Legionella maintains host cell ubiquitin homeostasis by effectors with unique catalytic mechanisms

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 15, 2024

Abstract The intracellular bacterial pathogen Legionella pneumophila modulates host cell functions by secreting multiple effectors with diverse biochemical activities. In particular, of the SidE family interfere protein ubiquitination in a process that involves production phosphoribosyl ubiquitin (PR-Ub). Here, we show effector LnaB converts PR-Ub into ADP-ribosylated ubiquitin, which is further processed to ADP-ribose and functional (ADP-ribosyl)hydrolase MavL, thus maintaining homeostasis infected cells. Upon being activated actin, also undergoes self-AMPylation on tyrosine residues. activity requires motif consisting Ser, His Glu (SHxxxE) present large toxins from pathogens. Thus, our study sheds light mechanisms maintains identifies enzymes capable AMPylation.

Language: Английский

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The Legionella pneumophila Dot/Icm type IV secretion system and its effectors

Microbiology, Journal Year: 2022, Volume and Issue: 168(5)

Published: May 23, 2022

To prevail in the interaction with eukaryotic hosts, many bacterial pathogens use protein secretion systems to release virulence factors at host–pathogen interface and/or deliver them directly into host cells. An outstanding example of complexity and sophistication diversity their substrates, effectors, is Defective organelle trafficking/Intracellular multiplication (Dot/Icm) Type IVB system (T4BSS) Legionella pneumophila related species. species are facultative intracellular environmental protozoa opportunistic human respiratory pathogens. The Dot/Icm T4BSS translocates an exceptionally large number more than 300 per L. strain, essential for evasion phagolysosomal degradation exploitation macrophages as replicative niches. Recent technological advancements imaging complexes have provided new insight architecture allowed us propose models transport mechanism. At same time, significant progress has been made assigning functions about a third discovering unprecedented enzymatic activities concepts subversion. In this review, we describe current knowledge workings machinery provide overview to-date characterized effectors

Language: Английский

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Identification and classification of papain-like cysteine proteinases

Journal of Biological Chemistry, Journal Year: 2023, Volume and Issue: 299(6), P. 104801 - 104801

