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33
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Lawarée E, Jankevicius G, Cooper C, Ahel I, Uphoff S, Tang CM. DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair. Cell Rep 2020; 30:1373-1384.e4. [PMID: 32023456 PMCID: PMC7003065 DOI: 10.1016/j.celrep.2020.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/16/2019] [Accepted: 01/02/2020] [Indexed: 01/08/2023] Open
Abstract
ADP-ribosylation of proteins is crucial for fundamental cellular processes. Despite increasing examples of DNA ADP-ribosylation, the impact of this modification on DNA metabolism and cell physiology is unknown. Here, we show that the DarTG toxin-antitoxin system from enteropathogenic Escherichia coli (EPEC) catalyzes reversible ADP-ribosylation of single-stranded DNA (ssDNA). The DarT toxin recognizes specific sequence motifs. EPEC DarG abrogates DarT toxicity by two distinct mechanisms: removal of DNA ADP-ribose (ADPr) groups and DarT sequestration. Furthermore, we investigate how cells recognize and deal with DNA ADP-ribosylation. We demonstrate that DNA ADPr stalls replication and is perceived as DNA damage. Removal of ADPr from DNA requires the sequential activity of two DNA repair pathways, with RecF-mediated homologous recombination likely to transfer ADP-ribosylation from single- to double-stranded DNA (dsDNA) and subsequent nucleotide excision repair eliminating the lesion. Our work demonstrates that these DNA repair pathways prevent the genotoxic effects of DNA ADP-ribosylation.
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Affiliation(s)
- Emeline Lawarée
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Charles Cooper
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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34
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Sutcu HH, Matta E, Ishchenko AA. Role of PARP-catalyzed ADP-ribosylation in the Crosstalk Between DNA Strand Breaks and Epigenetic Regulation. J Mol Biol 2019:S0022-2836(19)30719-3. [PMID: 31866292 DOI: 10.1016/j.jmb.2019.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022]
Abstract
Covalent linkage of ADP-ribose units to proteins catalyzed by poly(ADP-ribose) polymerases (PARPs) plays important signaling functions in a plethora of cellular processes including DNA damage response, chromatin organization, and gene transcription. Poly- and mono-ADP-ribosylation of target macromolecules are often responsible both for the initiation and for coordination of these processes in mammalian cells. Currently, the number of cellular targets for ADP-ribosylation is rapidly expanding, and the molecular mechanisms underlying the broad substrate specificity of PARPs present enormous interest. In this review, the roles of PARP-mediated modifications of protein and nucleic acids, the readers of ADP-ribosylated structures, and the origin and function of programmed DNA strand breaks in PARP activation, transcription regulation, and DNA demethylation are discussed.
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Affiliation(s)
- Haser H Sutcu
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Elie Matta
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France.
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35
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Subbarayan S, Subramanian S, Senthil Kumar N. Recombinant Pierisin-5 Induces Apoptosis and Differential Expression of Bcl-2, Bax, and p53 in Human Cancer Cells. DNA Cell Biol 2019; 38:773-785. [DOI: 10.1089/dna.2018.4520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
| | - Selvi Subramanian
- Department of Biotechnology, PSG College of Technology, Coimbatore, India
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36
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Munir A, Banerjee A, Shuman S. NAD+-dependent synthesis of a 5'-phospho-ADP-ribosylated RNA/DNA cap by RNA 2'-phosphotransferase Tpt1. Nucleic Acids Res 2019; 46:9617-9624. [PMID: 30202863 PMCID: PMC6182162 DOI: 10.1093/nar/gky792] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
RNA 2′-phosphotransferase Tpt1 converts an internal RNA 2′-monophosphate to a 2′-OH via a two-step NAD+-dependent mechanism in which: (i) the 2′-phosphate attacks the C1″ of NAD+ to expel nicotinamide and form a 2′-phospho-ADP-ribosylated RNA intermediate; and (ii) the ADP-ribose O2″ attacks the phosphate of the RNA 2′-phospho-ADPR intermediate to expel the RNA 2′-OH and generate ADP-ribose 1″–2″ cyclic phosphate. Tpt1 is an essential component of the fungal tRNA splicing pathway that generates a unique 2′-PO4, 3′-5′ phosphodiester splice junction during tRNA ligation. The wide distribution of Tpt1 enzymes in taxa that have no fungal-type RNA ligase raises the prospect that Tpt1 might catalyze reactions other than RNA 2′-phosphate removal. A survey of Tpt1 enzymes from diverse sources reveals that whereas all of the Tpt1 enzymes are capable of NAD+-dependent conversion of an internal RNA 2′-PO4 to a 2′-OH (the canonical Tpt1 reaction), a subset of Tpt1 enzymes also catalyzed NAD+-dependent ADP-ribosylation of an RNA or DNA 5′-monophosphate terminus. Aeropyrum pernix Tpt1 (ApeTpt1) is particularly adept in this respect. One-step synthesis of a 5′-phospho-ADP-ribosylated cap structure by ApeTpt1 (with no subsequent 5′-phosphotransferase step) extends the repertoire of the Tpt1 enzyme family and the catalogue of ADP-ribosylation reactions involving nucleic acid acceptors.
