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Pan Y, Chen H, Fu J, Zhang J, Wang P, Chen R, Geng S, Che J, Dong X, Zhou Y, Huang W. Discovery of N-Benzylpiperidinol derivatives as USP7 inhibitors against Hematology. Bioorg Chem 2024; 153:107807. [PMID: 39293304 DOI: 10.1016/j.bioorg.2024.107807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024]
Abstract
USP7 has been recognized as a potential target for the treatment of hematologic malignancies by stabilizing multiple cancer-relevant proteins. Nevertheless, drug-like USP7 inhibitors are still lacking. Herein, compound J21 (USP7 IC50: 41.35 ± 2.16 nM) was discovered based on the structure of L55 and its co-crystal complex with USP7. Additionally, J21 exhibited greater metabolic stability (T1/2: 1.25 h, Cmax: 394.1 ± 48.3 ng/mL, and AUC0-t: 597.8 ± 44.8 ng/mL∙h) compared to L55. These findings may further pave the way for the development of USP7 inhibitors for the treatment of hematologic malignancies.
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Affiliation(s)
- Youlu Pan
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou 310058, China
| | - Haifeng Chen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingfeng Fu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medical, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Jingyu Zhang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou First People's Hospital, Cancer Center of Zhejiang University, Hangzhou 310006, China
| | - Peipei Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medical, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Runmei Chen
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou 310058, China
| | - Shuangshuang Geng
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yubo Zhou
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medical, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China.
| | - Wenhai Huang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou 310058, China.
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2
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Huang L, Rojas-Pierce M. Rapid depletion of target proteins in plants by an inducible protein degradation system. THE PLANT CELL 2024; 36:3145-3161. [PMID: 38446628 PMCID: PMC11371150 DOI: 10.1093/plcell/koae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Inducible protein knockdowns are excellent tools to test the function of essential proteins in short time scales and to capture the role of proteins in dynamic events. Current approaches destroy or sequester proteins by exploiting plant biological mechanisms such as the activity of photoreceptors for optogenetics or auxin-mediated ubiquitination in auxin degrons. It follows that these are not applicable for plants as light and auxin are strong signals for plant cells. We describe here an inducible protein degradation system in plants named E3-DART for E3-targeted Degradation of Plant Proteins. The E3-DART system is based on the specific and well-characterized interaction between the Salmonella-secreted protein H1 (SspH1) and its human target protein kinase N1 (PKN1). This system harnesses the E3 catalytic activity of SspH1 and the SspH1-binding activity of the homology region 1b (HR1b) domain from PKN1. Using Nicotiana benthamiana and Arabidopsis (Arabidopsis thaliana), we show that a chimeric protein containing the leucine-rich repeat and novel E3 ligase domains of SspH1 efficiently targets protein fusions of varying sizes containing HR1b for degradation. Target protein degradation was induced by transcriptional control of the chimeric E3 ligase using a glucocorticoid transactivation system, and target protein depletion was detected as early as 3 h after induction. This system could be used to study the loss of any plant protein with high-temporal resolution and may become an important tool in plant cell biology.
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Affiliation(s)
- Linzhou Huang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Marcela Rojas-Pierce
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
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3
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Pruneda JN, Nguyen JV, Nagai H, Kubori T. Bacterial usurpation of the OTU deubiquitinase fold. FEBS J 2024; 291:3303-3316. [PMID: 36636866 PMCID: PMC10338644 DOI: 10.1111/febs.16725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/10/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023]
Abstract
The extensive cellular signalling events controlled by posttranslational ubiquitination are tightly regulated through the action of specialized proteases termed deubiquitinases. Among them, the OTU family of deubiquitinases can play very specialized roles in the regulation of discrete subtypes of ubiquitin signals that control specific cellular functions. To exert control over host cellular functions, some pathogenic bacteria have usurped the OTU deubiquitinase fold as a secreted virulence factor that interferes with ubiquitination inside infected cells. Herein, we provide a review of the function of bacterial OTU deubiquitinases during infection, the structural basis for their deubiquitinase activities and the bioinformatic approaches leading to their identification. Understanding bacterial OTU deubiquitinases holds the potential for discoveries not only in bacterial pathogenesis but in eukaryotic biology as well.
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Affiliation(s)
- Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Justine V. Nguyen
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu, Gifu 501-1194, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
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4
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Yang H, Chen W. Protease-Responsive Toolkit for Conditional Targeted Protein Degradation. ACS Synth Biol 2024; 13:2073-2080. [PMID: 38889440 DOI: 10.1021/acssynbio.4c00014] [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] [Indexed: 06/20/2024]
Abstract
BioPROTACs are heterobifunctional proteins designed for targeted protein degradation. While they offer a potential therapeutic avenue for modulating disease-related proteins, the current strategies are static in nature and lack the ability to modulate protein degradation dynamically. Here, we introduce a synthetic framework for dynamic fine-tuning of target protein levels using protease control switches. The idea is to utilize proteases as an interfacing layer between exogenous inputs and protein degradation by modulating the recruitment of target proteins to E3 ligase by separating the two binding domains on bioPROTACs. By decoupling the external inputs from the primary protease layer, new conditional degradation phenotypes can be readily adapted with minimal modifications to the design. We demonstrate the adaptability of this approach using two highly efficient "bioPROTAC" systems: AdPROM and IpaH9.8-based Ubiquibodies. Using the TEV protease as the transducer, we can interface small-molecule and optogenetic inputs for conditional targeted protein degradation. Our findings highlight the potential of bioPROTACs with protease-responsive linkers as a versatile tool for conditional targeted protein degradation.
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Affiliation(s)
- Hopen Yang
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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5
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Chambers LR, Ye Q, Cai J, Gong M, Ledvina HE, Zhou H, Whiteley AT, Suhandynata RT, Corbett KD. A eukaryotic-like ubiquitination system in bacterial antiviral defence. Nature 2024; 631:843-849. [PMID: 39020180 DOI: 10.1038/s41586-024-07730-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 06/18/2024] [Indexed: 07/19/2024]
Abstract
Ubiquitination pathways have crucial roles in protein homeostasis, signalling and innate immunity1-3. In these pathways, an enzymatic cascade of E1, E2 and E3 proteins conjugates ubiquitin or a ubiquitin-like protein (Ubl) to target-protein lysine residues4. Bacteria encode ancient relatives of E1 and Ubl proteins involved in sulfur metabolism5,6, but these proteins do not mediate Ubl-target conjugation, leaving open the question of whether bacteria can perform ubiquitination-like protein conjugation. Here we demonstrate that a bacterial operon associated with phage defence islands encodes a complete ubiquitination pathway. Two structures of a bacterial E1-E2-Ubl complex reveal striking architectural parallels with canonical eukaryotic ubiquitination machinery. The bacterial E1 possesses an amino-terminal inactive adenylation domain and a carboxy-terminal active adenylation domain with a mobile α-helical insertion containing the catalytic cysteine (CYS domain). One structure reveals a pre-reaction state with the bacterial Ubl C terminus positioned for adenylation, and a second structure mimics an E1-to-E2 transthioesterification state with the E1 CYS domain adjacent to the bound E2. We show that a deubiquitinase in the same pathway preprocesses the bacterial Ubl, exposing its C-terminal glycine for adenylation. Finally, we show that the bacterial E1 and E2 collaborate to conjugate Ubl to target-protein lysine residues. Together, these data reveal that bacteria possess bona fide ubiquitination systems with strong mechanistic and architectural parallels to canonical eukaryotic ubiquitination pathways, suggesting that these pathways arose first in bacteria.