Published: May 9, 2023

Papain-like cysteine peptidases form a big and highly diverse superfamily of proteins involved in many important biological functions, such as protein turnover, deubiquitination, tissue remodeling, blood clotting, virulence, defense, cell wall remodeling. High sequence structure diversity observed within these hinders their comprehensive classification well the identification new representatives. Moreover, general databases, families already classified papain like lack details regarding mechanism action or function. Here, we use transitive remote homology searches 3D modeling to newly classify 21 papain-like peptidase superfamily. We attempt predict function provide structural characterization 89 clusters defined based on similarity altogether spanning 106 families. systematically discuss sequences, structures, catalytic sites. Eventually, expand list human papain–related by seven representatives, including dopamine receptor–interacting 1 potential deubiquitinase, centriole duplication regulating CEP76 retaining catalytically active peptidase-like domain. The presented results not only structure-based rationales existing databases but also may inspire further experimental research focused peptidase-related processes. Peptidases constitute class enzymes catalyzing peptide bond breakage either other biologically relevant molecules. They are essentially indispensable for digestion, signaling, more. adopt two major mechanisms involving water molecule hydrophilic residue attack bond. Hence, most is very type: cysteine, serine, threonine, aspartate, glutamate. A separate utilize metal ions catalysis; those define clade named metalloproteases. This has been detailed at level clans compiled into today's reference, MEROPS database. currently known universe organized according detectable sequence, function, data. Each type be scaffolded range folds. For instance, retain proteinase, caspase-like, sortase, eIF1-like, Ntn hydrolase–like, trypsin-like serine protease In words, they belong multiple superfamilies. Furthermore, each cover families, which especially case proteinases, zincin-like metallopeptidases, proteases. On hand, given group types, proteases (cysteine type) hydrolase–like (cysteine, threonine), might indicate convergent evolution broader superfamilies, despite provided clear-cut classifications, it still challenging fully comprehend rationally describe light performed functions. subclass peptidases, large from all kingdoms life, viruses (1Page M.J. Di Cera E. Evolution diversity.J. Biol. Chem. 2008; 283: 30010-30014Google Scholar, 2Rawlings N.D. Bateman A. Origins peptidases.Biochimie. 2019; 166: 4-18Google Scholar). Papain, archetypal member superfamily, extracted papaya plant used native Indian countries tendering uncooked meat, was one first discovered (3Martin S.H. Papaïn-digestion.J. Physiol. 1885; 5: 213-230Google act endopeptidases, dipeptidases, exopeptidases (carboxypeptidases aminopeptidases) cleave amide groups outside protein's main chain, example, glutaminases, acyltransferases, peptidoglycan amidases. secreted play roles remodelers (4Vidak Javoršek U. Vizovišek M. Turk B. Cysteine cathepsins extracellular roles: shaping microenvironment.Cells. 8: 264Google Scholar) virulence/defense factors (5Peng C.W. Peremyslov V.V. Mushegian A.R. Dawson W.O. Dolja Functional specialization leader proteinases family Closteroviridae.J. Virol. 2001; 75: 12153-12160Google 6Jensen M.H. Otten H. Christensen Borchert T.V. L.L.H. Larsen S. et al.Structural biochemical studies elucidate rhamnogalacturonan lyase Aspergillus aculeatus.J. Mol. 2010; 404: 100-111Google deubiquitinases regulatory pathways (7Lin S.-C. Chung J.Y. Lamothe Rajashankar K. Lu Lo Y.-C. al.Molecular basis unique deubiquitinating activity NF-kappaB inhibitor A20.J. 376: 526-540Google accessory (8Choi G.H. Pawlyk D.M. Nuss D.L. autocatalytic p29 encoded hypovirulence-associated virus chestnut blight fungus resembles potyvirus-encoded HC-Pro.Virology. 1991; 183: 747-752Google 9Liang Y. Yao J. Gillam Rubella nonstructural domains trans- cis-cleavage activities.J. 2000; 74: 5412-5423Google 10Snijder E.J. Wassenaar A.L. van Dinten L.C. Spaan W.J. Gorbalenya A.E. arterivirus nsp4 prototype novel chymotrypsin-like enzymes, 3C-like proteases.J. 1996; 271: 4864-4871Google toxins bacterial species (11Ashida Sasakawa C. Suzuki T. tactic circumvent death crosstalk induced blockade caspase-8.EMBO 2020; 39e104469Google 12Gavin H.E. Beubier N.T. Satchell K.J.F. effector domain region Vibrio vulnificus MARTX toxin confers biphasic epithelial barrier disruption essential systemic spread intestine.PLoS Pathog. 