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Affiliation(s)
- Annum Munir
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Ankan Banerjee
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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37
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Sarathbabu S, Marimuthu SK, Ghatak S, Vidyalakshmi S, Gurusubramanian G, Ghosh SK, Subramanian S, Zhang W, Kumar NS. Induction of Apoptosis by Pierisin-6 in HPV Positive HeLa and HepG2 Cancer Cells is Mediated by the Caspase-3 Dependent Mitochondrial Pathway. Anticancer Agents Med Chem 2019; 19:337-346. [DOI: 10.2174/1871520619666181127113848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/18/2018] [Accepted: 11/14/2018] [Indexed: 11/22/2022]
Abstract
Background:
To explore the cytotoxic and apoptotic activity of the pierisin-6 protein in HPV HeLa
and HepG2 cell lines.
Methods:
In this study, isolation, and purification of cytotoxic Prierisin-6 from the larvae of Pieris napi by
affinity column chromatography techniques. Characterization of full-length mRNA of pierisin-6 gene was performed
using 3’/5’ RACE PCR. The quantitative RT-PCR used to study the developmental stage-specific expression
of pierisin-6 mRNA. The most effective concentration of Pierisin-6 protein was determined by measuring
cell proliferation. Apoptosis was assessed using AO/Et-Br, Propidium Iodide, and Rhodamine 123 assays,
whereas protein levels of caspase 3, cytochrome C were evaluated by ELISA method. Pierisin-6 induced cell
cycle arrest was determined using Propidium iodide by FACS.
Results:
In this study, Pierisin-6, a novel apoptotic protein was found to have cytotoxicity against HeLa, HepG2
human cancer cell lines and L-132 human lung epithelial cell line. Among the target cells, HeLa was the most
sensitive to Pierisin-6. Flow cytometry analysis confirms an increased percentage of apoptotic cells in sub G1
phase and cell cycle arrest at S phase. Alteration in the transmembrane potential of mitochondria, Cytochrome c
released from the mitochondrial membrane, and caspase substrate assay demonstrated the cleavage of Ac-
DEVD-pNA signifying the activation of Caspase-3. These findings suggested that Pierisin-6 significantly induce
apoptosis in HeLa and HepG2 cells and is attributed mainly through a mitochondrial pathway by activation of
caspases. The developmental and stage-specific expression of pierisin-6 mRNA was one thousand-fold increased
from second to third instar larvae and gradually declined before pupation.
Conclusion:
Pierisin-6 represents a promising therapeutic approach for liver cancer patients.
