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1.
Cell ; 175(5): 1380-1392.e14, 2018 11 15.
Artículo en Inglés | MEDLINE | ID: mdl-30343895

RESUMEN

ADP-ribosylation of proteins can profoundly impact their function and serves as an effective mechanism by which bacterial toxins impair eukaryotic cell processes. Here, we report the discovery that bacteria also employ ADP-ribosylating toxins against each other during interspecies competition. We demonstrate that one such toxin from Serratia proteamaculans interrupts the division of competing cells by modifying the essential bacterial tubulin-like protein, FtsZ, adjacent to its protomer interface, blocking its capacity to polymerize. The structure of the toxin in complex with its immunity determinant revealed two distinct modes of inhibition: active site occlusion and enzymatic removal of ADP-ribose modifications. We show that each is sufficient to support toxin immunity; however, the latter additionally provides unprecedented broad protection against non-cognate ADP-ribosylating effectors. Our findings reveal how an interbacterial arms race has produced a unique solution for safeguarding the integrity of bacterial cell division machinery against inactivating post-translational modifications.


Asunto(s)
ADP Ribosa Transferasas/metabolismo , Proteínas Bacterianas/metabolismo , Toxinas Bacterianas/metabolismo , Proteínas del Citoesqueleto/metabolismo , N-Glicosil Hidrolasas/metabolismo , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/genética , ADP-Ribosilación , Adenosina Difosfato/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/antagonistas & inhibidores , Toxinas Bacterianas/química , Toxinas Bacterianas/genética , Dominio Catalítico , Proteínas del Citoesqueleto/antagonistas & inhibidores , Escherichia coli/crecimiento & desarrollo , Escherichia coli/inmunología , Escherichia coli/metabolismo , Humanos , Mutagénesis Sitio-Dirigida , N-Glicosil Hidrolasas/química , N-Glicosil Hidrolasas/genética , Estructura Terciaria de Proteína , Subunidades de Proteína/genética , Subunidades de Proteína/metabolismo , Alineación de Secuencia , Serratia/metabolismo , Imagen de Lapso de Tiempo
2.
Mol Cell ; 82(18): 3484-3498.e11, 2022 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-36070765

RESUMEN

ADP-ribosyltransferases (ARTs) were among the first identified bacterial virulence factors. Canonical ART toxins are delivered into host cells where they modify essential proteins, thereby inactivating cellular processes and promoting pathogenesis. Our understanding of ARTs has since expanded beyond protein-targeting toxins to include antibiotic inactivation and DNA damage repair. Here, we report the discovery of RhsP2 as an ART toxin delivered between competing bacteria by a type VI secretion system of Pseudomonas aeruginosa. A structure of RhsP2 reveals that it resembles protein-targeting ARTs such as diphtheria toxin. Remarkably, however, RhsP2 ADP-ribosylates 2'-hydroxyl groups of double-stranded RNA, and thus, its activity is highly promiscuous with identified cellular targets including the tRNA pool and the RNA-processing ribozyme, ribonuclease P. Consequently, cell death arises from the inhibition of translation and disruption of tRNA processing. Overall, our data demonstrate a previously undescribed mechanism of bacterial antagonism and uncover an unprecedented activity catalyzed by ART enzymes.


Asunto(s)
ARN Catalítico , Sistemas de Secreción Tipo VI , ADP Ribosa Transferasas/química , Adenosina Difosfato/metabolismo , Antibacterianos/metabolismo , Bacterias/genética , Toxina Diftérica/genética , Toxina Diftérica/metabolismo , ARN Catalítico/genética , ARN Catalítico/metabolismo , ARN Bicatenario/metabolismo , Ribonucleasa P/genética , Sistemas de Secreción Tipo VI/metabolismo , Factores de Virulencia/metabolismo
3.
Nat Chem Biol ; 20(4): 463-472, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-37945894

RESUMEN

Ubiquitination plays essential roles in eukaryotic cellular processes. The effector protein CteC from Chromobacterium violaceum blocks host ubiquitination by mono-ADP-ribosylation of ubiquitin (Ub) at residue T66. However, the structural basis for this modification is unknown. Here we report three crystal structures of CteC in complexes with Ub, NAD+ or ADP-ribosylated Ub, which represent different catalytic states of CteC in the modification. CteC adopts a special 'D-E' catalytic motif for catalysis and binds NAD+ in a half-ligand binding mode. The specific recognition of Ub by CteC is determined by a relatively separate Ub-targeting domain and a long loop L6, not the classic ADP-ribosylating turn-turn loop. Structural analyses with biochemical results reveal that CteC represents a large family of poly (ADP-ribose) polymerase (PARP)-like ADP-ribosyltransferases, which harbors chimeric features from the R-S-E and H-Y-E classes of ADP-ribosyltransferases. The family of CteC-like ADP-ribosyltransferases has a common 'D-E' catalytic consensus and exists extensively in bacteria and eukaryotic microorganisms.