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Affiliation(s)
- Lydia R Chambers
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Qiaozhen Ye
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jiaxi Cai
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Minheng Gong
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hannah E Ledvina
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Huilin Zhou
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Aaron T Whiteley
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Raymond T Suhandynata
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
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6
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Bejan DS, Lacoursiere RE, Pruneda JN, Cohen MS. Discovery of ester-linked ubiquitylation of PARP10 mono-ADP-ribosylation in cells: a dual post-translational modification on Glu/Asp side chains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600929. [PMID: 38979324 PMCID: PMC11230417 DOI: 10.1101/2024.06.27.600929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The prevailing view on post-translational modifications (PTMs) is that amino acid side chains in proteins are modified with a single PTM at any given time. However, a growing body of work has demonstrated crosstalk between different PTMs, some occurring on the same residue. Such interplay is seen with ADP-ribosylation and ubiquitylation, where specialized E3 ligases ubiquitylate targets for proteasomal degradation in an ADP-ribosylation-dependent manner. More recently, the DELTEX family of E3 ligases was reported to catalyze ubiquitylation of the 3'- hydroxy group of the adenine-proximal ribose of free NAD + and ADP-ribose in vitro , generating a non-canonical ubiquitin ester-linked species. In this report, we show, for the first time, that this dual PTM occurs in cells on mono-ADP-ribosylated (MARylated) PARP10 on Glu/Asp sites to form a MAR ubiquitin ester (MARUbe). We term this process m ono- A DP-ribosyl ub iquit ylation or MARUbylation. Using chemical and enzymatic treatments, including a newly characterized bacterial deubiquitinase with esterase-specific activity, we discovered that PARP10 MARUbylation is extended with K11-linked polyubiquitin chains. Finally, mechanistic studies using proteasomal and ubiquitin-activating enzyme inhibitors demonstrated that PARP10 MARUbylation leads to its proteasomal degradation, providing a functional role for this new PTM in regulating protein turnover.
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7
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Franklin TG, Brzovic PS, Pruneda JN. Bacterial ligases reveal fundamental principles of polyubiquitin specificity. Mol Cell 2023; 83:4538-4554.e4. [PMID: 38091999 PMCID: PMC10872931 DOI: 10.1016/j.molcel.2023.11.017] [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: 06/29/2023] [Revised: 09/28/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
Homologous to E6AP C terminus (HECT) E3 ubiquitin (Ub) ligases direct substrates toward distinct cellular fates dictated by the specific form of monomeric or polymeric Ub (polyUb) signal attached. How polyUb specificity is achieved has been a long-standing mystery, despite extensive study in various hosts, ranging from yeast to human. The bacterial pathogens enterohemorrhagic Escherichia coli and Salmonella Typhimurium encode outlying examples of "HECT-like" (bHECT) E3 ligases, but commonalities to eukaryotic HECT (eHECT) mechanism and specificity had not been explored. We expanded the bHECT family with examples in human and plant pathogens. Three bHECT structures in primed, Ub-loaded states resolved key details of the entire Ub ligation process. One structure provided a rare glimpse into the act of ligating polyUb, yielding a means to rewire polyUb specificity of both bHECT and eHECT ligases. Studying this evolutionarily distinct bHECT family has revealed insight into the function of key bacterial virulence factors as well as fundamental principles underlying HECT-type Ub ligation.
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Affiliation(s)
- Tyler G Franklin
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA.
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8
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Dagar G, Kumar R, Yadav KK, Singh M, Pandita TK. Ubiquitination and deubiquitination: Implications on cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194979. [PMID: 37633647 DOI: 10.1016/j.bbagrm.2023.194979] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
The ubiquitin proteasomal system (UPS) represents a highly regulated protein degradation pathway essential for maintaining cellular homeostasis. This system plays a critical role in several cellular processes, which include DNA damage repair, cell cycle checkpoint control, and immune response regulation. Recently, the UPS has emerged as a promising target for cancer therapeutics due to its involvement in oncogenesis and tumor progression. Here we aim to summarize the key aspects of the UPS and its significance in cancer therapeutics. We begin by elucidating the fundamental components of the UPS, highlighting the role of ubiquitin, E1-E3 ligases, and the proteasome in protein degradation. Furthermore, we discuss the intricate process of ubiquitination and proteasomal degradation, emphasizing the specificity and selectivity achieved through various signaling pathways. The dysregulation of the UPS has been implicated in cancer development and progression. Aberrant ubiquitin-mediated degradation of key regulatory proteins, such as tumor suppressors and oncoproteins, can lead to uncontrolled cell proliferation, evasion of apoptosis, and metastasis. We outline the pivotal role of the UPS in modulating crucial oncogenic pathways, including the regulation of cyclins, transcription factors, Replication stress components and DNA damage response. The increasing recognition of the UPS as a target for cancer therapeutics has spurred the development of small molecules, peptides, and proteasome inhibitors with the potential to restore cellular balance and disrupt tumor growth. We provide an overview of current therapeutic strategies aimed at exploiting the UPS, including the use of proteasome inhibitors, deubiquitinating enzyme inhibitors, and novel E3 ligase modulators. We further discuss novel emerging strategies for the development of next-generation drugs that target proteasome inhibitors. Exploiting the UPS for cancer therapeutics offers promising avenues for developing innovative and effective treatment strategies, providing hope for improved patient outcomes in the fight against cancer.
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Affiliation(s)
- Gunjan Dagar
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir 182320, India.
| | - Kamlesh K Yadav
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA; School of Engineering Medicine, Texas A&M University, School of Medicine, Houston, TX 77030, USA.
| | - Mayank Singh
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Tej K Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA.
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9
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Sharma R, Adams M, Griffith-Jones S, Sahr T, Gomez-Valero L, Weis F, Hons M, Gharbi S, Berkane R, Stolz A, Buchrieser C, Bhogaraju S. Structural basis for the toxicity of Legionella pneumophila effector SidH. Nat Commun 2023; 14:7068. [PMID: 37923743 PMCID: PMC10624908 DOI: 10.1038/s41467-023-42683-8] [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: 04/26/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
Legionella pneumophila (LP) secretes more than 300 effectors into the host cytosol to facilitate intracellular replication. One of these effectors, SidH, 253 kDa in size with no sequence similarity to proteins of known function is toxic when overexpressed in host cells. SidH is regulated by the LP metaeffector LubX which targets SidH for degradation in a temporal manner during LP infection. The mechanism underlying the toxicity of SidH and its role in LP infection are unknown. Here, we determined the cryo-EM structure of SidH at 2.7 Å revealing a unique alpha helical arrangement with no overall similarity to known protein structures. Surprisingly, purified SidH came bound to a E. coli EF-Tu/t-RNA/GTP ternary complex which could be modeled into the cryo-EM density. Mutation of residues disrupting the SidH-tRNA interface and SidH-EF-Tu interface abolish the toxicity of overexpressed SidH in human cells, a phenotype confirmed in infection of Acanthamoeba castellani. We also present the cryo-EM structure of SidH in complex with a U-box domain containing ubiquitin ligase LubX delineating the mechanism of regulation of SidH. Our data provide the basis for the toxicity of SidH and into its regulation by the metaeffector LubX.