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Affiliation(s)
| | - Satheesh K. Marimuthu
- Department of Biotechnology, PSG College of Technology, Coimbatore-641004, TN, India
| | - Souvik Ghatak
- Department of Biotechnology, Mizoram University, Aizawl-796004, Mizoram, India
| | | | | | - Sankar K. Ghosh
- Department of Biotechnology, Assam University, Silchar-788011, Assam, India
| | - Selvi Subramanian
- Department of Biotechnology, PSG College of Technology, Coimbatore-641004, TN, India
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Nachimuthu S. Kumar
- Department of Biotechnology, Mizoram University, Aizawl-796004, Mizoram, India
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Munnur D, Bartlett E, Mikolčević P, Kirby IT, Matthias Rack JG, Mikoč A, Cohen MS, Ahel I. Reversible ADP-ribosylation of RNA. Nucleic Acids Res 2019; 47:5658-5669. [PMID: 31216043 PMCID: PMC6582358 DOI: 10.1093/nar/gkz305] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 12/17/2022] Open
Abstract
ADP-ribosylation is a reversible chemical modification catalysed by ADP-ribosyltransferases such as PARPs that utilize nicotinamide adenine dinucleotide (NAD+) as a cofactor to transfer monomer or polymers of ADP-ribose nucleotide onto macromolecular targets such as proteins and DNA. ADP-ribosylation plays an important role in several biological processes such as DNA repair, transcription, chromatin remodelling, host-virus interactions, cellular stress response and many more. Using biochemical methods we identify RNA as a novel target of reversible mono-ADP-ribosylation. We demonstrate that the human PARPs - PARP10, PARP11 and PARP15 as well as a highly diverged PARP homologue TRPT1, ADP-ribosylate phosphorylated ends of RNA. We further reveal that ADP-ribosylation of RNA mediated by PARP10 and TRPT1 can be efficiently reversed by several cellular ADP-ribosylhydrolases (PARG, TARG1, MACROD1, MACROD2 and ARH3), as well as by MACROD-like hydrolases from VEEV and SARS viruses. Finally, we show that TRPT1 and MACROD homologues in bacteria possess activities equivalent to the human proteins. Our data suggest that RNA ADP-ribosylation may represent a widespread and physiologically relevant form of reversible ADP-ribosylation signalling.
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Affiliation(s)
- Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Edward Bartlett
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ilsa T Kirby
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | | | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Michael S Cohen
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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Abstract
In this issue of The FEBS Journal, Munnur and Ahel describe the reversible mono-ADP-ribosylation of DNA by PARP3, a member of the poly-ADP-ribose-polymerase family known to modify proteins. They demonstrate a selective ADP-ribosylation of the 5'-phosphate group on DNA ends and show that the modification can be reversed by several known ADP-ribosylhydrolases including PARG.
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Affiliation(s)
- Christian Dölle
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
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40
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Insights into the biogenesis, function, and regulation of ADP-ribosylation. Nat Chem Biol 2019; 14:236-243. [PMID: 29443986 DOI: 10.1038/nchembio.2568] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 12/28/2017] [Indexed: 12/26/2022]
Abstract
ADP-ribosylation-the transfer of ADP-ribose (ADPr) from NAD+ onto target molecules-is catalyzed by members of the ADP-ribosyltransferase (ART) superfamily of proteins, found in all kingdoms of life. Modification of amino acids in protein targets by ADPr regulates critical cellular pathways in eukaryotes and underlies the pathogenicity of certain bacteria. Several members of the ART superfamily are highly relevant for disease; these include the poly(ADP-ribose) polymerases (PARPs), recently shown to be important cancer targets, and the bacterial toxins diphtheria toxin and cholera toxin, long known to be responsible for the symptoms of diphtheria and cholera that result in morbidity. In this Review, we discuss the functions of amino acid ADPr modifications and the ART proteins that make them, the nature of the chemical linkage between ADPr and its targets and how this impacts function and stability, and the way that ARTs select specific amino acids in targets to modify.
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41
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ADP-ribosylation and intracellular traffic: an emerging role for PARP enzymes. Biochem Soc Trans 2019; 47:357-370. [DOI: 10.1042/bst20180416] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/02/2018] [Accepted: 12/05/2018] [Indexed: 12/19/2022]
Abstract
AbstractADP-ribosylation is an ancient and reversible post-translational modification (PTM) of proteins, in which the ADP-ribose moiety is transferred from NAD+ to target proteins by members of poly-ADP-ribosyl polymerase (PARP) family. The 17 members of this family have been involved in a variety of cellular functions, where their regulatory roles are exerted through the modification of specific substrates, whose identification is crucial to fully define the contribution of this PTM. Evidence of the role of the PARPs is now available both in the context of physiological processes and of cell responses to stress or starvation. An emerging role of the PARPs is their control of intracellular transport, as it is the case for tankyrases/PARP5 and PARP12. Here, we discuss the evidence pointing at this novel aspect of PARPs-dependent cell regulation.