Asunto(s)
Treonina , Ubiquitina , Ubiquitina/química , Treonina/metabolismo , NAD/metabolismo , ADP-Ribosilación , ADP Ribosa Transferasas/química , Poli(ADP-Ribosa) Polimerasas/química , Bacterias/metabolismo , Adenosina Difosfato Ribosa
4.
J Biol Chem ; 300(2): 105604, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38159861

RESUMEN

ADP-ribosylation is a post-translational modification involved in regulation of diverse cellular pathways. Interestingly, many pathogens have been identified to utilize ADP-ribosylation as a way for host manipulation. A recent study found that CteC, an effector from the bacterial pathogen Chromobacterium violaceum, hinders host ubiquitin (Ub) signaling pathways via installing mono-ADP-ribosylation on threonine 66 of Ub. However, the molecular basis of substrate recognition by CteC is not well understood. In this article, we probed the substrate specificity of this effector at protein and residue levels. We also determined the crystal structure of CteC in complex with NAD+, which revealed a canonical mono-ADP-ribosyltransferase fold with an additional insertion domain. The AlphaFold-predicted model differed significantly from the experimentally determined structure, even in regions not used in crystal packing. Biochemical and biophysical studies indicated unique features of the NAD+ binding pocket, while showing selectivity distinction between Ub and structurally close Ub-like modifiers and the role of the insertion domain in substrate recognition. Together, this study provides insights into the enzymatic specificities and the key structural features of a novel bacterial ADP-ribosyltransferase involved in host-pathogen interaction.


Asunto(s)
ADP Ribosa Transferasas , Proteínas Bacterianas , Modelos Moleculares , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/genética , ADP Ribosa Transferasas/metabolismo , ADP-Ribosilación , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Chromobacterium/química , Chromobacterium/enzimología , Chromobacterium/genética , Cristalografía por Rayos X , NAD/química , NAD/metabolismo , Unión Proteica , Dominios Proteicos , Estructura Terciaria de Proteína , Especificidad por Sustrato , Ubiquitina/metabolismo
5.
Bioinformatics ; 40(7)2024 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-38885365

RESUMEN

MOTIVATION: ADP-ribosylation is a critical modification involved in regulating diverse cellular processes, including chromatin structure regulation, RNA transcription, and cell death. Bacterial ADP-ribosyltransferase toxins (bARTTs) serve as potent virulence factors that orchestrate the manipulation of host cell functions to facilitate bacterial pathogenesis. Despite their pivotal role, the bioinformatic identification of novel bARTTs poses a formidable challenge due to limited verified data and the inherent sequence diversity among bARTT members. RESULTS: We proposed a deep learning-based model, ARTNet, specifically engineered to predict bARTTs from bacterial genomes. Initially, we introduced an effective data augmentation method to address the issue of data scarcity in training ARTNet. Subsequently, we employed a data optimization strategy by utilizing ART-related domain subsequences instead of the primary full sequences, thereby significantly enhancing the performance of ARTNet. ARTNet achieved a Matthew's correlation coefficient (MCC) of 0.9351 and an F1-score (macro) of 0.9666 on repeated independent test datasets, outperforming three other deep learning models and six traditional machine learning models in terms of time efficiency and accuracy. Furthermore, we empirically demonstrated the ability of ARTNet to predict novel bARTTs across domain superfamilies without sequence similarity. We anticipate that ARTNet will greatly facilitate the screening and identification of novel bARTTs from bacterial genomes. AVAILABILITY AND IMPLEMENTATION: ARTNet is publicly accessible at http://www.mgc.ac.cn/ARTNet/. The source code of ARTNet is freely available at https://github.com/zhengdd0422/ARTNet/.


Asunto(s)
ADP Ribosa Transferasas , Biología Computacional , Aprendizaje Profundo , ADP Ribosa Transferasas/metabolismo , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/genética , Biología Computacional/métodos , Toxinas Bacterianas/química , Toxinas Bacterianas/metabolismo , Toxinas Bacterianas/genética , Genoma Bacteriano , Bacterias/genética
6.
Nature ; 557(7707): 674-678, 2018 05.
Artículo en Inglés | MEDLINE | ID: mdl-29795342

RESUMEN

Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.


