1
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Urbanus ML, Zheng TM, Khusnutdinova AN, Banh D, O'Connor Mount H, Gupta A, Stogios PJ, Savchenko A, Isberg RR, Yakunin AF, Ensminger AW. A random mutagenesis screen enriched for missense mutations in bacterial effector proteins. G3 (BETHESDA, MD.) 2024; 14:jkae158. [PMID: 39028840 PMCID: PMC11373652 DOI: 10.1093/g3journal/jkae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
To remodel their hosts and escape immune defenses, many pathogens rely on large arsenals of proteins (effectors) that are delivered to the host cell using dedicated translocation machinery. Effectors hold significant insight into the biology of both the pathogens that encode them and the host pathways that they manipulate. One of the most powerful systems biology tools for studying effectors is the model organism, Saccharomyces cerevisiae. For many pathogens, the heterologous expression of effectors in yeast is growth inhibitory at a frequency much higher than housekeeping genes, an observation ascribed to targeting conserved eukaryotic proteins. Abrogation of yeast growth inhibition has been used to identify bacterial suppressors of effector activity, host targets, and functional residues and domains within effector proteins. We present here a yeast-based method for enriching for informative, in-frame, missense mutations in a pool of random effector mutants. We benchmark this approach against three effectors from Legionella pneumophila, an intracellular bacterial pathogen that injects a staggering >330 effectors into the host cell. For each protein, we show how in silico protein modeling (AlphaFold2) and missense-directed mutagenesis can be combined to reveal important structural features within effectors. We identify known active site residues within the metalloprotease RavK, the putative active site in SdbB, and previously unidentified functional motifs within the C-terminal domain of SdbA. We show that this domain has structural similarity with glycosyltransferases and exhibits in vitro activity consistent with this predicted function.
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Affiliation(s)
- Malene L Urbanus
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thomas M Zheng
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Doreen Banh
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Harley O'Connor Mount
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Alind Gupta
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02115, USA
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 1A4, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Alexander W Ensminger
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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2
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Ma K, Xian W, Liu H, Shu R, Ge J, Luo ZQ, Liu X, Qiu J. Bacterial ubiquitin ligases hijack the host deubiquitinase OTUB1 to inhibit MTORC1 signaling and promote autophagy. Autophagy 2024; 20:1968-1983. [PMID: 38818749 PMCID: PMC11346569 DOI: 10.1080/15548627.2024.2353492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/21/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024] Open
Abstract
Many bacterial pathogens have evolved effective strategies to interfere with the ubiquitination network to evade clearance by the innate immune system. Here, we report that OTUB1, one of the most abundant deubiquitinases (DUBs) in mammalian cells, is subjected to both canonical and noncanonical ubiquitination during Legionella pneumophila infection. The effectors SidC and SdcA catalyze OTUB1 ubiquitination at multiple lysine residues, resulting in its association with a Legionella-containing vacuole. Lysine ubiquitination by SidC and SdcA promotes interactions between OTUB1 and DEPTOR, an inhibitor of the MTORC1 pathway, thus suppressing MTORC1 signaling. The inhibition of MTORC1 leads to suppression of host protein synthesis and promotion of host macroautophagy/autophagy during L. pneumophila infection. In addition, members of the SidE family effectors (SidEs) induce phosphoribosyl (PR)-linked ubiquitination of OTUB1 at Ser16 and Ser18 and block its DUB activity. The levels of the lysine and serine ubiquitination of OTUB1 are further regulated by effectors that function to antagonize the activities of SidC, SdcA and SidEs, including Lem27, DupA, DupB, SidJ and SdjA. Our study reveals an effectors-mediated complicated mechanism in regulating the activity of a host DUB.Abbreviations: BafA1: bafilomycin A1; BMDMs: bone marrow-derived macrophages; DUB: deubiquitinase; Dot/Icm: defective for organelle trafficking/intracellular multiplication; DEPTOR: DEP domain containing MTOR interacting protein; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; L. pneumophila: Legionella pneumophila; LCV: Legionella-containing vacuole; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTORC1: mechanistic target of rapamycin kinase complex 1; OTUB1: OTU deubiquitinase, ubiquitin aldehyde binding 1; PR-Ub: phosphoribosyl (PR)-linked ubiquitin; PTM: posttranslational modification; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SidEs: SidE family effectors; Ub: ubiquitin.
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Affiliation(s)
- Kelong Ma
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Rundong Shu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
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3
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Kotewicz KM, Zhang M, Kim S, Martin MS, Roy Chowdhury A, Tai A, Scheck RA, Isberg RR. Sde proteins coordinate ubiquitin utilization and phosphoribosylation to establish and maintain the Legionella replication vacuole. Nat Commun 2024; 15:7479. [PMID: 39214970 PMCID: PMC11364549 DOI: 10.1038/s41467-024-51272-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
The Legionella pneumophila Sde family of translocated proteins promotes host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity is tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, prevents binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb results in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decays quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
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Affiliation(s)
- Kristin M Kotewicz
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Mengyun Zhang
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Seongok Kim
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Department of Food Science & Biotechnology, Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul, South Korea
| | | | - Atish Roy Chowdhury
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Albert Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | | | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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4
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Kotewicz KM, Zhang M, Kim S, Martin MS, Chowdhury AR, Tai A, Scheck RA, Isberg RR. Sde Proteins Coordinate Ubiquitin Utilization and Phosphoribosylation to Establish and Maintain the Legionella Replication Vacuole. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.07.553534. [PMID: 38645023 PMCID: PMC11030226 DOI: 10.1101/2023.09.07.553534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The Legionella pneumophila Sde family of translocated proteins promotes host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity is tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, prevents binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb results in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decays quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
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5
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Kubori T, Arasaki K, Oide H, Kitao T, Nagai H. Multi-tiered actions of Legionella effectors to modulate host Rab10 dynamics. eLife 2024; 12:RP89002. [PMID: 38771316 PMCID: PMC11108646 DOI: 10.7554/elife.89002] [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: 05/22/2024] Open
Abstract
Rab GTPases are representative targets of manipulation by intracellular bacterial pathogens for hijacking membrane trafficking. Legionella pneumophila recruits many Rab GTPases to its vacuole and exploits their activities. Here, we found that infection-associated regulation of Rab10 dynamics involves ubiquitin signaling cascades mediated by the SidE and SidC families of Legionella ubiquitin ligases. Phosphoribosyl-ubiquitination of Rab10 catalyzed by the SidE ligases is crucial for its recruitment to the bacterial vacuole. SdcB, the previously uncharacterized SidC-family effector, resides on the vacuole and contributes to retention of Rab10 at the late stages of infection. We further identified MavC as a negative regulator of SdcB. By the transglutaminase activity, MavC crosslinks ubiquitin to SdcB and suppresses its function, resulting in elimination of Rab10 from the vacuole. These results demonstrate that the orchestrated actions of many L. pneumophila effectors fine-tune the dynamics of Rab10 during infection.
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Affiliation(s)
- Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life SciencesHachiojiJapan
| | - Hiromu Oide
- School of Life Sciences, Tokyo University of Pharmacy and Life SciencesHachiojiJapan
| | - Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu UniversityGifuJapan
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6
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Zhang Z, Fu J, Rack JGM, Li C, Voorneveld J, Filippov DV, Ahel I, Luo ZQ, Das C. Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain. Nat Commun 2024; 15:2452. [PMID: 38503748 PMCID: PMC10951314 DOI: 10.1038/s41467-024-46649-2] [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: 11/05/2022] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster. Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.
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Affiliation(s)
- Zhengrui Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jiaqi Fu
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, EX4 4QD, Exeter, UK
| | - Chuang Li
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Jim Voorneveld
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Dmitri V Filippov
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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7
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van Overbeek NK, Aguirre T, van der Heden van Noort GJ, Blagoev B, Vertegaal ACO. Deciphering non-canonical ubiquitin signaling: biology and methodology. Front Mol Biosci 2024; 10:1332872. [PMID: 38414868 PMCID: PMC10897730 DOI: 10.3389/fmolb.2023.1332872] [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: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 02/29/2024] Open
Abstract
Ubiquitination is a dynamic post-translational modification that regulates virtually all cellular processes by modulating function, localization, interactions and turnover of thousands of substrates. Canonical ubiquitination involves the enzymatic cascade of E1, E2 and E3 enzymes that conjugate ubiquitin to lysine residues giving rise to monomeric ubiquitination and polymeric ubiquitination. Emerging research has established expansion of the ubiquitin code by non-canonical ubiquitination of N-termini and cysteine, serine and threonine residues. Generic methods for identifying ubiquitin substrates using mass spectrometry based proteomics often overlook non-canonical ubiquitinated substrates, suggesting that numerous undiscovered substrates of this modification exist. Moreover, there is a knowledge gap between in vitro studies and comprehensive understanding of the functional consequence of non-canonical ubiquitination in vivo. Here, we discuss the current knowledge about non-lysine ubiquitination, strategies to map the ubiquitinome and their applicability for studying non-canonical ubiquitination substrates and sites. Furthermore, we elucidate the available chemical biology toolbox and elaborate on missing links required to further unravel this less explored subsection of the ubiquitin system.