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Affiliation(s)
- Rahul Sharma
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Michael Adams
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042, Grenoble, France
| | | | - Tobias Sahr
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, 75724, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, 75724, Paris, France
| | - Felix Weis
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Michael Hons
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Sarah Gharbi
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Rayene Berkane
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Carmen Buchrieser
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, 75724, Paris, France
| | - Sagar Bhogaraju
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042, Grenoble, France.
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10
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Sharma S, Prasad A, Prasad M. Ubiquitination from the perspective of plant pathogens. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4367-4376. [PMID: 37226440 DOI: 10.1093/jxb/erad191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
The constant battle of survival between pathogens and host plants has played a crucial role in shaping the course of their co-evolution. However, the major determinants of the outcome of this ongoing arms race are the effectors secreted by pathogens into host cells. These effectors perturb the defense responses of plants to promote successful infection. In recent years, extensive research in the area of effector biology has reported an increase in the repertoire of pathogenic effectors that mimic or target the conserved ubiquitin-proteasome pathway. The role of the ubiquitin-mediated degradation pathway is well known to be indispensable for various aspects of a plant's life, and thus targeting or mimicking it seems to be a smart strategy adopted by pathogens. Therefore, this review summarizes recent findings on how some pathogenic effectors mimic or act as one of the components of the ubiquitin-proteasome machinery while others directly target the plant's ubiquitin-proteasome system.
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Affiliation(s)
| | - Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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11
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Patel R, Negrón Terón K, Zhou M, Nakayasu E, Drown B, Das C. Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin-Deubiquitylating Enzyme Interactions. Chembiochem 2023; 24:e202300305. [PMID: 37262077 PMCID: PMC11088939 DOI: 10.1002/cbic.202300305] [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: 04/18/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C-terminal electrophiles (Ub-E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub-Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p-benzoyl-L-phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub-based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine-based chemistries.
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Affiliation(s)
- Rishi Patel
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Kristos Negrón Terón
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Mowei Zhou
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA
| | - Ernesto Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA
| | - Bryon Drown
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
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12
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Mishra V, Crespo-Puig A, McCarthy C, Masonou T, Glegola-Madejska I, Dejoux A, Dow G, Eldridge MJG, Marinelli LH, Meng M, Wang S, Bennison DJ, Morrison R, Shenoy AR. IL-1β turnover by the UBE2L3 ubiquitin conjugating enzyme and HECT E3 ligases limits inflammation. Nat Commun 2023; 14:4385. [PMID: 37474493 PMCID: PMC10359330 DOI: 10.1038/s41467-023-40054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
The cytokine interleukin-1β (IL-1β) has pivotal roles in antimicrobial immunity, but also incites inflammatory disease. Bioactive IL-1β is released following proteolytic maturation of the pro-IL-1β precursor by caspase-1. UBE2L3, a ubiquitin conjugating enzyme, promotes pro-IL-1β ubiquitylation and proteasomal disposal. However, actions of UBE2L3 in vivo and its ubiquitin ligase partners in this process are unknown. Here we report that deletion of Ube2l3 in mice reduces pro-IL-1β turnover in macrophages, leading to excessive mature IL-1β production, neutrophilic inflammation and disease following inflammasome activation. An unbiased RNAi screen identified TRIP12 and AREL1 E3 ligases of the Homologous to E6 C-terminus (HECT) family in adding destabilising K27-, K29- and K33- poly-ubiquitin chains on pro-IL-1β. We show that precursor abundance determines mature IL-1β production, and UBE2L3, TRIP12 and AREL1 limit inflammation by shrinking the cellular pool of pro-IL-1β. Our study uncovers fundamental processes governing IL-1β homeostasis and provides molecular insights that could be exploited to mitigate its adverse actions in disease.
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Affiliation(s)
- Vishwas Mishra
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Anna Crespo-Puig
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Callum McCarthy
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Tereza Masonou
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Izabela Glegola-Madejska
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Alice Dejoux
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Gabriella Dow
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Matthew J G Eldridge
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Luciano H Marinelli
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Meihan Meng
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Shijie Wang
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Daniel J Bennison
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Rebecca Morrison
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Avinash R Shenoy
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK.
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13
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Franklin TG, Brzovic PS, Pruneda JN. Bacterial mimicry of eukaryotic HECT ubiquitin ligation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543783. [PMID: 37333152 PMCID: PMC10274628 DOI: 10.1101/2023.06.05.543783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
HECT E3 ubiquitin (Ub) ligases direct their modified substrates toward a range of cellular fates dictated by the specific form of monomeric or polymeric Ub (polyUb) signal that is attached. How polyUb specificity is achieved has been a longstanding mystery, despite extensive study ranging from yeast to human. Two outlying examples of bacterial "HECT-like" (bHECT) E3 ligases have been reported in the human pathogens Enterohemorrhagic Escherichia coli and Salmonella Typhimurium, but what parallels can be drawn to eukaryotic HECT (eHECT) mechanism and specificity had not been explored. Here, we expanded the bHECT family and identified catalytically active, bona fide examples in both human and plant pathogens. By determining structures for three bHECT complexes in their primed, Ub-loaded states, we resolved key details of the full bHECT Ub ligation mechanism. One structure provided the first glimpse of a HECT E3 ligase in the act of ligating polyUb, yielding a means to rewire the polyUb specificity of both bHECT and eHECT ligases. Through studying this evolutionarily distinct bHECT family, we have not only gained insight into the function of key bacterial virulence factors but also revealed fundamental principles underlying HECT-type Ub ligation.