Asunto(s)
Legionella pneumophila/enzimología , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Ubiquitina/metabolismo , Ubiquitinación , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/metabolismo , Arginina/metabolismo , Proteínas Bacterianas , Dominio Catalítico , Cristalografía por Rayos X , Modelos Moleculares , Chaperonas Moleculares/metabolismo , NAD/metabolismo , Hidrolasas Diéster Fosfóricas/química , Hidrolasas Diéster Fosfóricas/metabolismo , Procesamiento Proteico-Postraduccional , Especificidad por Sustrato , Ubiquitina/química
7.
Nature ; 557(7707): 734-738, 2018 05.
Artículo en Inglés | MEDLINE | ID: mdl-29795347

RESUMEN

Conventional ubiquitination regulates key cellular processes by catalysing the ATP-dependent formation of an isopeptide bond between ubiquitin (Ub) and primary amines in substrate proteins 1 . Recently, the SidE family of bacterial effector proteins (SdeA, SdeB, SdeC and SidE) from pathogenic Legionella pneumophila were shown to use NAD+ to mediate phosphoribosyl-linked ubiquitination of serine residues in host proteins2, 3. However, the molecular architecture of the catalytic platform that enables this complex multistep process remains unknown. Here we describe the structure of the catalytic core of SdeA, comprising mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains, and shed light on the activity of two distinct catalytic sites for serine ubiquitination. The mART catalytic site is composed of an α-helical lobe (AHL) that, together with the mART core, creates a chamber for NAD+ binding and ADP-ribosylation of ubiquitin. The catalytic site in the PDE domain cleaves ADP-ribosylated ubiquitin to phosphoribosyl ubiquitin (PR-Ub) and mediates a two-step PR-Ub transfer reaction: first to a catalytic histidine 277 (forming a transient SdeA H277-PR-Ub intermediate) and subsequently to a serine residue in host proteins. Structural analysis revealed a substrate binding cleft in the PDE domain, juxtaposed with the catalytic site, that is essential for positioning serines for ubiquitination. Using degenerate substrate peptides and newly identified ubiquitination sites in RTN4B, we show that disordered polypeptides with hydrophobic residues surrounding the target serine residues are preferred substrates for SdeA ubiquitination. Infection studies with L. pneumophila expressing substrate-binding mutants of SdeA revealed that substrate ubiquitination, rather than modification of the cellular ubiquitin pool, determines the pathophysiological effect of SdeA during acute bacterial infection.


Asunto(s)
Biocatálisis , Legionella pneumophila/enzimología , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Serina/metabolismo , Ubiquitinación , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/metabolismo , Adenosina Difosfato/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas , Sitios de Unión , Dominio Catalítico , Cristalografía por Rayos X , Legionella pneumophila/genética , Legionella pneumophila/patogenicidad , Enfermedad de los Legionarios/microbiología , Proteínas de la Membrana/genética , Modelos Moleculares , Hidrolasas Diéster Fosfóricas/química , Hidrolasas Diéster Fosfóricas/metabolismo , Estructura Secundaria de Proteína , Especificidad por Sustrato , Ubiquitina/metabolismo
8.
Nature ; 563(7730): 209-213, 2018 11.
Artículo en Inglés | MEDLINE | ID: mdl-30232455

RESUMEN

Tc toxins secrete toxic enzymes into host cells using a unique syringe-like injection mechanism. They are composed of three subunits, TcA, TcB and TcC. TcA forms the translocation channel and the TcB-TcC heterodimer functions as a cocoon that shields the toxic enzyme. Binding of the cocoon to the channel triggers opening of the cocoon and translocation of the toxic enzyme into the channel. Here we show in atomic detail how the assembly of the three components activates the toxin. We find that part of the cocoon completely unfolds and refolds into an alternative conformation upon binding. The presence of the toxic enzyme inside the cocoon is essential for its subnanomolar binding affinity for the TcA subunit. The enzyme passes through a narrow negatively charged constriction site inside the cocoon, probably acting as an extruder that releases the unfolded protein with its C terminus first into the translocation channel.


Asunto(s)
Toxinas Bacterianas/química , Toxinas Bacterianas/metabolismo , Microscopía por Crioelectrón , Complejos Multiproteicos/ultraestructura , Photorhabdus/ultraestructura , Replegamiento Proteico , Desplegamiento Proteico , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/metabolismo , ADP Ribosa Transferasas/ultraestructura , Toxinas Bacterianas/biosíntesis , Citotoxinas/biosíntesis , Citotoxinas/química , Citotoxinas/metabolismo , Modelos Biológicos , Modelos Moleculares , Complejos Multiproteicos/biosíntesis , Complejos Multiproteicos/química , Complejos Multiproteicos/metabolismo , Photorhabdus/química , Conformación Proteica , Transporte de Proteínas
9.
Nature ; 557(7707): 729-733, 2018 05.
Artículo en Inglés | MEDLINE | ID: mdl-29795346