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Affiliation(s)
- Nila K. van Overbeek
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Tim Aguirre
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
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8
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Yang Y, Mei L, Chen J, Chen X, Wang Z, Liu L, Yang A. Legionella pneumophila-mediated host posttranslational modifications. J Mol Cell Biol 2023; 15:mjad032. [PMID: 37156500 PMCID: PMC10720952 DOI: 10.1093/jmcb/mjad032] [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: 09/16/2022] [Revised: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023] Open
Abstract
Legionella pneumophila is a Gram-negative bacterium ubiquitously present in freshwater environments and causes a serious type of pneumonia called Legionnaires' disease. During infections, L. pneumophila releases over 300 effector proteins into host cells through an Icm/Dot type IV secretion system to manipulate the host defense system for survival within the host. Notably, certain effector proteins mediate posttranslational modifications (PTMs), serving as useful approaches exploited by L. pneumophila to modify host proteins. Some effectors catalyze the addition of host protein PTMs, while others mediate the removal of PTMs from host proteins. In this review, we summarize L. pneumophila effector-mediated PTMs of host proteins, including phosphorylation, ubiquitination, glycosylation, AMPylation, phosphocholination, methylation, and ADP-ribosylation, as well as dephosphorylation, deubiquitination, deAMPylation, deADP-ribosylation, dephosphocholination, and delipidation. We describe their molecular mechanisms and biological functions in the regulation of bacterial growth and Legionella-containing vacuole biosynthesis and in the disruption of host immune and defense machinery.
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Affiliation(s)
- Yi Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
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9
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Isberg R, Kotewicz K, Zheng M, Kim S, Tai A. Sde Proteins Coordinate Ubiquitin Utilization and Phosphoribosylation to Promote Establishment and Maintenance of the Legionella Replication Vacuole. RESEARCH SQUARE 2023:rs.3.rs-3269310. [PMID: 37790456 PMCID: PMC10543313 DOI: 10.21203/rs.3.rs-3269310/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Legionella pneumophilaSde family of translocated proteins promote host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity was tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, caused an absolute block in binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb resulted in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decayed quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
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10
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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11
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Ge J, Wang Y, Chen X, Yu K, Luo ZQ, Liu X, Qiu J. Phosphoribosyl-linked serine ubiquitination of USP14 by the SidE family effectors of Legionella excludes p62 from the bacterial phagosome. Cell Rep 2023; 42:112817. [PMID: 37471226 DOI: 10.1016/j.celrep.2023.112817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/19/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
Xenophagy is an evolutionarily conserved host defensive mechanism to eliminate invading microorganisms through autophagic machinery. The intracellular bacterial pathogen Legionella pneumophila can avoid clearance by the xenophagy pathway via the actions of multiple Dot/Icm effector proteins. Previous studies have shown that p62, an adaptor protein involved in xenophagy signaling, is excluded from Legionella-containing vacuoles (LCVs). Such defects are attributed to the multifunctional SidE family effectors (SidEs) that exhibit classic deubiquitinase (DUB) and phosphoribosyl ubiquitination (PR-ubiquitination) activities, yet the mechanism remains elusive. In the present study, we demonstrate that the host DUB USP14 is PR-ubiquitinated by SidEs at multiple serine residues, which impairs its DUB activity and its interactions with p62. The exclusion of p62 from the bacterial phagosome requires the ubiquitin ligase but not the DUB activity of SidEs. These results reveal that PR-ubiquitination of USP14 by SidEs contributes to the evasion of xenophagic clearance by L. pneumophila.
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Affiliation(s)
- Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun 130062, China
| | - Ying Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xindi Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun 130062, China
| | - Kaiwen Yu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing 100191, China.
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun 130062, China.
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12
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Xie Y, Zhang Y, Wang Y, Feng Y. Mechanism and Modulation of SidE Family Proteins in the Pathogenesis of Legionella pneumophila. Pathogens 2023; 12:pathogens12040629. [PMID: 37111515 PMCID: PMC10143409 DOI: 10.3390/pathogens12040629] [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: 02/19/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Legionella pneumophila is the causative agent of Legionnaires' disease, causing fever and lung infection, with a death rate up to 15% in severe cases. In the process of infection, Legionella pneumophila secretes over 330 effectors into host cell via the Dot/Icm type IV secretion system to modulate multiple host cellular physiological processes, thereby changing the environment of the host cell and promoting the growth and propagation of the bacterium. Among these effector proteins, SidE family proteins from Legionella pneumophila catalyze a non-canonical ubiquitination reaction, which combines mono-ADP-ribosylation and phosphodiesterase activities together to attach ubiquitin onto substrates. Meanwhile, the activity of SidE family proteins is also under multiple modulations by other effectors. Herein we summarize the key insights into recent studies in this area, emphasizing the tight link between the modular structure of SidE family proteins and the pathogen virulence as well as the fundamental mechanism and modulation network for further extensive research.
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Affiliation(s)
- Yongchao Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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13
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Wanford JJ, Odendall C. Ca 2+-calmodulin signalling at the host-pathogen interface. Curr Opin Microbiol 2023; 72:102267. [PMID: 36716574 DOI: 10.1016/j.mib.2023.102267] [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: 10/19/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/29/2023]
Abstract
Multiple eukaryotic cell processes are modulated by calcium ions (Ca2+). As such, Ca2+ is emerging as a crucial regulator of innate immunity in multicellular organisms. In particular, recent studies have identified roles of Ca2+ signalling at the host-bacteria interface. Following microbial exposure, Ca2+ signals mobilised from the extracellular milieu or intracellular stores are transduced into cell physiological responses. However, during infection with host-adapted pathogens, Ca2+ signals are often atypical, due to the activities of virulence factors, with varied consequences for both the pathogen and the host cell. In this review, we describe the Ca2+-dependent host factors regulating antibacterial immunity, in addition to bacterial effectors that promote, inhibit, or co-opt Ca2+-calmodulin signalling to promote infection.
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Affiliation(s)
- Joseph J Wanford
- School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Charlotte Odendall
- School of Immunology and Microbial Sciences, Kings College London, London, UK.
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14
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Zacharchenko T, Dorendorf T, Locker N, Van Dijk E, Katzemich A, Diederichs K, Bullard B, Mayans O. PK1 from Drosophila obscurin is an inactive pseudokinase with scaffolding properties. Open Biol 2023; 13:220350. [PMID: 37121260 PMCID: PMC10129394 DOI: 10.1098/rsob.220350] [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: 11/25/2022] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Obscurins are large filamentous proteins with crucial roles in the assembly, stability and regulation of muscle. Characteristic of these proteins is a tandem of two C-terminal kinase domains, PK1 and PK2, that are separated by a long intrinsically disordered sequence. The significance of this conserved domain arrangement is unknown. Our study of PK1 from Drosophila obscurin shows that this is a pseudokinase with features typical of the CAM-kinase family, but which carries a minimalistic regulatory tail that no longer binds calmodulin or has mechanosensory properties typical of other sarcomeric kinases. PK1 binds ATP with high affinity, but in the absence of magnesium and lacks detectable phosphotransfer activity. It also has a highly diverged active site, strictly conserved across arthropods, that might have evolved to accommodate an unconventional binder. We find that PK1 interacts with PK2, suggesting a functional relation to the latter. These findings lead us to speculate that PK1/PK2 form a pseudokinase/kinase dual system, where PK1 might act as an allosteric regulator of PK2 and where mechanosensing properties, akin to those described for regulatory tails in titin-like kinases, might now reside on the unstructured interkinase segment. We propose that the PK1-interkinase-PK2 region constitutes an integrated functional unit in obscurin proteins.
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Affiliation(s)
- Thomas Zacharchenko
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Till Dorendorf
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Evert Van Dijk
- Biosynth B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
| | | | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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15
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Pon A, Osinski A, Sreelatha A. Redefining pseudokinases: A look at the untapped enzymatic potential of pseudokinases. IUBMB Life 2023; 75:370-376. [PMID: 36602414 PMCID: PMC10050101 DOI: 10.1002/iub.2698] [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: 09/30/2022] [Accepted: 11/19/2022] [Indexed: 01/06/2023]
Abstract
Catalytically inactive kinases, known as pseudokinases, are conserved in all three domains of life. Due to the lack of catalytic residues, pseudokinases are considered to act as allosteric regulators and scaffolding proteins with no enzymatic function. However, since these "dead" kinases are conserved along with their active counterparts, a role for pseudokinases may have been overlooked. In this review, we will discuss the recently characterized pseudokinases Selenoprotein O, Legionella effector SidJ, and the SARS-CoV2 protein nsp12 which catalyze AMPylation, glutamylation, and RNAylation, respectively. These studies provide structural and mechanistic insight into the versatility and diversity of the kinase fold.