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Affiliation(s)
- Tyler G. Franklin
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter S. Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
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14
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Abstract
Our understanding of the ubiquitin code has greatly evolved from conventional E1, E2 and E3 enzymes that modify Lys residues on specific substrates with a single type of ubiquitin chain to more complex processes that regulate and mediate ubiquitylation. In this Review, we discuss recently discovered endogenous mechanisms and unprecedented pathways by which pathogens rewrite the ubiquitin code to promote infection. These processes include unconventional ubiquitin modifications involving ester linkages with proteins, lipids and sugars, or ubiquitylation through a phosphoribosyl bridge involving Arg42 of ubiquitin. We also introduce the enzymatic pathways that write and reverse these modifications, such as the papain-like proteases of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Furthermore, structural studies have revealed that the ultimate functions of ubiquitin are mediated not simply by straightforward recognition by ubiquitin-binding domains. Instead, elaborate multivalent interactions between ubiquitylated targets or ubiquitin chains and their readers (for example, the proteasome, the MLL1 complex or DOT1L) can elicit conformational changes that regulate protein degradation or transcription. The newly discovered mechanisms provide opportunities for innovative therapeutic interventions for diseases such as cancer and infectious diseases.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
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15
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The DarT/DarG Toxin-Antitoxin ADP-Ribosylation System as a Novel Target for a Rational Design of Innovative Antimicrobial Strategies. Pathogens 2023; 12:pathogens12020240. [PMID: 36839512 PMCID: PMC9967889 DOI: 10.3390/pathogens12020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The chemical modification of cellular macromolecules by the transfer of ADP-ribose unit(s), known as ADP-ribosylation, is an ancient homeostatic and stress response control system. Highly conserved across the evolution, ADP-ribosyltransferases and ADP-ribosylhydrolases control ADP-ribosylation signalling and cellular responses. In addition to proteins, both prokaryotic and eukaryotic transferases can covalently link ADP-ribosylation to different conformations of nucleic acids, thus highlighting the evolutionary conservation of archaic stress response mechanisms. Here, we report several structural and functional aspects of DNA ADP-ribosylation modification controlled by the prototype DarT and DarG pair, which show ADP-ribosyltransferase and hydrolase activity, respectively. DarT/DarG is a toxin-antitoxin system conserved in many bacterial pathogens, for example in Mycobacterium tuberculosis, which regulates two clinically important processes for human health, namely, growth control and the anti-phage response. The chemical modulation of the DarT/DarG system by selective inhibitors may thus represent an exciting strategy to tackle resistance to current antimicrobial therapies.
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16
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Shariq M, Quadir N, Alam A, Zarin S, Sheikh JA, Sharma N, Samal J, Ahmad U, Kumari I, Hasnain SE, Ehtesham NZ. The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection. Autophagy 2023; 19:3-23. [PMID: 35000542 PMCID: PMC9809970 DOI: 10.1080/15548627.2021.2021495] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca2+-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Neha Quadir
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Sheeba Zarin
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid A. Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Neha Sharma
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Uzair Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), New Delhi, India,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India,Seyed E. Hasnain ; ; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110 016, India
| | - Nasreen Z. Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,CONTACT Nasreen Z. Ehtesham ; ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi110029, India
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17
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Maillot G, Szadkowski E, Massire A, Brunaud V, Rigaill G, Caromel B, Chadœuf J, Bachellez A, Touhami N, Hein I, Lamour K, Balzergue S, Lefebvre V. Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper. FRONTIERS IN PLANT SCIENCE 2022; 13:980587. [PMID: 36479518 PMCID: PMC9721114 DOI: 10.3389/fpls.2022.980587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper (Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici.
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Affiliation(s)
| | | | | | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- LaMME, Université d'Evry Val d'Essonne, INRAE, Evry, France
| | | | | | | | | | - Ingo Hein
- Division Plant Sciences at the JHI, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute (JHI), Dundee, United Kingdom
| | - Kurt Lamour
- INRAE, GAFL, Montfavet, France
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
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18
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Bilkei‐Gorzo O, Heunis T, Marín‐Rubio JL, Cianfanelli FR, Raymond BBA, Inns J, Fabrikova D, Peltier J, Oakley F, Schmid R, Härtlova A, Trost M. The E3 ubiquitin ligase RNF115 regulates phagosome maturation and host response to bacterial infection. EMBO J 2022; 41:e108970. [PMID: 36281581 PMCID: PMC9713710 DOI: 10.15252/embj.2021108970] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/01/2022] [Accepted: 10/06/2022] [Indexed: 01/15/2023] Open
Abstract
Phagocytosis is a key process in innate immunity and homeostasis. After particle uptake, newly formed phagosomes mature by acquisition of endolysosomal enzymes. Macrophage activation by interferon gamma (IFN-γ) increases microbicidal activity, but delays phagosomal maturation by an unknown mechanism. Using quantitative proteomics, we show that phagosomal proteins harbour high levels of typical and atypical ubiquitin chain types. Moreover, phagosomal ubiquitylation of vesicle trafficking proteins is substantially enhanced upon IFN-γ activation of macrophages, suggesting a role in regulating phagosomal functions. We identified the E3 ubiquitin ligase RNF115, which is enriched on phagosomes of IFN-γ activated macrophages, as an important regulator of phagosomal maturation. Loss of RNF115 protein or ligase activity enhanced phagosomal maturation and increased cytokine responses to bacterial infection, suggesting that both innate immune signalling from the phagosome and phagolysosomal trafficking are controlled through ubiquitylation. RNF115 knock-out mice show less tissue damage in response to S. aureus infection, indicating a role of RNF115 in inflammatory responses in vivo. In conclusion, RNF115 and phagosomal ubiquitylation are important regulators of innate immune functions during bacterial infections.
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Affiliation(s)
- Orsolya Bilkei‐Gorzo
- Wallenberg Centre for Molecular and Translational Medicine, Department of Microbiology and Immunology at Institute of BiomedicineUniversity of GothenburgGothenburgSweden,MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK
| | - Tiaan Heunis
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | | | | | | | - Joseph Inns
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Daniela Fabrikova
- Wallenberg Centre for Molecular and Translational Medicine, Department of Microbiology and Immunology at Institute of BiomedicineUniversity of GothenburgGothenburgSweden
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK,Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Fiona Oakley
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK,Newcastle Fibrosis Research GroupNewcastle UniversityNewcastle upon TyneUK
| | - Ralf Schmid
- Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK,Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | - Anetta Härtlova
- Wallenberg Centre for Molecular and Translational Medicine, Department of Microbiology and Immunology at Institute of BiomedicineUniversity of GothenburgGothenburgSweden,MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK,Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK,Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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19
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Abstract
Ubiquitination is a posttranslational modification that regulates a multitude of cellular functions. Pathogens, such as bacteria and viruses, have evolved sophisticated mechanisms that evade or counteract ubiquitin-dependent host responses, or even exploit the ubiquitin system to their own advantage. This is largely done by numerous pathogen virulence factors that encode E3 ligases and deubiquitinases, which are often used as weapons in pathogen-host cell interactions. Moreover, upon pathogen attack, host cellular signaling networks undergo major ubiquitin-dependent changes to protect the host cell, including coordination of innate immunity, remodeling of cellular organelles, reorganization of the cytoskeleton, and reprogramming of metabolic pathways to restrict growth of the pathogen. Here we provide mechanistic insights into ubiquitin regulation of host-pathogen interactions and how it affects bacterial and viral pathogenesis and the organization and response of the host cell.