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42
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Yoshida T, Tsuge H. Substrate N 2 atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP. J Biol Chem 2018; 293:13768-13774. [PMID: 30072382 DOI: 10.1074/jbc.ac118.004412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
ScARP from the bacterium Streptomyces coelicolor belongs to the pierisin family of DNA-targeting ADP-ribosyltransferases (ARTs). These enzymes ADP-ribosylate the N2 amino groups of guanine residues in DNA to yield N2-(ADP-ribos-1-yl)-2'-deoxyguanosine. Although the structures of pierisin-1 and Scabin were revealed recently, the substrate recognition mechanisms remain poorly understood because of the lack of a substrate-binding structure. Here, we report the apo structure of ScARP and of ScARP bound to NADH and its GDP substrate at 1.50 and 1.57 Å resolutions, respectively. The bound structure revealed that the guanine of GDP is trapped between N-ribose of NADH and Trp-159. Interestingly, N2 and N3 of guanine formed hydrogen bonds with the OE1 and NE2 atoms of Gln-162, respectively. We directly observed that the ADP-ribosylating toxin turn-turn (ARTT)-loop, including Trp-159 and Gln-162, plays a key role in the specificity of DNA-targeting, guanine-specific ARTs as well as protein-targeting ARTs such as the C3 exoenzyme. We propose that the ARTT-loop recognition is a common substrate-recognition mechanism in the pierisin family. Furthermore, this complex structure sheds light on similarities and differences among two subclasses that are distinguished by conserved structural motifs: H-Y-E in the ARTD subfamily and R-S-E in the ARTC subfamily. The spatial arrangements of the electrophile and nucleophile were the same, providing the first evidence for a common reaction mechanism in these ARTs. ARTC (including ScARP) uses the ARTT-loop for substrate recognition, whereas ARTD (represented by Arr) uses the C-terminal helix instead of the ARTT-loop. These observations could help inform efforts to improve ART inhibitors.
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Affiliation(s)
- Toru Yoshida
- From the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences.,Institute for Protein Dynamics, and
| | - Hideaki Tsuge
- From the Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, .,Institute for Protein Dynamics, and.,Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kyoto 603-8555, Japan
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Goodman RP, Calvo SE, Mootha VK. Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. J Biol Chem 2018; 293:7508-7516. [PMID: 29514978 PMCID: PMC5961030 DOI: 10.1074/jbc.tm117.000258] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Compartmentalization is a fundamental design principle of eukaryotic metabolism. Here, we review the compartmentalization of NAD+/NADH and NADP+/NADPH with a focus on the liver, an organ that experiences the extremes of biochemical physiology each day. Historical studies of the liver, using classical biochemical fractionation and measurements of redox-coupled metabolites, have given rise to the prevailing view that mitochondrial NAD(H) pools tend to be oxidized and important for energy homeostasis, whereas cytosolic NADP(H) pools tend to be highly reduced for reductive biosynthesis. Despite this textbook view, many questions still remain as to the relative size of these subcellular pools and their redox ratios in different physiological states, and to what extent such redox ratios are simply indicators versus drivers of metabolism. By performing a bioinformatic survey, we find that the liver expresses 352 known or predicted enzymes composing the hepatic NAD(P)ome, i.e. the union of all predicted enzymes producing or consuming NADP(H) or NAD(H) or using them as a redox co-factor. Notably, less than half are predicted to be localized within the cytosol or mitochondria, and a very large fraction of these genes exhibit gene expression patterns that vary during the time of day or in response to fasting or feeding. A future challenge lies in applying emerging new genetic tools to measure and manipulate in vivo hepatic NADP(H) and NAD(H) with subcellular and temporal resolution. Insights from such fundamental studies will be crucial in deciphering the pathogenesis of very common diseases known to involve alterations in hepatic NAD(P)H, such as diabetes and fatty liver disease.