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Affiliation(s)
- Alex Pon
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Anju Sreelatha
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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16
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Hou Y, Zeng H, Li Z, Feng N, Meng F, Xu Y, Li L, Shao F, Ding J. Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis. Nat Struct Mol Biol 2023; 30:261-272. [PMID: 36624349 DOI: 10.1038/s41594-022-00888-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/03/2022] [Indexed: 01/11/2023]
Abstract
The caspase-4/11-GSDMD pyroptosis axis recognizes cytosolic lipopolysaccharide for antibacterial defenses. Shigella flexneri employs an OspC3 effector to block pyroptosis by catalyzing NAD+-dependent arginine ADP-riboxanation of caspase-4/11. Here, we identify Ca2+-free calmodulin (CaM) that binds and stimulates OspC3 ADP-riboxanase activity. Crystal structures of OspC3-CaM and OspC3-caspase-4 binary complexes reveal unique CaM binding to an OspC3 N-terminal domain featuring an ADP-ribosyltransferase-like fold and specific recognition of caspase-4 by an OspC3 ankryin repeat domain, respectively. CaM-OspC3-caspase-4 ternary complex structures show that NAD+ binding reorganizes the catalytic pocket, in which D231 and D177 activate the substrate arginine for initial ADP-ribosylation and ribosyl 2'-OH in the ADP-ribosylated arginine, respectively, for subsequent deamination. We also determine structures of unmodified and OspC3-ADP-riboxanated caspase-4. Mechanisms derived from this series of structures covering the entire process of OspC3 action are supported by biochemical analyses in vitro and functional validation in S. flexneri-infected mice.
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Affiliation(s)
- Yanjie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huan Zeng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Zilin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China
| | - Na Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fanyi Meng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Xu
- National Institute of Biological Sciences, Beijing, Beijing, China
- Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, Beijing, China
| | - Feng Shao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- National Institute of Biological Sciences, Beijing, Beijing, China.
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
| | - Jingjin Ding
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Institute of Biological Sciences, Beijing, Beijing, China.
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17
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Luo J, Ruan X, Huang Z, Li Z, Ye L, Wu Y, Zhen X, Ouyang S. Structural basis for the dual catalytic activity of the Legionella pneumophila ovarian-tumor (OTU) domain deubiquitinase LotA. J Biol Chem 2022; 298:102414. [PMID: 36007613 PMCID: PMC9486567 DOI: 10.1016/j.jbc.2022.102414] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022] Open
Abstract
Legionella pneumophila, a bacterial pathogen that causes a severe pneumonia known as Legionnaires’ disease, extensively exploits the ubiquitin (Ub) pathway in the infected host cells through certain virulence effectors excreted by the Dot/Icm system. To date, several Dot/Icm effectors have been found to act as Ub ligases, and four effectors, including LotA, LotB, LotC, and Ceg7, have been identified as deubiquitinases (DUBs) from the ovarian tumor (OTU) domain family. LotA is unique among other OTU DUBs because it possesses two distinct DUB domains and exclusively exhibits catalytic activity against K6-linked diUb and polyUb chains. However, the structure of LotA and the molecular mechanism for the dual DUB activity remains elusive. In this study, we solved the structure of LotA in complex with proximally bound Ub and distal covalently bound Ub. Both Ub molecules are bound to the DUB1 domain and mimic a K6-linked diUb. Structural analysis reveals that the DUB1 domain utilizes a distinct mechanism for recognition of the K6-linked diUb within a large S1′ binding site that is uncommon to OTU DUBs. Structural fold of the LotA DUB2 domain closely resembles LotB and LotC, similarly containing an extra α-helix lobe that has been demonstrated to play an important role in Ub binding. Collectively, our study uncovers the structural basis for the dual catalytic activity of the unique OTU family DUB LotA.
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Affiliation(s)
- Jiwei Luo
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xinglin Ruan
- Department of Neurology, Fujian Medical University Union Hospital, 29 Xinquan Road Gulou District, Fuzhou 350001, China
| | - Zhijie Huang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Zekai Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Le Ye
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Yongyu Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiangkai Zhen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
| | - Songying Ouyang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
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18
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Alphonse N, Wanford JJ, Voak AA, Gay J, Venkhaya S, Burroughs O, Mathew S, Lee T, Evans SL, Zhao W, Frowde K, Alrehaili A, Dickenson RE, Munk M, Panina S, Mahmood IF, Llorian M, Stanifer ML, Boulant S, Berchtold MW, Bergeron JRC, Wack A, Lesser CF, Odendall C. A family of conserved bacterial virulence factors dampens interferon responses by blocking calcium signaling. Cell 2022; 185:2354-2369.e17. [PMID: 35568036 PMCID: PMC9596379 DOI: 10.1016/j.cell.2022.04.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/22/2022] [Accepted: 04/20/2022] [Indexed: 02/06/2023]
Abstract
Interferons (IFNs) induce an antimicrobial state, protecting tissues from infection. Many viruses inhibit IFN signaling, but whether bacterial pathogens evade IFN responses remains unclear. Here, we demonstrate that the Shigella OspC family of type-III-secreted effectors blocks IFN signaling independently of its cell death inhibitory activity. Rather, IFN inhibition was mediated by the binding of OspC1 and OspC3 to the Ca2+ sensor calmodulin (CaM), blocking CaM kinase II and downstream JAK/STAT signaling. The growth of Shigella lacking OspC1 and OspC3 was attenuated in epithelial cells and in a murine model of infection. This phenotype was rescued in both models by the depletion of IFN receptors. OspC homologs conserved in additional pathogens not only bound CaM but also inhibited IFN, suggesting a widespread virulence strategy. These findings reveal a conserved but previously undescribed molecular mechanism of IFN inhibition and demonstrate the critical role of Ca2+ and IFN targeting in bacterial pathogenesis.
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Affiliation(s)
- Noémie Alphonse
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK; Immunoregulation Laboratory, Francis Crick Institute, London, UK
| | - Joseph J Wanford
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Andrew A Voak
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jack Gay
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Shayla Venkhaya
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Owen Burroughs
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Sanjana Mathew
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Truelian Lee
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sasha L Evans
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Weiting Zhao
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Kyle Frowde
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Abrar Alrehaili
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Mads Munk
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Svetlana Panina
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ishraque F Mahmood
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Miriam Llorian
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Megan L Stanifer
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
| | | | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Andreas Wack
- Immunoregulation Laboratory, Francis Crick Institute, London, UK
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Odendall
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
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19
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Lockwood DC, Amin H, Costa TRD, Schroeder GN. The Legionella pneumophila Dot/Icm type IV secretion system and its effectors. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35639581 DOI: 10.1099/mic.0.001187] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To prevail in the interaction with eukaryotic hosts, many bacterial pathogens use protein secretion systems to release virulence factors at the host–pathogen interface and/or deliver them directly into host cells. An outstanding example of the complexity and sophistication of secretion systems and the diversity of their protein substrates, effectors, is the Defective in organelle trafficking/Intracellular multiplication (Dot/Icm) Type IVB secretion system (T4BSS) of
Legionella pneumophila
and related species.
Legionella
species are facultative intracellular pathogens of environmental protozoa and opportunistic human respiratory pathogens. The Dot/Icm T4BSS translocates an exceptionally large number of effectors, more than 300 per
L. pneumophila
strain, and is essential for evasion of phagolysosomal degradation and exploitation of protozoa and human macrophages as replicative niches. Recent technological advancements in the imaging of large protein complexes have provided new insight into the architecture of the T4BSS and allowed us to propose models for the transport mechanism. At the same time, significant progress has been made in assigning functions to about a third of
L. pneumophila
effectors, discovering unprecedented new enzymatic activities and concepts of host subversion. In this review, we describe the current knowledge of the workings of the Dot/Icm T4BSS machinery and provide an overview of the activities and functions of the to-date characterized effectors in the interaction of
L. pneumophila
with host cells.
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Affiliation(s)
- Daniel C Lockwood
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
| | - Himani Amin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Gunnar N Schroeder
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
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20
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Black MH, Gradowski M, Pawłowski K, Tagliabracci VS. Methods for discovering catalytic activities for pseudokinases. Methods Enzymol 2022; 667:575-610. [PMID: 35525554 DOI: 10.1016/bs.mie.2022.03.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pseudoenzymes resemble active enzymes, but lack key catalytic residues believed to be required for activity. Many pseudoenzymes appear to be inactive in conventional enzyme assays. However, an alternative explanation for their apparent lack of activity is that pseudoenzymes are being assayed for the wrong reaction. We have discovered several new protein kinase-like families which have revealed how different binding orientations of adenosine triphosphate (ATP) and active site residue migration can generate a novel reaction from a common kinase scaffold. These results have exposed the catalytic versatility of the protein kinase fold and suggest that atypical kinases and pseudokinases should be analyzed for alternative transferase activities. In this chapter, we discuss a general approach for bioinformatically identifying divergent or atypical members of an enzyme superfamily, then present an experimental approach to characterize their catalytic activity.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Marcin Gradowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland.