2017; 13e1006119Google 13Kitadokoro Kamitani Miyazawa Hanajima-Ozawa Fukui Miyake al.Crystal structures reveal thiol protease-like triad C-terminal Pasteurella multocida toxin.Proc. Natl. Acad. Sci. 2007; 104: 5139-5144Google 14Zhang D. de Souza R.F. Anantharaman V. Iyer L.M. Aravind L. Polymorphic systems: trafficking modes, processing, action, immunity ecology using comparative genomics.Biol. Direct. 2012; 7: 18Google Some underwent significant expansions, with paralogs specialized particular substrates (15Komander Clague Urbé Breaking chains: deubiquitinases.Nat. Rev. Cell 2009; 10: 550-563Google 16Nijman S.M.B. Luna-Vargas M.P.A. Velds Brummelkamp T.R. Dirac A.M.G. Sixma T.K. al.A genomic functional inventory enzymes.Cell. 2005; 123: 773-786Google share common core SCOP database (17Murzin A.G. Brenner S.E. Hubbard Chothia SCOP: investigation sequences structures.J. 1995; 247: 536-540Google an α + β fold (d.3—cysteine proteinases) comprising α-helix followed antiparallel β-sheet composed four/five β-strands (depending version) 43215 topology (Fig. 1). site located between helix providing its N terminus 2 3 delivering histidine polar group, respectively. These strands slightly bent away creating convenient pocket aligning incoming substrate catalysis. minimal canonical formed cysteine–histidine dyad (18Barrett A.J. Rawlings Evolutionary lines peptidases.Biol. 382: 727-733Google 19Storer A.C. Ménard R. Catalytic peptidases.Met. Enzymol. 1994; 244: 486-500Google acts nucleophile, whereas base forms reactive thiolate–imidazolium ion pair during catalysis (20Rzychon Chmiel Stec-Niemczyk Modes inhibition proteases.Acta Biochim. Pol. 2004; 51: 861-873Google Scholar), although some proteins, distance too big, limits this effect suggesting that nucleophilicity α-helix, primarily increased dipole itself (21Davies Heath R.J. White S.W. Rock C.O. 1.8 crystal active-site architecture beta-ketoacyl-acyl carrier synthase III (FabH) Escherichia coli.Structure. 185-195Google Still, majority deploy additional orienting histidine's imidazole ring toward increasing basicity (22Moult Sussman F. James M.N. Electron density calculations extension refinement. Streptomyces griseus 1.5 resolution.J. 1985; 182: 555-566Google dyad–triad conserved across few exceptions studies. GP42 transglutaminase Phytophthora sojae lacks position—this immediately after salt bridge aspartate another nearby (23Reiss Kirchner Gijzen Zocher G. Löffelhardt Nürnberger phylogenetic analyses evolutionary relationship oomycetes marine bacteria.J. 2011; 286: 42585-42593Google Scholar); Atg4b third β-strand, positions before (24Kumanomidou Mizushima Komatsu Tanida I. Sou Y.-S. al.The Atg4b, processing de-conjugating enzyme autophagosome-forming modifiers.J. 2006; 355: 612-618Google mobaraense residues swapped (25Kashiwagi Yokoyama K.-I. Ishikawa Ono Ejima Matsui microbial Streptoverticillium mobaraense.J. 2002; 277: 44252-44260Google abundance specificities, taxonomic distributions, ecological contexts entails great peptidases. Despite sharing core, display remarkably rich repertoire insertions (e.g., "fingers" (26Avvakumov G.V. Walker J.R. Xue Finerty Jr., P.J. Mackenzie Newman E.M. al.Amino-terminal dimerization, NRDP1-rhodanese interaction, inhibited conformation ubiquitin-specific 8 (USP8).J. 281: 38061-38070Google Scholar)), deletions viral (27Sun Guo Ma Hao N. Zhang X.C. porcine reproductive respiratory syndrome Nsp1alpha.J. 83: 10931-10940Google permutations (28Iyer Koonin E.V. Novel predicted role ubiquitin signaling pathway.Cell Cycle. 3: 1440-1450Google 29Xu Q. Chiu H.-J. Jaroszewski Klock Knuth M.W. analysis NlpC/P60 circularly permuted reveals lipid binding sites.PLoS One. 6e22013Google 30Anantharaman history, features enzymes.Genome 2003; 4: R11Google overall spatial deteriorations. representatives even tend surpassing capabilities automated comparison approaches. project aims collect distill set describing identify members. assigns 24 "cysteine proteinases" (d.3.1), Pfam, database, classifies 78 Peptidase_CA clan (CL0125), proteases, acetyltransferases, transglutaminases, deubiquitinases, amidases, unknown (DUFs). defines five (CA, CE, CN, CO, CP) 54 crosslinked 40 Pfam clan. addition, more is, C7, C23, C27, C36, C42, remain unassigned any linking aforementioned There have reviews discussing date. 1994, Barrett (31Rawlings Families 461-486Google identified which, authors, three were related (C1, C2, C10). From current point view, dataset included 12 papain-like, recognized differ His–Cys order amino acid sequences; however, because data, hardly possible recognize circular time. year later, 35 clans: CA, CB, CC, CD, CE (32Barrett peptidases.Perspect. Drug Discov. Des. 6: 1-11Google next follow-up article covered 48 27 1999, Koonin's (33Makarova K.S. archaeal, bacterial, eukaryotic homologous animal transglutaminases.Protein 1999; 1714-1719Google described transglutaminases containing families; now Transglut_core PF01841 (families numbered 1, 4, 5, 6, 7 original article), DUF553 PF04473 (no. 3), yet therein). Further work done al. (30Anantharaman who papain. report four families: NLPC_P60, CHAP, C92, lecithin retinol acyltransferase (LRAT) discussed relationships context analyses, PPPDE could works aimed view history universe. 