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Affiliation(s)
- Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany; .,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany; .,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany
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20
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Borbora SM, Rajmani RS, Balaji KN. PRMT5 epigenetically regulates the E3 ubiquitin ligase ITCH to influence lipid accumulation during mycobacterial infection. PLoS Pathog 2022; 18:e1010095. [PMID: 35658060 PMCID: PMC9200362 DOI: 10.1371/journal.ppat.1010095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 06/15/2022] [Accepted: 04/27/2022] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), triggers enhanced accumulation of lipids to generate foamy macrophages (FMs). This process has been often attributed to the surge in the expression of lipid influx genes with a concomitant decrease in those involved in lipid efflux. Here, we define an Mtb-orchestrated modulation of the ubiquitination of lipid accumulation markers to enhance lipid accretion during infection. We find that Mtb infection represses the expression of the E3 ubiquitin ligase, ITCH, resulting in the sustenance of key lipid accrual molecules viz. ADRP and CD36, that are otherwise targeted by ITCH for proteasomal degradation. In line, overexpressing ITCH in Mtb-infected cells was found to suppress Mtb-induced lipid accumulation. Molecular analyses including loss-of-function and ChIP assays demonstrated a role for the concerted action of the transcription factor YY1 and the arginine methyl transferase PRMT5 in restricting the expression of Itch gene by conferring repressive symmetrical H4R3me2 marks on its promoter. Consequently, siRNA-mediated depletion of YY1 or PRMT5 rescued ITCH expression, thereby compromising the levels of Mtb-induced ADRP and CD36 and limiting FM formation during infection. Accumulation of lipids within the host has been implicated as a pro-mycobacterial process that aids in pathogen persistence and dormancy. In line, we found that perturbation of PRMT5 enzyme activity resulted in compromised lipid levels and reduced mycobacterial survival in mouse peritoneal macrophages (ex vivo) and in a therapeutic mouse model of TB infection (in vivo). These findings provide new insights into the role of PRMT5 and YY1 in augmenting mycobacterial pathogenesis. Thus, we posit that our observations could help design novel adjunct therapies and combinatorial drug regimen for effective anti-TB strategies. Mycobacterium tuberculosis infection leads to the formation of lipid-laden cells (foamy macrophages-FMs) that offer a favorable shelter for its persistence. During infection, we observe a significant reduction in the expression of the E3 ubiquitin ligase, ITCH. This repression allows the sustenance of key lipid accretion molecules (ADRP and CD36), by curbing their proteasomal degradation. Further, we show the repression of ITCH to be dependent on the concerted action of the bifunctional transcription factor, YY1 and the arginine methyl transferase, PRMT5. NOTCH signaling pathway was identified as a master-regulator of YY1 expression. In vitro and in vivo analyses revealed the significance of PRMT5 in regulating FM formation and consequently mycobacterial burden.
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Affiliation(s)
- Salik Miskat Borbora
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Raju S. Rajmani
- Center for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka, India
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21
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Bacteria and tumor: Understanding the roles of bacteria in tumor genesis and immunology. Microbiol Res 2022; 261:127082. [PMID: 35660471 DOI: 10.1016/j.micres.2022.127082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/08/2021] [Accepted: 05/26/2022] [Indexed: 02/05/2023]
Abstract
In the past, tumor and microbial infection were commonly regarded as independent diseases with few interrelations. The discovery of bacteria in tumor tissue changed the knowledge of bacteria-tumor relationship. Recently, more and more findings have demonstrated the significant effects of bacteria on the genesis, development and metastasis of tumor. Particularly, the influence of bacteria on tumor immunity is of great interest. Bacteria can inhibit the function of immune system through multiple mechanisms. On the other hand, some bacteria can also enhance the immune response and inhibit tumor progression. Understanding the bacteria-tumor interactions is of great importance for developing novel anticancer approaches. Herein, we aim to provide a comprehensive understanding of the tumor/tumor immunology, the biogenesis of bacteria in tumor and the relation of tumorigenesis with bacteria. In addition, the roles of bacteria in tumor immunology and the potential approaches to use bacteria for cancer therapy are discussed.
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22
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Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Sci Rep 2022; 12:6868. [PMID: 35477739 PMCID: PMC9046306 DOI: 10.1038/s41598-022-10827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/31/2022] [Indexed: 11/08/2022] Open
Abstract
Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.
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23
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Haderer M, Neubert P, Rinner E, Scholtis A, Broncy L, Gschwendtner H, Kandulski A, Pavel V, Mehrl A, Brochhausen C, Schlosser S, Gülow K, Kunst C, Müller M. Novel pathomechanism for spontaneous bacterial peritonitis: disruption of cell junctions by cellular and bacterial proteases. Gut 2022; 71:580-592. [PMID: 33707230 PMCID: PMC8862089 DOI: 10.1136/gutjnl-2020-321663] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 02/17/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Spontaneous bacterial peritonitis (SBP) is a life-threatening complication of liver cirrhosis with a 1-year mortality of 66%. Bacterial translocation (BT) from the intestine to the mesenteric lymph nodes is crucial for the pathogenesis of SBP. DESIGN Since BT presupposes a leaky intestinal epithelium, the integrity of mucus and epithelial cell junctions (E-cadherin and occludin) was examined in colonic biopsies from patients with liver cirrhosis and controls. SBP-inducing Escherichia coli (E. coli) and Proteus mirabilis (P. mirabilis) were isolated from ascites of patients with liver cirrhosis and co-cultured with Caco-2 cells to characterise bacteria-to-cell effects. RESULTS SBP-derived E. coli and P. mirabilis led to a marked reduction of cell-to-cell junctions in a dose-dependent and time-dependent manner. This effect was enhanced by a direct interaction of live bacteria with epithelial cells. Degradation of occludin is mediated via increased ubiquitination by the proteasome. Remarkably, a novel bacterial protease activity is of pivotal importance for the cleavage of E-cadherin. CONCLUSION Patients with liver cirrhosis show a reduced thickness of colonic mucus, which allows bacteria-to-epithelial cell contact. Intestinal bacteria induce degradation of occludin by exploiting the proteasome of epithelial cells. We identified a novel bacterial protease activity of patient-derived SBP-inducing bacteria, which is responsible for the cleavage of E-cadherin structures. Inhibition of this protease activity leads to stabilisation of cell junctions. Thus, targeting these mechanisms by blocking the ubiquitin-proteasome system and/or the bacterial protease activity might interfere with BT and constitute a novel innovative therapeutic strategy to prevent SBP in patients with liver cirrhosis.