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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21
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Ge Z, Yuan P, Chen L, Chen J, Shen D, She Z, Lu Y. New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila. Mol Cell Proteomics 2022; 21:100233. [PMID: 35427813 PMCID: PMC9112007 DOI: 10.1016/j.mcpro.2022.100233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 01/11/2023] Open
Abstract
Legionella pneumophila, an environmental bacterium that parasitizes protozoa, causes Legionnaires’ disease in humans that is characterized by severe pneumonia. This bacterium adopts a distinct biphasic life cycle consisting of a nonvirulent replicative phase and a virulent transmissive phase in response to different environmental conditions. Hence, the timely and fine-tuned expression of growth and virulence factors in a life cycle–dependent manner is crucial for survival and replication. Here, we report that the completion of the biphasic life cycle and bacterial pathogenesis is greatly dependent on the protein homeostasis regulated by caseinolytic protease P (ClpP)-dependent proteolysis. We characterized the ClpP-dependent dynamic profiles of the regulatory and substrate proteins during the biphasic life cycle of L. pneumophila using proteomic approaches and discovered that ClpP-dependent proteolysis specifically and conditionally degraded the substrate proteins, thereby directly playing a regulatory role or indirectly controlling cellular events via the regulatory proteins. We further observed that ClpP-dependent proteolysis is required to monitor the abundance of fatty acid biosynthesis–related protein Lpg0102/Lpg0361/Lpg0362 and SpoT for the normal regulation of L. pneumophila differentiation. We also found that the control of the biphasic life cycle and bacterial virulence is independent. Furthermore, the ClpP-dependent proteolysis of Dot/Icm (defect in organelle trafficking/intracellular multiplication) type IVB secretion system and effector proteins at a specific phase of the life cycle is essential for bacterial pathogenesis. Therefore, our findings provide novel insights on ClpP-dependent proteolysis, which spans a broad physiological spectrum involving key metabolic pathways that regulate the transition of the biphasic life cycle and bacterial virulence of L. pneumophila, facilitating adaptation to aquatic and intracellular niches. ClpP is the major determinant of biphasic life cycle–dependent protein turnover. ClpP-dependent proteolysis monitors SpoT abundance for cellular differentiation. ClpP-dependent regulation of life cycle and bacterial virulence is independent. ClpP-dependent proteolysis of T4BSS and effector proteins is vital for virulence.
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Affiliation(s)
- Zhenhuang Ge
- School of Chemistry, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China
| | - Peibo Yuan
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lingming Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junyi Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China
| | - Dong Shen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhigang She
- School of Chemistry, Sun Yat-sen University, Guangzhou, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China.
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22
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Abstract
Polyglutamylation is a posttranslational modification (PTM) that adds several glutamates on glutamate residues in the form of conjugated peptide chains by a family of enzymes known as polyglutamylases. Polyglutamylation is well documented in microtubules. Polyglutamylated microtubules consist of different α- and β-tubulin subunits with varied number of added glutamate residues. Kinetic control and catalytic rates of tubulin modification by polyglutamylases influence the polyglutamylation pattern of functional microtubules. The recent studies uncovered catalytic mechanisms of the glutamylation enzymes family, particularly tubulin tyrosine ligase-like (TTLL). Variable length polyglutamylation of primary sequence glutamyl residues have been mapped with a multitude of protein chemistry and proteomics approaches. Although polyglutamylation was initially considered a tubulin-specific modification, the recent studies have uncovered a calmodulin-dependent glutamylase, SidJ. Nano-electrospray ionization (ESI) proteomic approaches have identified quantifiable polyglutamylated sites in specific substrates. Indeed, conjugated glutamylated peptides were used in nano-liquid chromatography gradient delivery due to their relative hydrophobicity for their tandem mass spectrometry (MS/MS) characterization. The recent polyglutamylation characterization has revealed three major sites: E445 in α-tubulin, E435 in β-tubulin, and E860 in SdeA. In this review, we have summarized the progress made using proteomic approaches for large-scale detection of polyglutamylated peptides, including biology and analysis.
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Song L, Luo J, Wang H, Huang D, Tan Y, Liu Y, Wang Y, Yu K, Zhang Y, Liu X, Li D, Luo ZQ. Legionella pneumophila regulates host cell motility by targeting Phldb2 with a 14-3-3ζ-dependent protease effector. eLife 2022; 11:73220. [PMID: 35175192 PMCID: PMC8871388 DOI: 10.7554/elife.73220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 11/18/2022] Open
Abstract
The cytoskeleton network of eukaryotic cells is essential for diverse cellular processes, including vesicle trafficking, cell motility, and immunity, thus is a common target for bacterial virulence factors. A number of effectors from the bacterial pathogen Legionella pneumophila have been shown to modulate the function of host actin cytoskeleton to construct the Legionella-containing vacuole (LCV) permissive for its intracellular replication. In this study, we found that the Dot/Icm effector Lem8 (Lpg1290) is a protease whose activity is catalyzed by a Cys-His-Asp motif known to be associated with diverse biochemical activities. Intriguingly, we found that Lem8 interacts with the host regulatory protein 14-3-3ζ, which activates its protease activity. Furthermore, Lem8 undergoes self-cleavage in a process that requires 14-3-3ζ. We identified the Pleckstrin homology-like domain-containing protein Phldb2 involved in cytoskeleton organization as a target of Lem8 and demonstrated that Lem8 plays a role in the inhibition of host cell migration by attacking Phldb2.
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Affiliation(s)
- Lei Song
- Department of Respiratory Medicine, Jilin University, Changchun, China
| | - Jingjing Luo
- Department of Respiratory Medicine, Jilin University, Changchun, China
| | - Hongou Wang
- Department of Microbiology, Peking University Health Science Center, Peking, China
| | - Dan Huang
- Department of Respiratory Medicine, Jilin University, Changchun, China
| | - Yunhao Tan
- Department of Biological Sciences, Purdue University, West Lafayette, United States
| | - Yao Liu
- Department of Biological Sciences, Purdue University, West Lafayette, United States
| | - Yingwu Wang
- Department of Respiratory Medicine, Jilin University, Changchun, China
| | - Kaiwen Yu
- Department of Microbiology, Peking University Health Science Center, Peking, China
| | - Yong Zhang
- Department of Respiratory Medicine, Jilin University, Changchun, China
| | - Xiaoyun Liu
- Department of Microbiology, Peking University Health Science Center, Peking, China
| | - Dan Li
- Department of Respiratory Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Biological Science, Purdue University, West Lafayette, United States
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Luo J, Wang L, Song L, Luo ZQ. Exploitation of the Host Ubiquitin System: Means by Legionella pneumophila. Front Microbiol 2022; 12:790442. [PMID: 35003021 PMCID: PMC8727461 DOI: 10.3389/fmicb.2021.790442] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/30/2021] [Indexed: 01/12/2023] Open
Abstract
Ubiquitination is a commonly used post-translational modification (PTM) in eukaryotic cells, which regulates a wide variety of cellular processes, such as differentiation, apoptosis, cell cycle, and immunity. Because of its essential role in immunity, the ubiquitin network is a common target of infectious agents, which have evolved various effective strategies to hijack and co-opt ubiquitin signaling for their benefit. The intracellular pathogen Legionella pneumophila represents one such example; it utilizes a large cohort of virulence factors called effectors to modulate diverse cellular processes, resulting in the formation a compartment called the Legionella-containing vacuole (LCV) that supports its replication. Many of these effectors function to re-orchestrate ubiquitin signaling with distinct biochemical activities. In this review, we highlight recent progress in the mechanism of action of L. pneumophila effectors involved in ubiquitination and discuss their roles in bacterial virulence and host cell biology.
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Affiliation(s)
- Jingjing Luo
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lidong Wang
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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25
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Gao WND, Gao C, Deane JE, Carpentier DCJ, Smith GL, Graham SC. The crystal structure of vaccinia virus protein E2 and perspectives on the prediction of novel viral protein folds. J Gen Virol 2022; 103:001716. [PMID: 35020582 PMCID: PMC8895614 DOI: 10.1099/jgv.0.001716] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
The morphogenesis of vaccinia virus (VACV, family Poxviridae), the smallpox vaccine, is a complex process involving multiple distinct cellular membranes and resulting in multiple different forms of infectious virion. Efficient release of enveloped virions, which promote systemic spread of infection within hosts, requires the VACV protein E2 but the molecular basis of E2 function remains unclear and E2 lacks sequence homology to any well-characterised family of proteins. We solved the crystal structure of VACV E2 to 2.3 Å resolution, revealing that it comprises two domains with novel folds: an N-terminal annular (ring) domain and a C-terminal globular (head) domain. The C-terminal head domain displays weak structural homology with cellular (pseudo)kinases but lacks conserved surface residues or kinase features, suggesting that it is not enzymatically active, and possesses a large surface basic patch that might interact with phosphoinositide lipid headgroups. Recent deep learning methods have revolutionised our ability to predict the three-dimensional structures of proteins from primary sequence alone. VACV E2 is an exemplar 'difficult' viral protein target for structure prediction, being comprised of multiple novel domains and lacking sequence homologues outside Poxviridae. AlphaFold2 nonetheless succeeds in predicting the structures of the head and ring domains with high and moderate accuracy, respectively, allowing accurate inference of multiple structural properties. The advent of highly accurate virus structure prediction marks a step-change in structural virology and beckons a new era of structurally-informed molecular virology.
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Affiliation(s)
- William N. D. Gao
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Chen Gao
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Janet E. Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - David C. J. Carpentier
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Geoffrey L. Smith
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Stephen C. Graham
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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26
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Osinski A, Black MH, Pawłowski K, Chen Z, Li Y, Tagliabracci VS. Structural and mechanistic basis for protein glutamylation by the kinase fold. Mol Cell 2021; 81:4527-4539.e8. [PMID: 34407442 DOI: 10.1016/j.molcel.2021.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active-site Glu in SidE, resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation.