RESUMEN

Ubiquitination is a post-translational modification that regulates many cellular processes in eukaryotes1-4. The conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein, usually on a lysine side chain1,5. Recent studies of the Legionella pneumophila SidE family of effector proteins revealed a ubiquitination method in which a phosphoribosyl ubiquitin (PR-Ub) is conjugated to a serine residue on substrates via a phosphodiester bond6-8. Here we present the crystal structure of a fragment of the SidE family member SdeA that retains ubiquitination activity, and determine the mechanism of this unique post-translational modification. The structure reveals that the catalytic module contains two distinct functional units: a phosphodiesterase domain and a mono-ADP-ribosyltransferase domain. Biochemical analysis shows that the mono-ADP-ribosyltransferase domain-mediated conversion of Ub to ADP-ribosylated Ub (ADPR-Ub) and the phosphodiesterase domain-mediated ligation of PR-Ub to substrates are two independent activities of SdeA. Furthermore, we present two crystal structures of a homologous phosphodiesterase domain from the SidE family member SdeD 9 in complexes with Ub and ADPR-Ub. The structures suggest a mechanism for how SdeA processes ADPR-Ub to PR-Ub and AMP, and conjugates PR-Ub to a serine residue in substrates. Our study establishes the molecular mechanism of phosphoribosyl-linked ubiquitination and will enable future studies of this unusual type of ubiquitination in eukaryotes.


Asunto(s)
ADP Ribosa Transferasas/metabolismo , Legionella pneumophila/enzimología , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Hidrolasas Diéster Fosfóricas/metabolismo , Ubiquitinación , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/genética , Adenosina Difosfato/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Cristalografía por Rayos X , Legionella pneumophila/genética , Lisina/metabolismo , Proteínas de la Membrana/genética , Modelos Moleculares , Hidrolasas Diéster Fosfóricas/química , Hidrolasas Diéster Fosfóricas/genética , Dominios Proteicos , Procesamiento Proteico-Postraduccional , Serina/metabolismo , Ubiquitina/química , Ubiquitina/metabolismo
10.
Mol Cell ; 64(6): 1109-1116, 2016 12 15.
Artículo en Inglés | MEDLINE | ID: mdl-27939941

RESUMEN

The discovery and study of toxin-antitoxin (TA) systems helps us advance our understanding of the strategies prokaryotes employ to regulate cellular processes related to the general stress response, such as defense against phages, growth control, biofilm formation, persistence, and programmed cell death. Here we identify and characterize a TA system found in various bacteria, including the global pathogen Mycobacterium tuberculosis. The toxin of the system (DarT) is a domain of unknown function (DUF) 4433, and the antitoxin (DarG) a macrodomain protein. We demonstrate that DarT is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. We also show that this modification can be removed by DarG. Our results provide an example of reversible DNA ADP-ribosylation, and we anticipate potential therapeutic benefits by targeting this enzyme-enzyme TA system in bacterial pathogens such as M. tuberculosis.


Asunto(s)
ADP Ribosa Transferasas/metabolismo , Antitoxinas/metabolismo , Toxinas Bacterianas/metabolismo , ADN de Cadena Simple/metabolismo , Mycobacterium tuberculosis/genética , ADP Ribosa Transferasas/antagonistas & inhibidores , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/genética , Adenosina Difosfato/metabolismo , Secuencias de Aminoácidos , Antitoxinas/química , Antitoxinas/genética , Toxinas Bacterianas/antagonistas & inhibidores , Toxinas Bacterianas/química , Toxinas Bacterianas/genética , Sitios de Unión , Clonación Molecular , Cristalografía por Rayos X , ADN de Cadena Simple/química , ADN de Cadena Simple/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Modelos Moleculares , Mycobacterium tuberculosis/metabolismo , Mycobacterium tuberculosis/patogenicidad , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidad por Sustrato , Timidina/metabolismo
11.
Nucleic Acids Res ; 50(22): 13114-13127, 2022 12 09.
Artículo en Inglés | MEDLINE | ID: mdl-36484105

RESUMEN

Rearrangement hot spot (Rhs) proteins are members of the broad family of polymorphic toxins. Polymorphic toxins are modular proteins composed of an N-terminal region that specifies their mode of secretion into the medium or into the target cell, a central delivery module, and a C-terminal domain that has toxic activity. Here, we structurally and functionally characterize the C-terminal toxic domain of the antibacterial Rhsmain protein, TreTu, which is delivered by the type VI secretion system of Salmonella enterica Typhimurium. We show that this domain adopts an ADP-ribosyltransferase fold and inhibits protein synthesis by transferring an ADP-ribose group from NAD+ to the elongation factor Tu (EF-Tu). This modification is specifically placed on the side chain of the conserved D21 residue located on the P-loop of the EF-Tu G-domain. Finally, we demonstrate that the TriTu immunity protein neutralizes TreTu activity by acting like a lid that closes the catalytic site and traps the NAD+.