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Affiliation(s)
- Marika Haderer
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Philip Neubert
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Eva Rinner
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Annika Scholtis
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Lucile Broncy
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Heidi Gschwendtner
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Arne Kandulski
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Vlad Pavel
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Alexander Mehrl
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Christoph Brochhausen
- Department of Pathology, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Sophie Schlosser
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Karsten Gülow
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Claudia Kunst
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Martina Müller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious diseases, University Hospital Regensburg, Regensburg, Bavaria, Germany
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24
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Sura T, Surabhi S, Maaß S, Hammerschmidt S, Siemens N, Becher D. The global proteome and ubiquitinome of bacterial and viral co-infected bronchial epithelial cells. J Proteomics 2022; 250:104387. [PMID: 34600154 DOI: 10.1016/j.jprot.2021.104387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/26/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Viral infections facilitate bacterial trafficking to the lower respiratory tract resulting in bacterial-viral co-infections. Bacterial dissemination to the lower respiratory tract is enhanced by influenza A virus induced epithelial cell damage and dysregulation of immune responses. Epithelial cells act as a line of defense and detect pathogens by a high variety of pattern recognition receptors. The post-translational modification ubiquitin is involved in almost every cellular process. Moreover, ubiquitination contributes to the regulation of host immune responses, influenza A virus uncoating and transport within host cells. We applied proteomics with a special focus on ubiquitination to assess the impact of single bacterial and viral as well as bacterial-viral co-infections on bronchial epithelial cells. We used Tandem Ubiquitin Binding Entities to enrich polyubiquitinated proteins and assess changes in the ubiquitinome. Infecting 16HBE cells with Streptococcus pyogenes led to an increased abundance of proteins related to mitochondrial translation and energy metabolism in proteome and ubiquitinome. In contrast, influenza A virus infection mainly altered the ubiquitinome. Co-infections had no additional impact on protein abundances or affected pathways. Changes in protein abundance and enriched pathways were assigned to imprints of both infecting pathogens. SIGNIFICANCE: Viral and bacterial co-infections of the lower respiratory tract are a burden for health systems worldwide. Therefore, it is necessary to elucidate the complex interplay between the host and the infecting pathogens. Thus, we analyzed the proteome and the ubiquitinome of co-infected bronchial epithelial cells to elaborate a potential synergism of the two infecting organisms. The results presented in this work can be used as a starting point for further analyses.
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Affiliation(s)
- Thomas Sura
- University of Greifswald, Center for Functional Genomics of Microbes, Institute of Microbiology, Department of Microbial Proteomics, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Surabhi Surabhi
- University of Greifswald, Center for Functional Genomics of Microbes, Interfaculty Institute for Genetics and Functional Genomics, Department of Molecular Genetics and Infection Biology, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Sandra Maaß
- University of Greifswald, Center for Functional Genomics of Microbes, Institute of Microbiology, Department of Microbial Proteomics, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Sven Hammerschmidt
- University of Greifswald, Center for Functional Genomics of Microbes, Interfaculty Institute for Genetics and Functional Genomics, Department of Molecular Genetics and Infection Biology, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Nikolai Siemens
- University of Greifswald, Center for Functional Genomics of Microbes, Interfaculty Institute for Genetics and Functional Genomics, Department of Molecular Genetics and Infection Biology, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Dörte Becher
- University of Greifswald, Center for Functional Genomics of Microbes, Institute of Microbiology, Department of Microbial Proteomics, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany.
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25
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Iyer S, Das C. The unity of opposites: Strategic interplay between bacterial effectors to regulate cellular homeostasis. J Biol Chem 2021; 297:101340. [PMID: 34695417 PMCID: PMC8605245 DOI: 10.1016/j.jbc.2021.101340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Legionella pneumophila is a facultative intracellular pathogen that uses the Dot/Icm Type IV secretion system (T4SS) to translocate many effectors into its host and establish a safe, replicative lifestyle. The bacteria, once phagocytosed, reside in a vacuolar structure known as the Legionella-containing vacuole (LCV) within the host cells and rapidly subvert organelle trafficking events, block inflammatory responses, hijack the host ubiquitination system, and abolish apoptotic signaling. This arsenal of translocated effectors can manipulate the host factors in a multitude of different ways. These proteins also contribute to bacterial virulence by positively or negatively regulating the activity of one another. Such effector-effector interactions, direct and indirect, provide the delicate balance required to maintain cellular homeostasis while establishing itself within the host. This review summarizes the recent progress in our knowledge of the structure-function relationship and biochemical mechanisms of select effector pairs from Legionella that work in opposition to one another, while highlighting the diversity of biochemical means adopted by this intracellular pathogen to establish a replicative niche within host cells.
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Affiliation(s)
- Shalini Iyer
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
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26
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Grohmann C, Marapana DS, Ebert G. Targeted protein degradation at the host-pathogen interface. Mol Microbiol 2021; 117:670-681. [PMID: 34816514 DOI: 10.1111/mmi.14849] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022]
Abstract
Infectious diseases remain a major burden to global health. Despite the implementation of successful vaccination campaigns and efficient drugs, the increasing emergence of pathogenic vaccine or treatment resistance demands novel therapeutic strategies. The development of traditional therapies using small-molecule drugs is based on modulating protein function and activity through the occupation of active sites such as enzyme inhibition or ligand-receptor binding. These prerequisites result in the majority of host and pathogenic disease-relevant, nonenzymatic and structural proteins being labeled "undruggable." Targeted protein degradation (TPD) emerged as a powerful strategy to eliminate proteins of interest including those of the undruggable variety. Proteolysis-targeting chimeras (PROTACs) are rationally designed heterobifunctional small molecules that exploit the cellular ubiquitin-proteasome system to specifically mediate the highly selective and effective degradation of target proteins. PROTACs have shown remarkable results in the degradation of various cancer-associated proteins, and several candidates are already in clinical development. Significantly, PROTAC-mediated TPD holds great potential for targeting and modulating pathogenic proteins, especially in the face of increasing drug resistance to the best-in-class treatments. In this review, we discuss advances in the development of TPD in the context of targeting the host-pathogen interface and speculate on their potential use to combat viral, bacterial, and parasitic infection.
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Affiliation(s)
- Christoph Grohmann
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Danushka S Marapana
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Gregor Ebert
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
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27
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Tripathi-Giesgen I, Behrends C, Alpi AF. The ubiquitin ligation machinery in the defense against bacterial pathogens. EMBO Rep 2021; 22:e52864. [PMID: 34515402 PMCID: PMC8567218 DOI: 10.15252/embr.202152864] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin system is an important part of the host cellular defense program during bacterial infection. This is in particular evident for a number of bacteria including Salmonella Typhimurium and Mycobacterium tuberculosis which—inventively as part of their invasion strategy or accidentally upon rupture of seized host endomembranes—become exposed to the host cytosol. Ubiquitylation is involved in the detection and clearance of these bacteria as well as in the activation of innate immune and inflammatory signaling. Remarkably, all these defense responses seem to emanate from a dense layer of ubiquitin which coats the invading pathogens. In this review, we focus on the diverse group of host cell E3 ubiquitin ligases that help to tailor this ubiquitin coat. In particular, we address how the divergent ubiquitin conjugation mechanisms of these ligases contribute to the complexity of the anti‐bacterial coating and the recruitment of different ubiquitin‐binding effectors. We also discuss the activation and coordination of the different E3 ligases and which strategies bacteria evolved to evade the activities of the host ubiquitin system.
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Affiliation(s)
- Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, München, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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28
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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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29
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Maculins T, Dikic I. Gasdermin B in the host-pathogen tug-of-war. Cell Res 2021; 31:1043-1044. [PMID: 34341491 PMCID: PMC8486812 DOI: 10.1038/s41422-021-00544-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Timurs Maculins
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA.