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Affiliation(s)
- Russell P Goodman
- From the Division of Gastroenterology and
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
| | - Sarah E Calvo
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
- the Broad Institute, Cambridge, Massachusetts 02142
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 and
- the Broad Institute, Cambridge, Massachusetts 02142
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44
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Lugo MR, Lyons B, Lento C, Wilson DJ, Merrill AR. Dynamics of Scabin toxin. A proposal for the binding mode of the DNA substrate. PLoS One 2018; 13:e0194425. [PMID: 29543870 PMCID: PMC5854381 DOI: 10.1371/journal.pone.0194425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/04/2018] [Indexed: 12/29/2022] Open
Abstract
Scabin is a mono-ADP-ribosyltransferase enzyme and is a putative virulence factor produced by the plant pathogen, Streptomyces scabies. Previously, crystal structures of Scabin were solved in the presence and absence of substrate analogues and inhibitors. Herein, experimental (hydrogen-deuterium exchange), simulated (molecular dynamics), and theoretical (Gaussian Network Modeling) approaches were systematically applied to study the dynamics of apo-Scabin in the context of a Scabin·NAD+·DNA model. MD simulations revealed that the apo-Scabin solution conformation correlates well with the X-ray crystal structure, beyond the conformation of the exposed, mobile regions. In turn, the MD fluctuations correspond with the crystallographic B-factors, with the fluctuations derived from a Gaussian network model, and with the experimental H/D exchange rates. An Essential Dynamics Analysis identified the dynamic aspects of the toxin as a crab-claw-like mechanism of two topological domains, along with coupled deformations of exposed motifs. The “crab-claw” movement resembles the motion of C3-like toxins and emerges as a property of the central β scaffold of catalytic single domain toxins. The exposure and high mobility of the cis side motifs in the Scabin β-core suggest involvement in DNA substrate binding. A ternary Scabin·NAD+·DNA model was produced via an independent docking methodology, where the intermolecular interactions correspond to the region of high mobility identified by dynamics analyses and agree with binding and kinetic data reported for wild-type and Scabin variants. Based on data for the Pierisin-like toxin group, the sequence motif Rβ1–RLa–NLc–STTβ2–WPN–WARTT–(QxE)ARTT emerges as a catalytic signature involved in the enzymatic activity of these DNA-acting toxins. However, these results also show that Scabin possesses a unique DNA-binding motif within the Pierisin-like toxin group.
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Affiliation(s)
- Miguel R Lugo
- Department of Molecular and Cell Biology, University of Guelph, Guelph, Ontario, Canada
| | - Bronwyn Lyons
- Department of Molecular and Cell Biology, University of Guelph, Guelph, Ontario, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cristina Lento
- Chemistry Department, York University, Toronto, Ontario, Canada.,The Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
| | - Derek J Wilson
- Chemistry Department, York University, Toronto, Ontario, Canada.,The Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
| | - A Rod Merrill
- Department of Molecular and Cell Biology, University of Guelph, Guelph, Ontario, Canada
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45
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Crawford K, Bonfiglio JJ, Mikoč A, Matic I, Ahel I. Specificity of reversible ADP-ribosylation and regulation of cellular processes. Crit Rev Biochem Mol Biol 2018; 53:64-82. [PMID: 29098880 DOI: 10.1080/10409238.2017.1394265] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 02/08/2023]
Abstract
Proper and timely regulation of cellular processes is fundamental to the overall health and viability of organisms across all kingdoms of life. Thus, organisms have evolved multiple highly dynamic and complex biochemical signaling cascades in order to adapt and survive diverse challenges. One such method of conferring rapid adaptation is the addition or removal of reversible modifications of different chemical groups onto macromolecules which in turn induce the appropriate downstream outcome. ADP-ribosylation, the addition of ADP-ribose (ADPr) groups, represents one of these highly conserved signaling chemicals. Herein we outline the writers, erasers and readers of ADP-ribosylation and dip into the multitude of cellular processes they have been implicated in. We also review what we currently know on how specificity of activity is ensured for this important modification.
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Affiliation(s)
- Kerryanne Crawford
- a Sir William Dunn School of Pathology , University of Oxford , Oxford , UK
| | | | - Andreja Mikoč
- c Division of Molecular Biology , Ruđer Bošković Institute , Zagreb , Croatia
| | - Ivan Matic
- b Max Planck Institute for Biology of Ageing , Cologne , Germany
| | - Ivan Ahel
- a Sir William Dunn School of Pathology , University of Oxford , Oxford , UK
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46
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Characterization of the catalytic signature of Scabin toxin, a DNA-targeting ADP-ribosyltransferase. Biochem J 2018; 475:225-245. [PMID: 29208763 DOI: 10.1042/bcj20170818] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 01/27/2023]
Abstract
Scabin was previously identified as a novel DNA-targeting mono-ADP-ribosyltransferase (mART) toxin from the plant pathogen 87.22 strain of Streptomyces scabies Scabin is a member of the Pierisin-like subgroup of mART toxins, since it targets DNA. An in-depth characterization of both the glycohydrolase and transferase enzymatic activities of Scabin was conducted. Several protein variants were developed based on an initial Scabin·DNA molecular model. Consequently, three residues were deemed important for DNA-binding and transferase activity. Trp128 and Trp155 are important for binding the DNA substrate and participate in the reaction mechanism, whereas Tyr129 was shown to be important only for DNA binding, but was not involved in the reaction mechanism. Trp128 and Trp155 are both conserved within the Pierisin-like toxins, whereas Tyr129 is a unique substitution within the group. Scabin showed substrate specificity toward double-stranded DNA containing a single-base overhang, as a model for single-stranded nicked DNA. The crystal structure of Scabin bound to NADH - a competitive inhibitor of Scabin - was determined, providing important insights into the active-site structure and Michaelis-Menten complex of the enzyme. Based on these results, a novel DNA-binding motif is proposed for Scabin with substrate and the key residues that may participate in the Scabin·NAD(+) complex are highlighted.