Asunto(s)
Dominio AAA , Factor Tu de Elongación Peptídica , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/metabolismo , ADP-Ribosilación , NAD/metabolismo , Factor Tu de Elongación Peptídica/química , Factor Tu de Elongación Peptídica/metabolismo , Salmonella , Pliegue de Proteína
12.
Appl Microbiol Biotechnol ; 107(5-6): 1765-1784, 2023 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-36808279

RESUMEN

The ADP-ribosyl transferase activity of P. aeruginosa PE24 moiety expressed by E. coli BL21 (DE3) was assessed on nitrobenzylidene aminoguanidine (NBAG) and in vitro cultured cancer cell lines. Gene encoding PE24 was isolated from P. aeruginosa isolates, cloned into pET22b( +) plasmid, and expressed in E. coli BL21 (DE3) under IPTG induction. Genetic recombination was confirmed by colony PCR, the appearance of insert post digestion of engineered construct, and protein electrophoresis using sodium dodecyl-sulfate polyacrylamide gel (SDS-PAGE). The chemical compound NBAG has been used to confirm PE24 extract ADP-ribosyl transferase action through UV spectroscopy, FTIR, c13-NMR, and HPLC before and after low-dose gamma irradiation (5, 10, 15, 24 Gy). The cytotoxicity of PE24 extract alone and in combination with paclitaxel and low-dose gamma radiation (both 5 Gy and one shot 24 Gy) was assessed on adherent cell lines HEPG2, MCF-7, A375, OEC, and Kasumi-1 cell suspension. Expressed PE24 moiety ADP-ribosylated NBAG as revealed by structural changes depicted by FTIR and NMR, and the surge of new peaks at different retention times from NBAG in HPLC chromatograms. Irradiating recombinant PE24 moiety was associated with a reduction in ADP-ribosylating activity. The PE24 extract IC50 values were < 10 µg/ml with an acceptable R2 value on cancer cell lines and acceptable cell viability at 10 µg/ml on normal OEC. Overall, the synergistic effects were observed upon combining PE24 extract with low-dose paclitaxel demonstrated by the reduction in IC50 whereas antagonistic effects and a rise in IC50 values were recorded after irradiation by low-dose gamma rays. KEY POINTS: • Recombinant PE24 moiety was successfully expressed and biochemically analyzed. • Low-dose gamma radiation and metal ions decreased the recombinant PE24 cytotoxic activity. • Synergism was observed upon combining recombinant PE24 with low-dose paclitaxel.


Asunto(s)
ADP Ribosa Transferasas , Pseudomonas aeruginosa , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/genética , ADP Ribosa Transferasas/metabolismo , Pseudomonas aeruginosa/genética , Rayos gamma , Escherichia coli/genética
13.
Biochem J ; 479(4): 463-477, 2022 02 17.
Artículo en Inglés | MEDLINE | ID: mdl-35175282

RESUMEN

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.


Asunto(s)
ADP-Ribosilación/fisiología , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/clasificación , ADP Ribosa Transferasas/fisiología , Adenosina Difosfato/metabolismo , Guanosina/metabolismo , N-Glicosil Hidrolasas/fisiología , Poli(ADP-Ribosa) Polimerasas/metabolismo , Secuencias Reguladoras de Ácido Ribonucleico , Transducción de Señal , Relación Estructura-Actividad , Timidina/metabolismo , Ubiquitina/metabolismo
14.
Proc Natl Acad Sci U S A ; 117(2): 1049-1058, 2020 01 14.
Artículo en Inglés | MEDLINE | ID: mdl-31896582

RESUMEN

Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single-particle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including a symmetric (SymCDTb; 3.14 Å) and an asymmetric form (AsymCDTb; 2.84 Å). Roles played by 2 receptor-binding domains of activated CDTb were of particular interest since the receptor-binding domain 1 lacks sequence homology to any other known toxin, and the receptor-binding domain 2 is completely absent in other well-studied heptameric toxins (i.e., anthrax). For AsymCDTb, a Ca2+ binding site was discovered in the first receptor-binding domain that is important for its stability, and the second receptor-binding domain was found to be critical for host cell toxicity and the di-heptamer fold for both forms of activated CDTb. Together, these studies represent a starting point for developing structure-based drug-design strategies to target the most severe strains of C. difficile.