2007, analyzed distribution sequenced genomes sets ubiquitous (16 families) kingdom-specific Similarly, 2019, (2Rawlings surveyed 271 tree life found 33 cellular organisms. neither diversity, would complex sequence-to-structure-to-function nor systematic aim members categorize proteins. By sequence-based detection methods, 28 16 Protein Data Bank (PDB90) belonging papain-like. Based manually curated superimpositions, alignments time outlining complete proteinase fold. Starting initial 59 30 25 Clusters Orthologous Groups (COG) 47 EuKaryotic Group (KOG) PDB90 (Table S1). counts over 4.8 million nonredundant 2.2 single PF08715 coronavirus Markov clustering (MCL) algorithm hmmscan scores closely represented PDB90, COG/KOG, MEROPS, Table HHsearch reflect distant similarities allowed us 10 bigger "meta" groups, least features.Figure 2Structure-guided alignment elements representing columns left: number, cluster clan, family, representative identifier—either National Center Biotechnology Information GenBank entry code. Tags written red font. numbers area denote omitted alignment: parentheses—insertions elements; square brackets—C-terminal part; without brackets—the number following block. Sequences italic elements, turquoise reverse correspond oriented direction space; number. Sequence conservation marked highlights follows: yellow—nonpolar, gray—charged, black/green/red—confirmed (red instead cysteine), magenta—Asp/Arg characteristic NlpC/P60-like proteins.View Large Image Figure ViewerDownload Hi-res image Download (PPT) being assigned CL0125 eight annotated DUFs no information probable sequence–structure domains. Peptidase C8 (PF03569) confirmed methods used. PF18021 PF18022, Trefoil (CL0066), probably beta-trefoil lectin-like preceding domain—here, them 13 residues, had previously Seven proteins: BIVM (Swiss-Prot [SP]: Q86UB2, basic immunoglobulin-like variable motif-containing protein), DRC7 (SP: Q8IY82, dynein subunit 7), Q8TAP6, centrosomal C2D2B Q6DHV5), C2D2A Q9P2K1), C14orf28 Q4W4Y0), VRTN Q9H8Y1, vertnin), sites (C2D2A, C2D2B, contain by, depending definition, forming β-sheet. whole add β-strand definition (β1'), variable, present 3A, PDB ID: 5JT8). Quite unusually classifications where definitions generally clear adequately represent parts extraordinary alterations, cases means alleged elements. Commonly alone together β1' 3B, 3EBQ, C, 3KW0) thoroughly for, (29Xu permutation events affect often associated reversed agglutinin mushroom Marasmius oreades (34Cordara Manna Krengel Family fungal chimerolectins distinct Ca2+-dependent activation mechanism.Biochemistry. 56: 4689-4700Google 3D, 5MU9) 1′ reversed; Legionella pneumophila SdeA deubiquitinase 3E, 5CRA (35Sheedlo Qiu Tan Paul L.N. Luo Z.-Q. Das Structural recognition dynamics phagosome ubiquitination.Proc. 2015; 112: 15090-15095Google Scholar)) 1′, 4 5 direction, latter addition permuted; OTUD5 3F, 3PFY) reversed, fourth missing, permuted—the reversed. Interestingly, harbors glutamine. Many severely reduced missing Nsp1 3G, 3IFU) minimized potyvirus helper–component 3H, 3RNV). Another peptidase/deubiquitinase turnip yellow mosaic (36Jupin Ayach Jomat Fieulaine Bressanelli mobile loop near switch dual activities protease/deubiquitinase.PLoS 13e1006714Google 3I, 5LWA) permuted. consists histidine, residue: asparagine, glutamine, glutamate, indeed 4A, Although always regardless aberrations, alternative architectures observed. obvious reduction C32, C31, C07, C06, C09, C34, C36 OTU-like (clusters V VII). beyond second (harboring histidine) retained remnant Nevertheless, β3 does impose can C33, Ceg23, LotA, presence requires triad, C10, Amidase_6 (PF12671), C115, DUF2459 (PF09601), C97, Calici_PP_N polyprotein (PF08405). migrate position lose 4B, 3IU0, 1IU4) switched (forming CDH triad), now, plays Bacillus 4C, 4P8I) uses glutamate histidine; operate another, directly (37Fernandes C.G. Plácido Lousa Brito J.A. Isidro Soares C.M. ancient sheds requirements cross-linking.Biochemistry. 54: 5723-5734Google DUF1839 4D, PF08893) C(T/S)H place threonine serine. According modeling, threonine/serine's hydroxyl interacts orients against cysteine. 4E, 2D1I) UfSP1 (38Ha B.H. Ahn H.-C. Kang Tanaka C.H. Kim E.E.K. Ufm1 UfSP1.J. 14893-14900Google deconjugating strand resulting "Asp–Pro–His" box defining uncommon 4F, 3TW5), moved location right "CH" motif interacting asparagine (located β2) noncore α-helix) al.Structur