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47
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Munnur D, Ahel I. Reversible mono-ADP-ribosylation of DNA breaks. FEBS J 2017; 284:4002-4016. [PMID: 29054115 PMCID: PMC5725667 DOI: 10.1111/febs.14297] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/14/2017] [Accepted: 10/17/2017] [Indexed: 12/30/2022]
Abstract
Adenosine diphosphate (ADP)-ribosylation is a chemical modification of macromolecules that plays an important role in regulation of quintessential biological processes such as DNA repair, transcription, chromatin remodelling, stress response, apoptosis, bacterial metabolism and many others. ADP-ribosylation is carried out by ADP-ribosyltransferase proteins, such as poly (ADP-ribose) polymerases (PARPs) that transfer either monomer or polymers of ADP-ribose onto the molecular targets by using nicotinamide adenine dinucleotide (NAD+ ) as a cofactor. Traditionally, proteins have been described as primary targets of ADP-ribosylation; however, there has been growing evidence that DNA may be a common target as well. Here, we show using biochemical studies that PARP3, a DNA damage-activated ADP-ribosyltransferase, can mono-ADP-ribosylate double-stranded DNA ends. ADP-ribosylation of DNA mediated by PARP3 attaches a single mono-ADP-ribose moiety to the phosphate group at the terminal ends of DNA. We further show that mono ADP-ribosylation at DNA ends can be efficiently reversed by several cellular hydrolases (PARG, MACROD2, TARG1 and ARH3). This suggests that mono ADP-ribosylated DNA adducts can be efficiently removed in cells by several mechanisms.
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Affiliation(s)
- Deeksha Munnur
- Sir William Dunn School of PathologyUniversity of OxfordUK
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordUK
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48
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Oda T, Hirabayashi H, Shikauchi G, Takamura R, Hiraga K, Minami H, Hashimoto H, Yamamoto M, Wakabayashi K, Shimizu T, Sato M. Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1. J Biol Chem 2017; 292:15445-15455. [PMID: 28765284 DOI: 10.1074/jbc.m117.776641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 07/25/2017] [Indexed: 01/10/2023] Open
Abstract
ADP-ribosyltransferases transfer the ADP-ribose moiety of βNAD+ to an acceptor molecule, usually a protein that modulates the function of the acceptor. Pierisin-1 is an ADP-ribosyltransferase from the cabbage butterfly Pieris rapae and is composed of N-terminal catalytic and C-terminal ricin B-like domains. Curiously, it ADP-ribosylates the DNA duplex, resulting in apoptosis of various cancer cells, which has raised interest in pierisin-1 as an anti-cancer agent. However, both the structure and the mechanism of DNA ADP-ribosylation are unclear. Here, we report the crystal structures of the N-terminal catalytic domain of pierisin-1, its complex with βNAD+, and the catalytic domain with the linker connecting it to the ricin B-like domains. We found that the catalytic domain possesses a defined, positively charged region on the molecular surface but that its overall structure is otherwise similar to those of protein-targeting ADP-ribosyltransferases. Electrophoretic mobility shift assays and site-directed mutagenesis indicated that pierisin-1 binds double-stranded but not single-stranded DNA and that Lys122, Lys123, and Lys124, which are found in a loop, and Arg181 and Arg187, located in a basic cleft near the loop, are required for DNA binding. Furthermore, the structure of the catalytic domain with the linker revealed an autoinhibitory mechanism in which the linker occupies and blocks both the βNAD+- and DNA-binding sites, suggesting that proteolytic cleavage to remove the linker is necessary for enzyme catalysis. Our study provides a structural basis for the DNA-acceptor specificity of pierisin-1 and reveals that a self-regulatory mechanism is required for its activity.