Asunto(s)
ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Toxinas Bacterianas/química , Toxinas Bacterianas/metabolismo , Clostridioides difficile/metabolismo , Enterotoxinas/química , Enterotoxinas/metabolismo , ADP Ribosa Transferasas/genética , Animales , Proteínas Bacterianas/genética , Sitios de Unión , Fenómenos Biofísicos , Chlorocebus aethiops , Microscopía por Crioelectrón , Cristalografía por Rayos X , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Conformación Proteica , Dominios Proteicos , Células Vero
15.
J Biol Chem ; 296: 100301, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33476647

RESUMEN

ADP-ribosyltransferases (ARTs) are a widespread superfamily of enzymes frequently employed in pathogenic strategies of bacteria. Legionella pneumophila, the causative agent of a severe form of pneumonia known as Legionnaire's disease, has acquired over 330 translocated effectors that showcase remarkable biochemical and structural diversity. However, the ART effectors that influence L. pneumophila have not been well defined. Here, we took a bioinformatic approach to search the Legionella effector repertoire for additional divergent members of the ART superfamily and identified an ART domain in Legionella pneumophila gene0181, which we hereafter refer to as Legionella ADP-Ribosyltransferase 1 (Lart1) (Legionella ART 1). We show that L. pneumophila Lart1 targets a specific class of 120-kDa NAD+-dependent glutamate dehydrogenase (GDH) enzymes found in fungi and protists, including many natural hosts of Legionella. Lart1 targets a conserved arginine residue in the NAD+-binding pocket of GDH, thereby blocking oxidative deamination of glutamate. Therefore, Lart1 could be the first example of a Legionella effector which directly targets a host metabolic enzyme during infection.


Asunto(s)
ADP Ribosa Transferasas/química , Proteínas Bacterianas/química , Glutamato Deshidrogenasa/química , Legionella pneumophila/genética , ADP Ribosa Transferasas/genética , ADP Ribosa Transferasas/metabolismo , ADP-Ribosilación , Secuencia de Aminoácidos , Amoeba/microbiología , Animales , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Clonación Molecular , Desaminación , Escherichia coli/genética , Escherichia coli/metabolismo , Hongos , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Glutamato Deshidrogenasa/genética , Glutamato Deshidrogenasa/metabolismo , Interacciones Huésped-Patógeno , Cinética , Legionella pneumophila/enzimología , Legionella pneumophila/patogenicidad , Modelos Moleculares , Oxidación-Reducción , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Especificidad por Sustrato
16.
Nature ; 533(7601): 120-4, 2016 May 05.
Artículo en Inglés | MEDLINE | ID: mdl-27049943

RESUMEN

Signalling by ubiquitination regulates virtually every cellular process in eukaryotes. Covalent attachment of ubiquitin to a substrate is catalysed by the E1, E2 and E3 three-enzyme cascade, which links the carboxy terminus of ubiquitin to the ε-amino group of, in most cases, a lysine of the substrate via an isopeptide bond. Given the essential roles of ubiquitination in the regulation of the immune system, it is not surprising that the ubiquitination network is a common target for diverse infectious agents. For example, many bacterial pathogens exploit ubiquitin signalling using virulence factors that function as E3 ligases, deubiquitinases or as enzymes that directly attack ubiquitin. The bacterial pathogen Legionella pneumophila utilizes approximately 300 effectors that modulate diverse host processes to create a permissive niche for its replication in phagocytes. Here we demonstrate that members of the SidE effector family of L. pneumophila ubiquitinate multiple Rab small GTPases associated with the endoplasmic reticulum. Moreover, we show that these proteins are capable of catalysing ubiquitination without the need for the E1 and E2 enzymes. A putative mono-ADP-ribosyltransferase motif critical for the ubiquitination activity is also essential for the role of the SidE family in intracellular bacterial replication in a protozoan host. The E1/E2-independent ubiquitination catalysed by these enzymes is energized by nicotinamide adenine dinucleotide, which activates ubiquitin by the formation of ADP-ribosylated ubiquitin. These results establish that ubiquitination can be catalysed by a single enzyme, the activity of which does not require ATP.


Asunto(s)
Proteínas Bacterianas/metabolismo , Legionella pneumophila/química , Ubiquitinación , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/metabolismo , Adenosina Difosfato Ribosa/metabolismo , Adenosina Trifosfato , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Carga Bacteriana , Biocatálisis , Retículo Endoplásmico/enzimología , Retículo Endoplásmico/metabolismo , Legionella pneumophila/citología , Legionella pneumophila/enzimología , Legionella pneumophila/patogenicidad , Proteínas de la Membrana/metabolismo , Datos de Secuencia Molecular , NAD/metabolismo , Ubiquitina/química , Ubiquitina/metabolismo , Enzimas Activadoras de Ubiquitina , Enzimas Ubiquitina-Conjugadoras , Factores de Virulencia/metabolismo , Proteínas de Unión al GTP rab/química , Proteínas de Unión al GTP rab/metabolismo
17.
Biochem J ; 478(15): 2999-3014, 2021 08 13.
Artículo en Inglés | MEDLINE | ID: mdl-34264286