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany.
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30
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Serine-ubiquitination regulates Golgi morphology and the secretory pathway upon Legionella infection. Cell Death Differ 2021; 28:2957-2969. [PMID: 34285384 PMCID: PMC8481228 DOI: 10.1038/s41418-021-00830-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/31/2022] Open
Abstract
SidE family of Legionella effectors catalyze non-canonical phosphoribosyl-linked ubiquitination (PR-ubiquitination) of host proteins during bacterial infection. SdeA localizes predominantly to ER and partially to the Golgi apparatus, and mediates serine ubiquitination of multiple ER and Golgi proteins. Here we show that SdeA causes disruption of Golgi integrity due to its ubiquitin ligase activity. The Golgi linking proteins GRASP55 and GRASP65 are PR-ubiquitinated on multiple serine residues, thus preventing their ability to cluster and form oligomeric structures. In addition, we found that the functional consequence of Golgi disruption is not linked to the recruitment of Golgi membranes to the growing Legionella-containing vacuoles. Instead, it affects the host secretory pathway. Taken together, our study sheds light on the Golgi manipulation strategy by which Legionella hijacks the secretory pathway and promotes bacterial infection.
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31
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Henneberg LT, Schulman BA. Decoding the messaging of the ubiquitin system using chemical and protein probes. Cell Chem Biol 2021; 28:889-902. [PMID: 33831368 PMCID: PMC7611516 DOI: 10.1016/j.chembiol.2021.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modification of proteins by ubiquitin is required for nearly all aspects of eukaryotic cell function. The numerous targets of ubiquitylation, and variety of ubiquitin modifications, are often likened to a code, where the ultimate messages are diverse responses to target ubiquitylation. E1, E2, and E3 multiprotein enzymatic assemblies modify specific targets and thus function as messengers. Recent advances in chemical and protein tools have revolutionized our ability to explore the ubiquitin system, through enabling new high-throughput screening methods, matching ubiquitylation enzymes with their cellular targets, revealing intricate allosteric mechanisms regulating ubiquitylating enzymes, facilitating structural revelation of transient assemblies determined by multivalent interactions, and providing new paradigms for inhibiting and redirecting ubiquitylation in vivo as new therapeutics. Here we discuss the development of methods that control, disrupt, and extract the flow of information across the ubiquitin system and have enabled elucidation of the underlying molecular and cellular biology.
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Affiliation(s)
- Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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32
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Zhang Z, Aweya JJ, Yao D, Zheng Z, Tran NT, Li S, Zhang Y. Ubiquitination as an Important Host-Immune Response Strategy in Penaeid Shrimp: Inferences From Other Species. Front Immunol 2021; 12:697397. [PMID: 34122458 PMCID: PMC8191737 DOI: 10.3389/fimmu.2021.697397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022] Open
Abstract
Shrimp aquaculture is an essential economic venture globally, but the industry faces numerous challenges, especially pathogenic infections. As invertebrates, shrimp rely mainly on their innate immune system for protection. An increasing number of studies have shown that ubiquitination plays a vital role in the innate immune response to microbial pathogens. As an important form of posttranslational modification (PTM), both hosts and pathogens have exploited ubiquitination and the ubiquitin system as an immune response strategy to outwit the other. This short review brings together recent findings on ubiquitination and how this PTM plays a critical role in immune modulation in penaeid shrimps. Key findings inferred from other species would help guide further studies on ubiquitination as an immune response strategy in shrimp-pathogen interactions.
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Affiliation(s)
- Zhaoxue Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Jude Juventus Aweya
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Defu Yao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Zhihong Zheng
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Ngoc Tuan Tran
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shengkang Li
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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33
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Tilocca B, Soggiu A, Greco V, Sacchini F, Garofolo G, Paci V, Bonizzi L, Urbani A, Tittarelli M, Roncada P. Comparative proteomics of Brucella melitensis is a useful toolbox for developing prophylactic interventions in a One-Health context. One Health 2021; 13:100253. [PMID: 33997237 PMCID: PMC8100217 DOI: 10.1016/j.onehlt.2021.100253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 11/28/2022] Open
Abstract
Brucellosis caused by Brucella melitensis is a zoonosis frequently reported in the Mediterranean and Middle-East regions and responsible for important economic losses and reduced animal welfare. To date, current strategies applied to control or eradicate the disease relies on diagnostic tests that suffer from limited specificity in non-vaccinated animals; while prophylactic measures, when applied, use a live attenuated bacterial strain characterized by residual virulence on adult pregnant animals and difficulties in distinguishing vaccinated from infected animals. To overcome these issues, studies are desired to elucidate the bacterial biology and the pathogenetic mechanisms of both the vaccinal strain and the pathogenic strains. Proteomics has a potential in tackling issues of One-Health concern; here, we employed label-free shotgun proteomics to investigate the protein repertoire of the vaccinal strain B. melitensis Rev.1 and compare it with the proteome of the Brucella melitensis 16 M, a reference strain representative of B. melitensis field strains. Comparative proteomics profiling underlines common and diverging traits between the two strains. Common features suggest the potential biochemical routes responsible for the residual virulence of the vaccinal strain, whilst the diverging traits are suggestive biochemical signatures to be further investigated to provide an optimized diagnostic capable of discriminating the vaccinated from infected animals. The data presented in this study are openly available in PRIDE data repository at https://www.ebi.ac.uk/pride/, reference number PXD022472.
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Affiliation(s)
- Bruno Tilocca
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, viale Europa, 88100 Catanzaro, Italy
| | - Alessio Soggiu
- Department of Biomedical, Surgical and Dental Sciences- One Health Unit, University of Milano, via Celoria 10, 20133 Milano, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli, Largo A. Gemelli, 8-00168 Rome, Italy
| | - Flavio Sacchini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Centro di Referenza Nazionale per le brucellosi animali, Via Campo Boario 1, 64100 Teramo, Italy
| | - Giuliano Garofolo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Centro di Referenza Nazionale per le brucellosi animali, Via Campo Boario 1, 64100 Teramo, Italy
| | - Valentina Paci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Centro di Referenza Nazionale per le brucellosi animali, Via Campo Boario 1, 64100 Teramo, Italy
| | - Luigi Bonizzi
- Department of Biomedical, Surgical and Dental Sciences- One Health Unit, University of Milano, via Celoria 10, 20133 Milano, Italy
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli, Largo A. Gemelli, 8-00168 Rome, Italy
| | - Manuela Tittarelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Centro di Referenza Nazionale per le brucellosi animali, Via Campo Boario 1, 64100 Teramo, Italy
| | - Paola Roncada
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, viale Europa, 88100 Catanzaro, Italy
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34
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Guo Y, Li L, Xu T, Guo X, Wang C, Li Y, Yang Y, Yang D, Sun B, Zhao X, Shao G, Qi X. HUWE1 mediates inflammasome activation and promotes host defense against bacterial infection. J Clin Invest 2021; 130:6301-6316. [PMID: 33104527 DOI: 10.1172/jci138234] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/11/2020] [Indexed: 02/05/2023] Open
Abstract
The mechanism by which inflammasome activation is modulated remains unclear. In this study, we identified an AIM2-interacting protein, the E3 ubiquitin ligase HUWE1, which was also found to interact with NLRP3 and NLRC4 through the HIN domain of AIM2 and the NACHT domains of NLRP3 and NLRC4. The BH3 domain of HUWE1 was important for its interaction with NLRP3, AIM2, and NLRC4. Caspase-1 maturation, IL-1β release, and pyroptosis were reduced in Huwe1-deficient bone marrow-derived macrophages (BMDMs) compared with WT BMDMs in response to stimuli to induce NLRP3, NLRC4, and AIM2 inflammasome activation. Furthermore, the activation of NLRP3, NLRC4, and AIM2 inflammasomes in both mouse and human cells was remarkably reduced by treatment with the HUWE1 inhibitor BI8622. HUWE1 mediated the K27-linked polyubiquitination of AIM2, NLRP3, and NLRC4, which led to inflammasome assembly, ASC speck formation, and sustained caspase-1 activation. Huwe1-deficient mice had an increased bacterial burden and decreased caspase-1 activation and IL-1β production upon Salmonella, Francisella, or Acinetobacter baumannii infection. Our study provides insights into the mechanisms of inflammasome activation as well as a potential therapeutic target against bacterial infection.