Language: Английский

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Ubiquitin‐targeted bacterial effectors: rule breakers of the ubiquitin system

The EMBO Journal, Journal Year: 2023, Volume and Issue: 42(18)

Published: Aug. 9, 2023

Language: Английский

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Ubiquitin and Legionella: From bench to bedside

Seminars in Cell and Developmental Biology, Journal Year: 2022, Volume and Issue: 132, P. 230 - 241

Published: Feb. 15, 2022

Legionella pneumophila, a Gram-negative intracellular bacterium, is one of the major causes Legionnaires' disease, specific type atypical pneumonia. Despite intensive research efforts that elucidated many relevant structural, molecular and medical insights into Legionella's pathogenicity, disease continues to present an ongoing public health concern. virulence based on its ability simultaneously hijack multiple pathways host cell ensure fast replication dissemination. usurps ubiquitin system through effector proteins, using advantage both conventional unconventional (phosphoribosyl-linked) ubiquitination, thus providing optimal conditions for replication. In this review, we summarize current understanding L. pneumophila from medical, biochemical perspectives. We describe clinical presentation, diagnostics treatment, as well host-pathogen interactions, with emphasis target upon infection. Furthermore, interdisciplinary use innovative technologies enables better pathogenesis provides new opportunities treatment prevention.

Language: Английский

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Host-acting antibacterial compounds combat cytosolic bacteria

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 30(8), P. 761 - 777

Published: Feb. 7, 2022

Language: Английский

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Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 19, 2024

Abstract ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being major family this category. The pathogen Legionella pneumophila mediates atypical ubiquitination host targets using the SidE effector process that involves ubiquitin on arginine 42 as an obligatory step. Here, we show MavL regulates pathway by reversing ADP-ribosylation, likely to minimize potential detrimental effects caused modified ubiquitin. We determine crystal structure ADP-ribose-bound MavL, providing structural insights into recognition ADP-ribosyl group and catalytic mechanism its removal. Further analyses reveal DUF4804 class MavL-like whose representative members unique selectivity for mono-ADP-ribosylated residue synthetic substrates. find such are also present eukaryotes, exemplified two previously uncharacterized (ADP-ribosyl)hydrolases Drosophila melanogaster . Crystal structures several proteins provide specificity shared mode ADP-ribose interaction distinct from characterized macrodomains. Collectively, our study reveals new regulatory layer SidE-catalyzed expands current understanding enzymes.