RESUMEN

We recently described a signal transduction pathway that contributes to androgen receptor (AR) regulation based on site-specific ADP-ribosylation by PARP7, a mono-ADP-ribosyltransferase implicated in several human cancers. ADP-ribosylated AR is recognized by PARP9/DTX3L, a heterodimeric complex that contains an ADP-ribose reader (PARP9) and a ubiquitin E3 ligase (DTX3L). Here, we have characterized the cellular and biochemical requirements for AR ADP-ribosylation by PARP7. We found that the reaction requires nuclear localization of PARP7 and an agonist-induced conformation of AR. PARP7 contains a Cys3His1-type zinc finger (ZF), which also is critical for AR ADP-ribosylation. The Parp7 ZF is required for efficient nuclear import by a nuclear localization signal encoded in PARP7, but rescue experiments indicate the ZF makes a contribution to AR ADP-ribosylation that is separable from the effect on nuclear transport. ZF mutations do not detectably reduce PARP7 catalytic activity and binding to AR, but they do result in the loss of PARP7 enhancement of AR-dependent transcription of the MYBPC1 gene. Our data reveals critical roles for AR conformation and the PARP7 ZF in AR ADP-ribosylation and AR-dependent transcription.


Asunto(s)
ADP Ribosa Transferasas/metabolismo , Andrógenos/metabolismo , Núcleo Celular/metabolismo , Proteínas de Transporte de Nucleósidos/metabolismo , Receptores Androgénicos/metabolismo , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/genética , ADP-Ribosilación , Andrógenos/química , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Dominio Catalítico , Expresión Génica/efectos de los fármacos , Células HEK293 , Humanos , Mutación , Proteínas de Neoplasias/metabolismo , Proteínas de Transporte de Nucleósidos/química , Proteínas de Transporte de Nucleósidos/genética , Poli(ADP-Ribosa) Polimerasas/metabolismo , Unión Proteica , Conformación Proteica , Receptores Androgénicos/química , Ubiquitina-Proteína Ligasas/metabolismo , Dedos de Zinc/genética
18.
Int J Mol Sci ; 23(13)2022 Jun 24.
Artículo en Inglés | MEDLINE | ID: mdl-35806028

RESUMEN

Due to its essential role in cellular processes, actin is a common target for bacterial toxins. One such toxin, TccC3, is an effector domain of the ABC-toxin produced by entomopathogenic bacteria of Photorhabdus spp. Unlike other actin-targeting toxins, TccC3 uniquely ADP-ribosylates actin at Thr-148, resulting in the formation of actin aggregates and inhibition of phagocytosis. It has been shown that the fully modified F-actin is resistant to depolymerization by cofilin and gelsolin, but their effects on partially modified actin were not explored. We found that only F-actin unprotected by tropomyosin is the physiological TccC3 substrate. Yet, ADP-ribosylated G-actin can be produced upon cofilin-accelerated F-actin depolymerization, which was only mildly inhibited in partially modified actin. The affinity of TccC3-ADP-ribosylated G-actin for profilin and thymosin-ß4 was weakened moderately but sufficiently to potentiate spontaneous polymerization in their presence. Interestingly, the Arp2/3-mediated nucleation was also potentiated by T148-ADP-ribosylation. Notably, even partially modified actin showed reduced bundling by plastins and α-actinin. In agreement with the role of these and other tandem calponin-homology domain actin organizers in the assembly of the cortical actin network, TccC3 induced intense membrane blebbing in cultured cells. Overall, our data suggest that TccC3 imposes a complex action on the cytoskeleton by affecting F-actin nucleation, recycling, and interaction with actin-binding proteins involved in the integration of actin filaments with each other and cellular elements.


Asunto(s)
Photorhabdus , ADP Ribosa Transferasas/química , Citoesqueleto de Actina/metabolismo , Factores Despolimerizantes de la Actina/metabolismo , Actinas/metabolismo , Adenosina Difosfato/metabolismo
19.
Hepatology ; 71(5): 1696-1711, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-31520528

RESUMEN

BACKGROUND AND AIMS: Treatment of hepatocellular carcinomas using our glypican-3 (GPC3)-targeting human nanobody (HN3) immunotoxins causes potent tumor regression by blocking protein synthesis and down-regulating the Wnt signaling pathway. However, immunogenicity and a short serum half-life may limit the ability of immunotoxins to transition to the clinic. APPROACH AND RESULTS: To address these concerns, we engineered HN3-based immunotoxins to contain various deimmunized Pseudomonas exotoxin (PE) domains. This included HN3-T20, which was modified to remove T-cell epitopes and contains a PE domain II truncation. We compared them to our previously reported B-cell deimmunized immunotoxin (HN3-mPE24) and our original HN3-immunotoxin with a wild-type PE domain (HN3-PE38). All of our immunotoxins displayed high affinity to human GPC3, with HN3-T20 having a KD value of 7.4 nM. HN3-T20 retained 73% enzymatic activity when compared with the wild-type immunotoxin in an adenosine diphosphate-ribosylation assay. Interestingly, a real-time cell growth inhibition assay demonstrated that a single dose of HN3-T20 at 62.5 ng/mL (1.6 nM) was capable of inhibiting nearly all cell proliferation during the 10-day experiment. To enhance HN3-T20's serum retention, we tested the effect of adding a streptococcal albumin-binding domain (ABD) and a llama single-domain antibody fragment specific for mouse and human serum albumin. For the detection of immunotoxin in mouse serum, we developed a highly sensitive enzyme-linked immunosorbent assay and found that HN3-ABD-T20 had a 45-fold higher serum half-life than HN3-T20 (326 minutes vs. 7.3 minutes); consequently, addition of an ABD resulted in HN3-ABD-T20-mediated tumor regression at 1 mg/kg. CONCLUSION: These data indicate that ABD-containing deimmunized HN3-T20 immunotoxins are high-potency therapeutics ready to be evaluated in clinical trials for the treatment of liver cancer.