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Affiliation(s)
- Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-787, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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27
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Adams M, Sharma R, Colby T, Weis F, Matic I, Bhogaraju S. Structural basis for protein glutamylation by the Legionella pseudokinase SidJ. Nat Commun 2021; 12:6174. [PMID: 34702826 PMCID: PMC8548325 DOI: 10.1038/s41467-021-26429-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/01/2021] [Indexed: 11/11/2022] Open
Abstract
Legionella pneumophila (LP) avoids phagocytosis by secreting nearly 300 effector proteins into the host cytosol. SidE family of effectors (SdeA, SdeB, SdeC and SidE) employ phosphoribosyl ubiquitination to target multiple host Rab GTPases and innate immune factors. To suppress the deleterious toxicity of SidE enzymes in a timely manner, LP employs a metaeffector named SidJ. Upon activation by host Calmodulin (CaM), SidJ executes an ATP-dependent glutamylation to modify the catalytic residue Glu860 in the mono-ADP-ribosyl transferase (mART) domain of SdeA. SidJ is a unique glutamylase that adopts a kinase-like fold but contains two nucleotide-binding pockets. There is a lack of consensus about the substrate recognition and catalytic mechanism of SidJ. Here, we determined the cryo-EM structure of SidJ in complex with its substrate SdeA in two different states of catalysis. Our structures reveal that both phosphodiesterase (PDE) and mART domains of SdeA make extensive contacts with SidJ. In the pre-glutamylation state structure of the SidJ-SdeA complex, adenylylated E860 of SdeA is inserted into the non-canonical (migrated) nucleotide-binding pocket of SidJ. Structure-based mutational analysis indicates that SidJ employs its migrated pocket for the glutamylation of SdeA. Finally, using mass spectrometry, we identified several transient autoAMPylation sites close to both the catalytic pockets of SidJ. Our data provide unique insights into the substrate recognition and the mechanism of protein glutamylation by the pseudokinase SidJ.
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Affiliation(s)
- Michael Adams
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Rahul Sharma
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Thomas Colby
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9b, 50931, Cologne, Germany
| | - Felix Weis
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9b, 50931, Cologne, Germany
| | - Sagar Bhogaraju
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France.
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28
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The Legionella Effector SdjA Is a Bifunctional Enzyme That Distinctly Regulates Phosphoribosyl Ubiquitination. mBio 2021; 12:e0231621. [PMID: 34488448 PMCID: PMC8546864 DOI: 10.1128/mbio.02316-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Legionella pneumophila promotes its survival and replication in phagocytes by actively modulating cellular processes using effectors injected into host cells by its Dot/Icm type IV secretion system. Many of these effectors function to manipulate the ubiquitin network of infected cells, thus contributing to the biogenesis of the Legionella-containing vacuole (LCV), which is permissive for bacterial replication. Among these, members of the SidE effector family (SidEs) catalyze ubiquitination of functionally diverse host proteins by a mechanism that is chemically distinct from the canonical three-enzyme cascade. The activity of SidEs is regulated by two mechanisms: reversal of the phosphoribosyl ubiquitination by DupA and DupB and direct inactivation by SidJ, which is a calmodulin-dependent glutamylase. In many L. pneumophila strains, SidJ belongs to a two-member protein family. Its homolog SdjA appears to function differently from SidJ despite the high-level similarity in their primary sequences. Here, we found that SdjA is a bifunctional enzyme that exhibits distinct activities toward members of the SidE family. It inhibits the activity of SdeB and SdeC by glutamylation. Unexpectedly, it also functions as a deglutamylase that reverses SidJ-induced glutamylation on SdeA. Our results reveal that an enzyme can catalyze two completely opposite biochemical reactions, which highlights the distinct regulation of phosphoribosyl ubiquitination by the SidJ effector family. IMPORTANCE One unique feature of L. pneumophila Dot/Icm effectors is the existence of protein families with members of high-level similarity. Whereas members of some families are functionally redundant, as suggested by their primary sequences, the relationship between SidJ and SdjA, the two members of the SidJ family, has remained mysterious. Despite their sharing 57% identity, sdjA cannot complement the defects in virulence displayed by a mutant lacking sidJ. SidJ inhibits the activity of the SidE family by a calmodulin (CaM)-dependent glutamylase activity. Here, we found that SdjA is a dual function protein: it is a CaM-dependent glutamylase against SdeB and SdeC but exhibits deglutamylase activity toward SdeA that has been modified by SidJ, indicating that SdjA functions to fine-tune the activity of SidEs. These findings have paved the way for future structural and functional analysis of SdjA, which may reveal novel mechanism for isopeptide bond cleavage and provide insights into the study of protein evolution.
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29
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Linsky M, Segal G. A horizontally acquired Legionella genomic island encoding a LuxR type regulator and effector proteins displays variation in gene content and regulation. Mol Microbiol 2021; 116:766-782. [PMID: 34120381 DOI: 10.1111/mmi.14770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/30/2022]
Abstract
The intracellular pathogen Legionella pneumophila translocates >300 effector proteins into host cells, many of which are regulated at the transcriptional level. Here, we describe a novel L. pneumophila genomic island, which undergoes horizontal gene transfer within the Legionella genus. This island encodes two Icm/Dot effectors: LegK3 and a previously uncharacterized effector which we named CegK3, as well as a LuxR type regulator, which we named RegK3. Analysis of this island in different Legionella species revealed a conserved regulatory element located upstream to the effector-encoding genes in the island. Further analyses, including gene expression analysis, mutagenesis of the RegK3 regulatory element, controlled expression studies, and gel-mobility shift assays, all demonstrate that RegK3 directly activates the expression levels of legK3 and cegK3 effector-encoding genes. Additionally, the expression of all the components of the island is silenced by the Fis repressors. Comparison of expression profiles of these three genes among different Legionella species revealed variability in the activation levels mediated by RegK3, which were positively correlated with the Fis-mediated repression. Furthermore, LegK3 and CegK3 effectors moderately inhibit yeast growth, and importantly, they have a strong synergistic inhibitory effect on yeast growth, suggesting these two effectors are not only co-regulated but also might function together.
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Affiliation(s)
- Marika Linsky
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Gil Segal
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
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30
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Allombert J, Jaboulay C, Michard C, Andréa C, Charpentier X, Vianney A, Doublet P. Deciphering Legionella effector delivery by Icm/Dot secretion system reveals a new role for c-di-GMP signaling. J Mol Biol 2021; 433:166985. [PMID: 33845084 DOI: 10.1016/j.jmb.2021.166985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022]
Abstract
Secretion of bacterial effector proteins into host cells plays a key role in bacterial virulence. Yet, the dynamics of the secretion systems activity remains poorly understood, especially when machineries deal with the export of numerous effectors. We address the question of multi-effector secretion by focusing on the Legionella pneumophila Icm/Dot T4SS that translocates a record number of 300 effectors. We set up a kinetic translocation assay, based on the β-lactamase translocation reporter system combined with the effect of the protonophore CCCP. When used for translocation analysis of Icm/Dot substrates constitutively produced by L. pneumophila, this assay allows a fine monitoring of the secretion activity of the T4SS, independently of the expression control of the effectors. We observed that effectors are translocated with a specific timing, suggesting a control of their docking/translocation by the T4SS. Their delivery is accurately organized to allow effective manipulation of the host cell, as exemplified by the sequential translocation of effectors targeting Rab1, namely SidM/DrrA, LidA, LepB. Remarkably, the timed delivery of effectors does not depend only on their interaction with chaperone proteins but implies cyclic-di-GMP signaling, as the diguanylate cyclase Lpl0780/Lpp0809, contributes to the timing of translocation.
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Affiliation(s)
- J Allombert
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - C Jaboulay
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - C Michard
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - C Andréa
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - X Charpentier
- CIRI, Centre International de Recherche en Infectiologie, (Team: Horigene), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - A Vianney
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France.
| | - P Doublet
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France.
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31
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Mikolčević P, Hloušek-Kasun A, Ahel I, Mikoč A. ADP-ribosylation systems in bacteria and viruses. Comput Struct Biotechnol J 2021; 19:2366-2383. [PMID: 34025930 PMCID: PMC8120803 DOI: 10.1016/j.csbj.2021.04.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/30/2022] Open
Abstract
ADP-ribosylation is an ancient posttranslational modification present in all kingdoms of life. The system likely originated in bacteria where it functions in inter- and intra-species conflict, stress response and pathogenicity. It was repeatedly adopted via lateral transfer by eukaryotes, including humans, where it has a pivotal role in epigenetics, DNA-damage repair, apoptosis, and other crucial pathways including the immune response to pathogenic bacteria and viruses. In other words, the same ammunition used by pathogens is adapted by eukaryotes to fight back. While we know quite a lot about the eukaryotic system, expanding rather patchy knowledge on bacterial and viral ADP-ribosylation would give us not only a better understanding of the system as a whole but a fighting advantage in this constant arms race. By writing this review we hope to put into focus the available information and give a perspective on how this system works and can be exploited in the search for therapeutic targets in the future. The relevance of the subject is especially highlighted by the current situation of being amid the world pandemic caused by a virus harbouring and dependent on a representative of such a system.
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Affiliation(s)
- Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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32
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Chauhan D, Shames SR. Pathogenicity and Virulence of Legionella: Intracellular replication and host response. Virulence 2021; 12:1122-1144. [PMID: 33843434 PMCID: PMC8043192 DOI: 10.1080/21505594.2021.1903199] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bacteria of the genus Legionella are natural pathogens of amoebae that can cause a severe pneumonia in humans called Legionnaires’ Disease. Human disease results from inhalation of Legionella-contaminated aerosols and subsequent bacterial replication within alveolar macrophages. Legionella pathogenicity in humans has resulted from extensive co-evolution with diverse genera of amoebae. To replicate intracellularly, Legionella generates a replication-permissive compartment called the Legionella-containing vacuole (LCV) through the concerted action of hundreds of Dot/Icm-translocated effector proteins. In this review, we present a collective overview of Legionella pathogenicity including infection mechanisms, secretion systems, and translocated effector function. We also discuss innate and adaptive immune responses to L. pneumophila, the implications of Legionella genome diversity and future avenues for the field.