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Affiliation(s)
- Takashi Oda
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hirokazu Hirabayashi
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Gen Shikauchi
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryouma Takamura
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kiyoshi Hiraga
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Minami
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Hashimoto
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,the School of Pharmaceutical Sciences and
| | - Masafumi Yamamoto
- the Central Institute for Experimental Animals, Kawasaki 210-0821, Japan, and
| | - Keiji Wakabayashi
- the Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Toshiyuki Shimizu
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,the Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
| | - Mamoru Sato
- From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan,
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49
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Bioengineered silkworms with butterfly cytotoxin-modified silk glands produce sericin cocoons with a utility for a new biomaterial. Proc Natl Acad Sci U S A 2017; 114:6740-6745. [PMID: 28607081 DOI: 10.1073/pnas.1703449114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetically manipulated organisms with dysfunction of specific tissues are crucial for the study of various biological applications and mechanisms. However, the bioengineering of model organisms with tissue-specific dysfunction has not progressed because the challenges of expression of proteins, such as cytotoxins, in living cells of individual organisms need to be overcome first. Here, we report the establishment of a transgenic silkworm (Bombyx mori) with posterior silk glands (PSGs) that was designed to express the cabbage butterfly (Pieris rapae) cytotoxin pierisin-1A (P1A). P1A, a homolog of the apoptosis inducer pierisin-1, had relatively lower DNA ADP ribosyltransferase activity than pierisin-1; it also induced the repression of certain protein synthesis when expressed in B. mori-derived cultured cells. The transgene-derived P1A domain harboring enzymatic activity was successfully expressed in the transgenic silkworm PSGs. The glands showed no apoptosis-related morphological changes; however, an abnormal appearance was evident. The introduced truncated P1A resulted in the dysfunction of PSGs in that they failed to produce the silk protein fibroin. Cocoons generated by the silkworms solely consisted of the glue-like glycoprotein sericin, from which soluble sericin could be prepared to form hydrogels. Embryonic stem cells could be maintained on the hydrogels in an undifferentiated state and proliferated through stimulation by the cytokines introduced into the hydrogels. Thus, bioengineering with targeted P1A expression successfully produced silkworms with a biologically useful trait that has significant application potential.
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50
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Shen J, Cong Q, Kinch LN, Borek D, Otwinowski Z, Grishin NV. Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. F1000Res 2016; 5:2631. [PMID: 28163896 PMCID: PMC5247789 DOI: 10.12688/f1000research.9765.1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/27/2016] [Indexed: 11/20/2022] Open
Abstract
The Small Cabbage White ( Pieris rapae) is originally a Eurasian butterfly. Being accidentally introduced into North America, Australia, and New Zealand a century or more ago, it spread throughout the continents and rapidly established as one of the most abundant butterfly species. Although it is a serious pest of cabbage and other mustard family plants with its caterpillars reducing crops to stems, it is also a source of pierisin, a protein unique to the Whites that shows cytotoxicity to cancer cells. To better understand the unusual biology of this omnipresent agriculturally and medically important butterfly, we sequenced and annotated the complete genome from USA specimens. At 246 Mbp, it is among the smallest Lepidoptera genomes reported to date. While 1.5% positions in the genome are heterozygous, they are distributed highly non-randomly along the scaffolds, and nearly 20% of longer than 1000 base-pair segments are SNP-free (median length: 38000 bp). Computational simulations of population evolutionary history suggest that American populations started from a very small number of introduced individuals, possibly a single fertilized female, which is in agreement with historical literature. Comparison to other Lepidoptera genomes reveals several unique families of proteins that may contribute to the unusual resilience of Pieris. The nitrile-specifier proteins divert the plant defense chemicals to non-toxic products. The apoptosis-inducing pierisins could offer a defense mechanism against parasitic wasps. While only two pierisins from Pieris rapae were characterized before, the genome sequence revealed eight, offering additional candidates as anti-cancer drugs. The reference genome we obtained lays the foundation for future studies of the Cabbage White and other Pieridae species.
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Affiliation(s)
- Jinhui Shen
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, USA
| | - Qian Cong
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, USA
| | - Dominika Borek
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, USA
| | - Zbyszek Otwinowski
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, USA
| | - Nick V Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, USA
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