Asunto(s)
ADP Ribosa Transferasas/uso terapéutico , Toxinas Bacterianas/uso terapéutico , Carcinoma Hepatocelular/terapia , Exotoxinas/uso terapéutico , Glipicanos/antagonistas & inhibidores , Inmunotoxinas/uso terapéutico , Neoplasias Hepáticas/terapia , Anticuerpos de Dominio Único/uso terapéutico , Factores de Virulencia/uso terapéutico , ADP Ribosa Transferasas/química , ADP Ribosa Transferasas/farmacología , Animales , Toxinas Bacterianas/química , Toxinas Bacterianas/farmacología , Línea Celular Tumoral , Exotoxinas/química , Exotoxinas/farmacología , Humanos , Inmunotoxinas/química , Inmunotoxinas/farmacología , Ratones , Ratones Desnudos , Anticuerpos de Dominio Único/química , Anticuerpos de Dominio Único/farmacología , Factores de Virulencia/química , Factores de Virulencia/farmacología , Ensayos Antitumor por Modelo de Xenoinjerto , Exotoxina A de Pseudomonas aeruginosa
20.
J Cell Physiol ; 235(4): 3711-3720, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-31578716

RESUMEN

Bacterial toxins have received a great deal of attention in the development of antitumor agents. Currently, these protein toxins were used in the immunotoxins as a cancer therapy strategy. Despite the successful use of immunotoxins, immunotherapy strategies are still expensive and limited to hematologic malignancies. In the current study, for the first time, a nano-toxin comprised of truncated pseudomonas exotoxin (PE38) loaded silver nanoparticles (AgNPs) were prepared and their cytotoxicity effect was investigated on human breast cancer cells. The PE38 protein was cloned into pET28a and expressed in Escherichia coli, BL21 (DE3), and purified using metal affinity chromatography and was analyzed by 15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis. AgNPs were biologically prepared using cell-free supernatant of E. Coli K12 strain. Nanoparticle formation was characterized by energy dispersive spectroscopy, transmission electron microscopy, and dynamic light scattering. The PE38 protein was loaded on AgNPs and prepared the PE38-AgNPs nano-toxin. Additionally, in vitro release indicated a partial slow release of toxin in about 100 hr. The nano-toxin exhibited dose-dependent cytotoxicity on MCF-7 cells. Also, real-time polymerase chain reaction results demonstrated the ability of nano-toxin to upregulate Bax/Bcl-2 ratio and caspase-3, -8, -9, and P53 apoptotic genes in the MCF-7 tumor cells. Apoptosis induction was determined by Annexin-V/propidium flow cytometry and caspases activity assay after treatment of cancer cells with the nano-toxin. In general, in the current study, the nano-toxin exhibit an inhibitory effect on the viability of breast cancer cells through apoptosis, which suggests that AgNPs could be used as a delivery system for targeting of toxins to cancer cells.


Asunto(s)
ADP Ribosa Transferasas/farmacología , Toxinas Bacterianas/farmacología , Neoplasias de la Mama/tratamiento farmacológico , Citotoxinas/farmacocinética , Exotoxinas/farmacología , Nanopartículas del Metal/química , Factores de Virulencia/farmacología , ADP Ribosa Transferasas/química , Antineoplásicos/química , Apoptosis/efectos de los fármacos , Toxinas Bacterianas/química , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Caspasa 3/genética , Caspasas/genética , Proliferación Celular/efectos de los fármacos , Citotoxinas/química , Escherichia coli/genética , Exotoxinas/química , Femenino , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Humanos , Células MCF-7 , Microscopía Electrónica de Transmisión , Proteínas Proto-Oncogénicas c-bcl-2/genética , Plata/química , Plata/farmacología , Factores de Virulencia/química , Proteína X Asociada a bcl-2/genética , Exotoxina A de Pseudomonas aeruginosa
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