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Affiliation(s)
- Deepika Chauhan
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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33
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Grishin A, Voth K, Gagarinova A, Cygler M. Structural biology of the invasion arsenal of Gram-negative bacterial pathogens. FEBS J 2021; 289:1385-1427. [PMID: 33650300 DOI: 10.1111/febs.15794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
In the last several years, there has been a tremendous progress in the understanding of host-pathogen interactions and the mechanisms by which bacterial pathogens modulate behavior of the host cell. Pathogens use secretion systems to inject a set of proteins, called effectors, into the cytosol of the host cell. These effectors are secreted in a highly regulated, temporal manner and interact with host proteins to modify a multitude of cellular processes. The number of effectors varies between pathogens from ~ 30 to as many as ~ 350. The functional redundancy of effectors encoded by each pathogen makes it difficult to determine the cellular effects or function of individual effectors, since their individual knockouts frequently produce no easily detectable phenotypes. Structural biology of effector proteins and their interactions with host proteins, in conjunction with cell biology approaches, has provided invaluable information about the cellular function of effectors and underlying molecular mechanisms of their modes of action. Many bacterial effectors are functionally equivalent to host proteins while being structurally divergent from them. Other effector proteins display new, previously unobserved functionalities. Here, we summarize the contribution of the structural characterization of effectors and effector-host protein complexes to our understanding of host subversion mechanisms used by the most commonly investigated Gram-negative bacterial pathogens. We describe in some detail the enzymatic activities discovered among effector proteins and how they affect various cellular processes.
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Affiliation(s)
- Andrey Grishin
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Kevin Voth
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
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34
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The metaeffector MesI regulates the activity of the Legionella effector SidI through direct protein-protein interactions. Microbes Infect 2021; 23:104794. [PMID: 33571674 DOI: 10.1016/j.micinf.2021.104794] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/10/2020] [Accepted: 01/26/2021] [Indexed: 12/25/2022]
Abstract
To create an intracellular niche permissive for its replication, Legionella pneumophila uses hundreds of effectors to target a wide variety of host proteins and manipulate specific host processes such as immune response, and vesicle trafficking. To avoid unwanted disruption of host physiology, this pathogen also imposes precise control of its virulence by the use of effectors called metaeffectors to regulate the activity of other effectors. A number of effector/metaeffector pairs with distinct regulatory mechanisms have been characterized, including abrogation of protein modifications, direct modification of the effector and direct binding to the catalytic pocket of the cognate effector. Recently, MesI (Lpg2505) was found to be a metaeffector of SidI, an effector involved in inhibiting host protein translation. Here we demonstrate that MesI functions by inhibiting the activity of SidI via direct protein-protein interactions. We show that this interaction occurs within L. pneumophila and thus interferes with the translocation of SidI into host cells. We also solved the structure of MesI, which suggests that this protein does not have an active site similar to any known enzymes. Analysis of deletion mutants allowed the identification of regions within SidI and MesI that are important for their interactions.
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35
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Kim RQ, Misra M, Gonzalez A, Tomašković I, Shin D, Schindelin H, Filippov DV, Ovaa H, Đikić I, van der Heden van Noort GJ. Development of ADPribosyl Ubiquitin Analogues to Study Enzymes Involved in Legionella Infection. Chemistry 2021; 27:2506-2512. [PMID: 33075184 PMCID: PMC7898697 DOI: 10.1002/chem.202004590] [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: 10/15/2020] [Indexed: 11/18/2022]
Abstract
Legionnaires' disease is caused by infection with the intracellularly replicating Gram-negative bacterium Legionella pneumophila. This pathogen uses an unconventional way of ubiquitinating host proteins by generating a phosphoribosyl linkage between substrate proteins and ubiquitin by making use of an ADPribosylated ubiquitin (UbADPr ) intermediate. The family of SidE effector enzymes that catalyze this reaction is counteracted by Legionella hydrolases, which are called Dups. This unusual ubiquitination process is important for Legionella proliferation and understanding these processes on a molecular level might prove invaluable in finding new treatments. Herein, a modular approach is used for the synthesis of triazole-linked UbADPr , and analogues thereof, and their affinity towards the hydrolase DupA is determined and hydrolysis rates are compared to natively linked UbADPr . The inhibitory effects of modified Ub on the canonical eukaryotic E1-enzyme Uba1 are investigated and rationalized in the context of a high-resolution crystal structure reported herein. Finally, it is shown that synthetic UbADPr analogues can be used to effectively pull-down overexpressed DupA from cell lysate.
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Affiliation(s)
- Robbert Q. Kim
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Mohit Misra
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
- Rudolf Virchow Center for Integrative and Translational BioimagingUniversity of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Alexis Gonzalez
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
| | - Ines Tomašković
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
| | - Donghyuk Shin
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
- Current Address: Department of Nano-BioengineeringIncheon National UniversityAcademyro 11922012IncheonSouth Korea
| | - Hermann Schindelin
- Rudolf Virchow Center for Integrative and Translational BioimagingUniversity of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Dmitri V. Filippov
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Ivan Đikić
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
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Li G, Liu H, Luo ZQ, Qiu J. Modulation of phagosome phosphoinositide dynamics by a Legionella phosphoinositide 3-kinase. EMBO Rep 2021; 22:e51163. [PMID: 33492731 DOI: 10.15252/embr.202051163] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/06/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
The phagosome harboring the bacterial pathogen Legionella pneumophila is known to be enriched with phosphatidylinositol 4-phosphate (PtdIns4P), which is important for anchoring a subset of its virulence factors and potentially for signaling events implicated in the biogenesis of the Legionella-containing vacuole (LCV) that supports intracellular bacterial growth. Here we demonstrate that the effector MavQ is a phosphoinositide 3-kinase that specifically catalyzes the conversion of phosphatidylinositol (PtdIns) into PtdIns3P. The product of MavQ is subsequently phosphorylated by the effector LepB to yield PtdIns(3,4)P2, whose 3-phosphate is then removed by another effector SidF to generate PtdIns4P. We also show that MavQ is associated with the LCV and the ∆mavQ mutant displays phenotypes in the anchoring of a PtdIns4P-binding effector similar to those of ∆lepB or ∆sidF mutants. Our results establish a mechanism of de novo PtdIns4P biosynthesis by L. pneumophila via a catalysis axis comprised of MavQ, LepB, and SidF on the surface of its phagosome.
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Affiliation(s)
- Gen Li
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongtao Liu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
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Affecting the Effectors: Regulation of Legionella pneumophila Effector Function by Metaeffectors. Pathogens 2021; 10:pathogens10020108. [PMID: 33499048 PMCID: PMC7911563 DOI: 10.3390/pathogens10020108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/24/2022] Open
Abstract
Many bacterial pathogens utilize translocated virulence factors called effectors to successfully infect their host. Within the host cell, effector proteins facilitate pathogen replication through subversion of host cell targets and processes. Legionella pneumophila is a Gram-negative intracellular bacterial pathogen that relies on hundreds of translocated effectors to replicate within host phagocytes. Within this large arsenal of translocated effectors is a unique subset of effectors called metaeffectors, which target and regulate other effectors. At least one dozen metaeffectors are encoded by L. pneumophila; however, mechanisms by which they promote virulence are largely unknown. This review details current knowledge of L pneumophila metaeffector function, challenges associated with their identification, and potential avenues to reveal the contribution of metaeffectors to bacterial pathogenesis.
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Price CT, Abu Kwaik Y. Evolution and Adaptation of Legionella pneumophila to Manipulate the Ubiquitination Machinery of Its Amoebae and Mammalian Hosts. Biomolecules 2021; 11:biom11010112. [PMID: 33467718 PMCID: PMC7830128 DOI: 10.3390/biom11010112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin pathway is highly conserved across the eukaryotic domain of life and plays an essential role in a plethora of cellular processes. It is not surprising that many intracellular bacterial pathogens often target the essential host ubiquitin pathway. The intracellular bacterial pathogen Legionella pneumophila injects into the host cell cytosol multiple classes of classical and novel ubiquitin-modifying enzymes that modulate diverse ubiquitin-related processes in the host cell. Most of these pathogen-injected proteins, designated as effectors, mimic known E3-ubiquitin ligases through harboring F-box or U-box domains. The classical F-box effector, AnkB targets host proteins for K48-linked polyubiquitination, which leads to excessive proteasomal degradation that is required to generate adequate supplies of amino acids for metabolism of the pathogen. In contrast, the SidC and SdcA effectors share no structural similarity to known eukaryotic ligases despite having E3-ubiquitin ligase activity, suggesting that the number of E3-ligases in eukaryotes is under-represented. L. pneumophila also injects into the host many novel ubiquitin-modifying enzymes, which are the SidE family of effectors that catalyze phosphoribosyl-ubiquitination of serine residue of target proteins, independently of the canonical E1-2-3 enzymatic cascade. Interestingly, the environmental bacterium, L. pneumophila, has evolved within a diverse range of amoebal species, which serve as the natural hosts, while accidental transmission through contaminated aerosols can cause pneumonia in humans. Therefore, it is likely that the novel ubiquitin-modifying enzymes of L. pneumophila were acquired by the pathogen through interkingdom gene transfer from the diverse natural amoebal hosts. Furthermore, conservation of the ubiquitin pathway across eukaryotes has enabled these novel ubiquitin-modifying enzymes to function similarly in mammalian cells. Studies on the biological functions of these effectors are likely to reveal further novel ubiquitin biology and shed further lights on the evolution of ubiquitin.