Language: Английский

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Bacterial ubiquitin ligases hijack the host deubiquitinase OTUB1 to inhibit MTORC1 signaling and promote autophagy

Autophagy, Journal Year: 2024, Volume and Issue: 20(9), P. 1968 - 1983

Published: May 31, 2024

Many bacterial pathogens have evolved effective strategies to interfere with the ubiquitination network evade clearance by innate immune system. Here, we report that OTUB1, one of most abundant deubiquitinases (DUBs) in mammalian cells, is subjected both canonical and noncanonical during Legionella pneumophila infection. The effectors SidC SdcA catalyze OTUB1 at multiple lysine residues, resulting its association a Legionella-containing vacuole. Lysine promotes interactions between DEPTOR, an inhibitor MTORC1 pathway, thus suppressing signaling. inhibition leads suppression host protein synthesis promotion macroautophagy/autophagy L. In addition, members SidE family (SidEs) induce phosphoribosyl (PR)-linked Ser16 Ser18 block DUB activity. levels serine are further regulated function antagonize activities SidC, SidEs, including Lem27, DupA, DupB, SidJ SdjA. Our study reveals effectors-mediated complicated mechanism regulating activity DUB.

Language: Английский

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Phosphoribosyl modification of poly-ubiquitin chains at the Legionella-containing vacuole prohibiting autophagy adaptor recognition

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 30, 2024

Ubiquitination is a posttranslational modification in eukaryotes that plays significant role the infection of intracellular microbial pathogens, such as Legionella pneumophila. While Legionella-containing vacuole (LCV) coated with ubiquitin (Ub), it avoids recognition by autophagy adaptors. Here, we report Sdc and Sde families effectors work together to build ubiquitinated species around LCV. The catalyze canonical polyubiquitination directly on host targets or phosphoribosyl-Ub conjugated Sde. Remarkably, Ub moieties within poly-Ub chains are either modified phosphoribosyl group PDE domain-containing covalently attached other substrates via Sde-mediated phosphoribosyl-ubiquitination. Furthermore, these modifications prevent adaptors therefore exclude from In this work, shed light nature poly-ubiquitinated present at surface LCV provide molecular mechanism for avoidance Ub-decorated

Language: Английский

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Divergence of Legionella Effectors Reversing Conventional and Unconventional Ubiquitination

Frontiers in Cellular and Infection Microbiology, Journal Year: 2020, Volume and Issue: 10

Published: Aug. 21, 2020

The intracellular bacterial pathogen Legionella pneumophila employs bacteria-derived effector proteins in a variety of functions to exploit host cellular systems. ubiquitination machinery constitutes crucial eukaryotic system for the regulation numerous processes and is representative target effector-mediated manipulation. L. transports more than 300 into cells through type IV secretion system. Among these, several have been found function as ubiquitin ligases, including unprecedented enzymes that catalyze unconventional mechanisms. Recent studies identified many can interfere ubiquitination. These effectors include are distantly related ovarian tumor protein superfamily described deubiquitinases (DUBs), which regulate important signaling cascades human cells. Intriguingly, DUBs not limited exhibit canonical DUB activity. Some cleavage linkage substrates. Furthermore, novel mechanisms adversely affect specific ligases; instance, an posttranslational modification ligases results inhibition their Bacterial inhibit ligase activity, cognate DUBs, examples effector/metaeffector sets due opposing functional relationship. In context infection, existence reverse mainly relates fine tuning biogenesis remodeling Legionella-containing vacuole replicative niche. complexity arrays reflects sophisticated strategies bacteria adopted adapt its environment enable survival This review summarizes current state knowledge on divergent ubiquitination, mediated by other well machinery.

Language: Английский

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