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Affiliation(s)
- Christopher T.D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, KY 40202, USA
- Correspondence:
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Mace PD, Murphy JM. There's more to death than life: Noncatalytic functions in kinase and pseudokinase signaling. J Biol Chem 2021; 296:100705. [PMID: 33895136 PMCID: PMC8141879 DOI: 10.1016/j.jbc.2021.100705] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Protein kinases are present in all domains of life and play diverse roles in cellular signaling. Whereas the impact of substrate phosphorylation by protein kinases has long been appreciated, it is becoming increasingly clear that protein kinases also play other, noncatalytic, functions. Here, we review recent developments in understanding the noncatalytic functions of protein kinases. Many noncatalytic activities are best exemplified by protein kinases that are devoid of enzymatic activity altogether-known as pseudokinases. These dead proteins illustrate that, beyond conventional notions of kinase function, catalytic activity can be dispensable for biological function. Through key examples we illustrate diverse mechanisms of noncatalytic kinase activity: as allosteric modulators; protein-based switches; scaffolds for complex assembly; and as competitive inhibitors in signaling pathways. In common, these noncatalytic mechanisms exploit the nature of the protein kinase fold as a versatile protein-protein interaction module. Many examples are also intrinsically linked to the ability of the protein kinase to switch between multiple states, a function shared with catalytic protein kinases. Finally, we consider the contemporary landscape of small molecules to modulate noncatalytic functions of protein kinases, which, although challenging, has significant potential given the scope of noncatalytic protein kinase function in health and disease.
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Affiliation(s)
- Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
| | - James M Murphy
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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40
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Black MH, Osinski A, Park GJ, Gradowski M, Servage KA, Pawłowski K, Tagliabracci VS. A Legionella effector ADP-ribosyltransferase inactivates glutamate dehydrogenase. J Biol Chem 2021; 296:100301. [PMID: 33476647 PMCID: PMC7949102 DOI: 10.1016/j.jbc.2021.100301] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
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.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gina J Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Marcin Gradowski
- Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Howard Hughes Medical Institute, Dallas, Texas, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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41
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Sulpizio AG, Minelli ME, Mao Y. In vitro Glutamylation Inhibition of Ubiquitin Modification and Phosphoribosyl-Ubiquitin Ligation Mediated by Legionella pneumophila Effectors. Bio Protoc 2020; 10:e3811. [PMID: 33659464 DOI: 10.21769/bioprotoc.3811] [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: 04/24/2020] [Revised: 07/25/2020] [Accepted: 08/17/2020] [Indexed: 11/02/2022] Open
Abstract
Glutamylation is a posttranslational modification where the amino group of a free glutamate amino acid is conjugated to the carboxyl group of a glutamate side chain within a target protein. SidJ is a Legionella kinase-like protein that has recently been identified to perform protein polyglutamylation of the Legionella SdeA Phosphoribosyl-Ubiquitin (PR-Ub) ligase to inhibit SdeA's activity. The attachment of multiple glutamate amino acids to the catalytic glutamate residue of SdeA by SidJ inhibits SdeA's modification of ubiquitin (Ub) and ligation activity. In this protocol, we will discuss a SidJ non-radioactive, in vitro glutamylation assay using its substrate SdeA. This will also include a second reaction to assay the inhibition of SdeA by using both modification of free Ub and ligation of ADP-ribosylated Ubiquitin (ADPR-Ub) to SdeA's substrate Rab33b. Prior to the identification and publication of SidJ's activity, no SdeA inhibition assays existed. Our group and others have demonstrated various methods to display inhibition of SdeA's activity. The alternatives include measurement of ADP-ribosylation of Ub using radioactive NAD, NAD hydrolysis, and Western blot analysis of HA-Ub ligation by SdeA. This protocol will describe the inhibition of both ubiquitin modification and the PR-Ub ligation by SdeA using inexpensive standard gels and Coomassie staining.
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Affiliation(s)
- Alan G Sulpizio
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca NY, United States
| | - Marena E Minelli
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca NY, United States
| | - Yuxin Mao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca NY, United States
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42
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Liu S, Luo J, Zhen X, Qiu J, Ouyang S, Luo ZQ. Interplay between bacterial deubiquitinase and ubiquitin E3 ligase regulates ubiquitin dynamics on Legionella phagosomes. eLife 2020; 9:58114. [PMID: 33136002 PMCID: PMC7669269 DOI: 10.7554/elife.58114] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/01/2020] [Indexed: 12/12/2022] Open
Abstract
Legionella pneumophila extensively modulates the host ubiquitin network to create the Legionella-containing vacuole (LCV) for its replication. Many of its virulence factors function as ubiquitin ligases or deubiquitinases (DUBs). Here, we identify Lem27 as a DUB that displays a preference for diubiquitin formed by K6, K11, or K48. Lem27 is associated with the LCV where it regulates Rab10 ubiquitination in concert with SidC and SdcA, two bacterial E3 ubiquitin ligases. Structural analysis of the complex formed by an active fragment of Lem27 and the substrate-based suicide inhibitor ubiquitin-propargylamide (PA) reveals that it harbors a fold resembling those in the OTU1 DUB subfamily with a Cys-His catalytic dyad and that it recognizes ubiquitin via extensive hydrogen bonding at six contact sites. Our results establish Lem27 as a DUB that functions to regulate protein ubiquitination on L. pneumophila phagosomes by counteracting the activity of bacterial ubiquitin E3 ligases.
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Affiliation(s)
- Shuxin Liu
- Department of Respiratory Medicine and Center of Infection and Immunity, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital, Jilin University, Changchun, China
| | - Jiwei Luo
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xiangkai Zhen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Zhao-Qing Luo
- Department of Respiratory Medicine and Center of Infection and Immunity, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital, Jilin University, Changchun, China.,Department of Biological Sciences, Purdue University, West Lafayette, United States
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Abstract
Through coevolution with host cells, microorganisms have acquired mechanisms to avoid the detection by the host surveillance system and to use the cell's supplies to establish themselves. Indeed, certain pathogens have evolved proteins that imitate specific eukaryotic cell proteins, allowing them to manipulate host pathways, a phenomenon termed molecular mimicry. Bacterial "eukaryotic-like proteins" are a remarkable example of molecular mimicry. They are defined as proteins that strongly resemble eukaryotic proteins or that carry domains that are predominantly present in eukaryotes and that are generally absent from prokaryotes. The widest diversity of eukaryotic-like proteins known to date can be found in members of the bacterial genus Legionella, some of which cause a severe pneumonia in humans. The characterization of a number of these proteins shed light on their importance during infection. The subsequent identification of eukaryotic-like genes in the genomes of other amoeba-associated bacteria and bacterial symbionts suggested that eukaryotic-like proteins are a common means of bacterial evasion and communication, shaped by the continuous interactions between bacteria and their protozoan hosts. In this review, we discuss the concept of molecular mimicry using Legionella as an example and show that eukaryotic-like proteins effectively manipulate host cell pathways. The study of the function and evolution of such proteins is an exciting field of research that is leading us toward a better understanding of the complex world of bacterium-host interactions. Ultimately, this knowledge will teach us how host pathways are manipulated and how infections may possibly be tackled.
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Sulpizio AG, Shin JH, Minelli ME, Mao Y. Radioactive Assay of in vitro Glutamylation Activity of the Legionella pneumophila Effector Protein SidJ. Bio Protoc 2020; 10:e3770. [PMID: 33659428 DOI: 10.21769/bioprotoc.3770] [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: 04/24/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 11/02/2022] Open
Abstract
The Legionella effector protein SidJ has recently been identified to perform polyglutamylation on another Legionella effector, SdeA, ablating SdeA's activity. SidJ is a kinase-like protein that requires the small eukaryotic protein calmodulin to perform glutamylation. Glutamylation is a relatively uncommon type of post-translational modification, where the amino group of a free glutamate amino acid is covalently linked to the γ-carboxyl group of a glutamate sidechain in a substrate protein. This protocol describes the SidJ glutamylation reaction using radioactive [U-14C] glutamate and its substrate SdeA, the separation of proteins by gel electrophoresis, preparation of gels for radioactive exposure, and relative quantification of glutamylation activity. This procedure is useful for the identification of substrates for glutamylation, characterization of substrate and glutamylase activities due to mutations, and identification of proteins with glutamylation activity. Some studies have assayed glutamylation with the use of [3H] glutamate (Regnard et al., 1998) and the use of the GT335 antibody (Wolff et al., 1992). However, the use of [U-14C] glutamate requires a shorter radioactive exposure time with no dependence on antibody specificity.
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Affiliation(s)
- Alan G Sulpizio
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca NY, United States
| | - Jung-Ho Shin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca NY, United States
| | - Marena E Minelli
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca NY, United States
| | - Yuxin Mao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca NY, United States
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Kitao T, Nagai H, Kubori T. Divergence of Legionella Effectors Reversing Conventional and Unconventional Ubiquitination. Front Cell Infect Microbiol 2020; 10:448. [PMID: 32974222 PMCID: PMC7472693 DOI: 10.3389/fcimb.2020.00448] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila employs bacteria-derived effector proteins in a variety of functions to exploit host cellular systems. The ubiquitination machinery constitutes a crucial eukaryotic system for the regulation of numerous cellular processes, and is a representative target for effector-mediated bacterial manipulation. L. pneumophila transports over 300 effector proteins into host cells through its Dot/Icm type IV secretion system. Among these, several effector proteins have been found to function as ubiquitin ligases, including unprecedented enzymes that catalyze ubiquitination through unconventional mechanisms. Recent studies have identified many L. pneumophila effector proteins that can interfere with ubiquitination. These effectors include proteins that are distantly related to the ovarian tumor protein superfamily described as deubiquitinases (DUBs), which regulate important signaling cascades in human cells. Intriguingly, L. pneumophila DUBs are not limited to enzymes that exhibit canonical DUB activity. Some L. pneumophila DUBs can catalyze the cleavage of the unconventional linkage between ubiquitin and substrates. Furthermore, novel mechanisms have been found that adversely affect the function of specific ubiquitin ligases; for instance, effector-mediated posttranslational modifications of ubiquitin ligases result in the inhibition of their activity. In the context of L. pneumophila infection, the existence of enzymes that reverse ubiquitination primarily relates to a fine tuning of biogenesis and remodeling of the Legionella-containing vacuole as a replicative niche. The complexity of the effector arrays reflects sophisticated strategies that bacteria have adopted to adapt their host environment and enable their survival in host cells. This review summarizes the current state of knowledge on the divergent mechanisms of the L. pneumophila effectors that can reverse ubiquitination, which is mediated by other effectors as well as the host ubiquitin machinery.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
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46
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Insights into catalysis and regulation of non-canonical ubiquitination and deubiquitination by bacterial deamidase effectors. Nat Commun 2020; 11:2751. [PMID: 32488130 PMCID: PMC7265302 DOI: 10.1038/s41467-020-16587-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/11/2020] [Indexed: 02/01/2023] Open
Abstract
The bacterial effector MavC catalyzes non-canonical ubiquitination of host E2 enzyme UBE2N without engaging any of the conventional ubiquitination machinery, thereby abolishing UBE2N’s function in forming K63-linked ubiquitin (Ub) chains and dampening NF-кB signaling. We now report the structures of MavC in complex with conjugated UBE2N~Ub and an inhibitor protein Lpg2149, as well as the structure of its ortholog, MvcA, bound to Lpg2149. Recognition of UBE2N and Ub depends on several unique features of MavC, which explains the inability of MvcA to catalyze ubiquitination. Unexpectedly, MavC and MvcA also possess deubiquitinase activity against MavC-mediated ubiquitination, highlighting MavC as a unique enzyme possessing deamidation, ubiquitination, and deubiquitination activities. Further, Lpg2149 directly binds and inhibits both MavC and MvcA by disrupting the interactions between enzymes and Ub. These results provide detailed insights into catalysis and regulation of MavC-type enzymes and the molecular mechanisms of this non-canonical ubiquitination machinery. The bacterial effector MavC can ubiquitinate the host E2 enzyme UBE2N to dampen the host immune response. Here, the authors provide mechanistic insight into this non-canonical ubiquitination machinery and reveal the structural basis for the functional differences between MavC and its close homolog MvcA.
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47
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Sreelatha A, Nolan C, Park BC, Pawłowski K, Tomchick DR, Tagliabracci VS. A Legionella effector kinase is activated by host inositol hexakisphosphate. J Biol Chem 2020; 295:6214-6224. [PMID: 32229585 DOI: 10.1074/jbc.ra120.013067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
The transfer of a phosphate from ATP to a protein substrate, a modification known as protein phosphorylation, is catalyzed by protein kinases. Protein kinases play a crucial role in virtually every cellular activity. Recent studies of atypical protein kinases have highlighted the structural similarity of the kinase superfamily despite notable differences in primary amino acid sequence. Here, using a bioinformatics screen, we searched for putative protein kinases in the intracellular bacterial pathogen Legionella pneumophila and identified the type 4 secretion system effector Lpg2603 as a remote member of the protein kinase superfamily. Employing an array of biochemical and structural biology approaches, including in vitro kinase assays and isothermal titration calorimetry, we show that Lpg2603 is an active protein kinase with several atypical structural features. Importantly, we found that the eukaryote-specific host signaling molecule inositol hexakisphosphate (IP6) is required for Lpg2603 kinase activity. Crystal structures of Lpg2603 in the apo-form and when bound to IP6 revealed an active-site rearrangement that allows for ATP binding and catalysis. Our results on the structure and activity of Lpg2603 reveal a unique mode of regulation of a protein kinase, provide the first example of a bacterial kinase that requires IP6 for its activation, and may aid future work on the function of this effector during Legionella pathogenesis.
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Affiliation(s)
- Anju Sreelatha
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390.
| | - Christine Nolan
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Krzysztof Pawłowski
- Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-787, Poland
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390.
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48
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"Make way": Pathogen exploitation of membrane traffic. Curr Opin Cell Biol 2020; 65:78-85. [PMID: 32234681 DOI: 10.1016/j.ceb.2020.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/20/2020] [Indexed: 01/18/2023]
Abstract
Intracellular pathogens have evolved numerous strategies to manipulate their host cells to survive and replicate in a hostile environment. They often exploit membrane trafficking pathways to enter the cell, establish a replicative niche, avoid degradation and immune response, acquire nutrients and lastly, egress. Recent studies on membrane trafficking exploitation by intracellular pathogens have led to the discovery of novel and fascinating cell biology, including a noncanonical mechanism of ubiquitination and a novel mitophagy receptor. Thus, studying how pathogens target host cell membrane trafficking pathways is not only important for the development of new therapeutics, but also helps understanding fundamental mechanisms of cell biology.
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49
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Puvar K, Saleh AM, Curtis RW, Zhou Y, R Nyalapatla P, Fu J, Rovira AR, Tor Y, Luo ZQ, Ghosh AK, Wirth MJ, Chmielewski J, Kinzer-Ursem TL, Das C. Fluorescent Probes for Monitoring Serine Ubiquitination. Biochemistry 2020; 59:1309-1313. [PMID: 32207972 DOI: 10.1021/acs.biochem.0c00067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a radical departure from the classical E1-E2-E3 three-enzyme mediated ubiquitination of eukaryotes, the recently described bacterial enzymes of the SidE family of Legionella pneumophila effectors utilize NAD+ to ligate ubiquitin onto target substrate proteins. This outcome is achieved via a two-step mechanism involving (1) ADP ribosylation of ubiquitin followed by (2) phosphotransfer to a target serine residue. Here, using fluorescent NAD+ analogues as well as synthetic substrate mimics, we have developed continuous assays enabling real-time monitoring of both steps of this mechanism. These assays are amenable to biochemical studies and high-throughput screening of inhibitors of these effectors, and the discovery and characterization of putative enzymes similar to members of the SidE family in other organisms. We also show their utility in studying enzymes that can reverse and inhibit this post-translational modification.
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Affiliation(s)
- Kedar Puvar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Aya M Saleh
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47906, United States
| | - Ryan W Curtis
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Yiyang Zhou
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Prasanth R Nyalapatla
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Jiaqi Fu
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47906, United States
| | - Alexander R Rovira
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Zhao-Qing Luo
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47906, United States
| | - Arun K Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Mary J Wirth
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47906, United States
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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50
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Deubiquitination of phosphoribosyl-ubiquitin conjugates by phosphodiesterase-domain-containing Legionella effectors. Proc Natl Acad Sci U S A 2019; 116:23518-23526. [PMID: 31690664 DOI: 10.1073/pnas.1916287116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Posttranslational protein modification by ubiquitin (Ub) is a central eukaryotic mechanism that regulates a plethora of physiological processes. Recent studies unveiled an unconventional type of ubiquitination mediated by the SidE family of Legionella pneumophila effectors, such as SdeA, that catalyzes the conjugation of Ub to a serine residue of target proteins via a phosphoribosyl linker (hence named PR-ubiquitination). Comparable to the deubiquitinases in the canonical ubiquitination pathway, here we show that 2 paralogous Legionella effectors, Lpg2154 (DupA; deubiquitinase for PR-ubiquitination) and Lpg2509 (DupB), reverse PR-ubiquitination by specific removal of phosphoribosyl-Ub from substrates. Both DupA and DupB are fully capable of rescuing the Golgi fragmentation phenotype caused by exogenous expression of SdeA in mammalian cells. We further show that deletion of these 2 genes results in significant accumulation of PR-ubiquitinated species in host cells infected with Legionella In addition, we have identified a list of specific PR-ubiquitinated host targets and show that DupA and DupB play a role in modulating the association of PR-ubiquitinated host targets with Legionella-containing vacuoles. Together, our data establish a complete PR-ubiquitination and deubiquitination cycle and demonstrate the intricate control that Legionella has over this unusual Ub-dependent posttranslational modification.
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