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Affiliation(s)
- Yu Guo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Longjun Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, China
| | - Tao Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaomin Guo
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chaoming Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, China
| | - Yihui Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, China
| | - Yanan Yang
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dong Yang
- Laboratory of Animal Tumor Models and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Bin Sun
- Laboratory of Animal Tumor Models and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xudong Zhao
- Laboratory of Animal Tumor Models and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Genze Shao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xiaopeng Qi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
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35
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Sheedlo MJ, Kenny S, Podkorytov IS, Brown K, Ma J, Iyer S, Hewitt CS, Arbough T, Mikhailovskii O, Flaherty DP, Wilson MA, Skrynnikov NR, Das C. Insights into Ubiquitin Product Release in Hydrolysis Catalyzed by the Bacterial Deubiquitinase SdeA. Biochemistry 2021; 60:584-596. [PMID: 33583181 DOI: 10.1021/acs.biochem.0c00760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the co-crystal structure of the (catalytic Cys)-to-Ala mutant of the deubiquitinase domain of the Legionella pneumophila effector SdeA (SdeADUB) with its ubiquitin (Ub) product. Most of the intermolecular interactions are preserved in this product-bound structure compared to that of the previously characterized complex of SdeADUB with the suicide inhibitor ubiquitin vinylmethyl ester (Ub-VME), whose structure models the acyl-enzyme thioester intermediate. Nuclear magnetic resonance (NMR) titration studies show a chemical shift perturbation pattern that suggests that the same interactions also exist in solution. Isothermal titration calorimetry and NMR titration data reveal that the affinity of wild-type (WT) SdeADUB for Ub is significantly lower than that of the Cys-to-Ala mutant. This is potentially due to repulsive interaction between the thiolate ion of the catalytic Cys residue in WT SdeADUB and the carboxylate group of the C-terminal Gly76 residue in Ub. In the context of SdeADUB catalysis, this electrostatic repulsion arises after the hydrolysis of the scissile isopeptide bond in the acyl-enzyme intermediate and the consequent formation of the C-terminal carboxylic group in the Ub fragment. We hypothesize that this electrostatic repulsion may expedite the release of the Ub product by SdeADUB. We note that similar repulsive interactions may also occur in other deubiquitinases and hydrolases of ubiquitin-like protein modifiers and may constitute a fairly general mechanism of product release within this family. This is a potentially important feature for a family of enzymes that form extensive protein-protein interactions during enzyme-substrate engagement.
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Affiliation(s)
- Michael J Sheedlo
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sebastian Kenny
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Kwame Brown
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jia Ma
- Bindley Bioscience Center, West Lafayette, Indiana 47906, United States
| | - Shalini Iyer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
| | - Trent Arbough
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Oleg Mikhailovskii
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, United States
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Nikolai R Skrynnikov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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36
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Rasaei R, Sarodaya N, Kim KS, Ramakrishna S, Hong SH. Importance of Deubiquitination in Macrophage-Mediated Viral Response and Inflammation. Int J Mol Sci 2020; 21:ijms21218090. [PMID: 33138315 PMCID: PMC7662591 DOI: 10.3390/ijms21218090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 01/14/2023] Open
Abstract
Ubiquitination and deubiquitination play a fundamental role in the signaling pathways associated with innate and adaptive immune responses. Macrophages are key sentinels for the host defense, triggering antiviral and inflammatory responses against various invading pathogens. Macrophages recognize the genetic material of these pathogens as pathogen-associated molecular patterns (PAMPs) and danger-associated molecular patterns (DAMPs) through the activation of its pattern recognition receptors (PRRs), initiating the cascade of immune signaling, which leads to the production of pro- and anti-inflammatory cytokines that initiates the appropriate immune response. Macrophage-mediated immune response is highly regulated and tightly controlled by the ubiquitin system since its abnormal activation or dysregulation may result in the severe pathogenesis of numerous inflammatory and autoimmune diseases. Deubiquitinating enzymes (DUBs) play a crucial role in reversing the ubiquitination and controlling the magnitude of the immune response. During infection, pathogens manipulate the host defense system by regulating DUBs to obtain nutrients and increase proliferation. Indeed, the regulation of DUBs by small molecule inhibitors has been proposed as an excellent way to control aberrant activation of immune signaling molecules. This review is focused on the complex role of DUBs in macrophage-mediated immune response, exploring the potential use of DUBs as therapeutic targets in autoimmune and inflammatory diseases by virtue of small molecule DUB inhibitors.
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Affiliation(s)
- Roya Rasaei
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (K.-S.K.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (K.-S.K.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (K.-S.K.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: or (S.R.); or (S.-H.H.)
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea;
- Correspondence: or (S.R.); or (S.-H.H.)
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37
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Saeed AFUH, Ouyang S. Ubiquitin: there's no quitting. Sci Bull (Beijing) 2020; 65:1327-1329. [PMID: 36659208 DOI: 10.1016/j.scib.2020.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 01/21/2023]
Affiliation(s)
- Abdullah F U H Saeed
- 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 Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, 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 Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
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38
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Nedal A, Ræder SB, Dalhus B, Helgesen E, Forstrøm RJ, Lindland K, Sumabe BK, Martinsen JH, Kragelund BB, Skarstad K, Bjørås M, Otterlei M. Peptides containing the PCNA interacting motif APIM bind to the β-clamp and inhibit bacterial growth and mutagenesis. Nucleic Acids Res 2020; 48:5540-5554. [PMID: 32347931 PMCID: PMC7261172 DOI: 10.1093/nar/gkaa278] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
In the fight against antimicrobial resistance, the bacterial DNA sliding clamp, β-clamp, is a promising drug target for inhibition of DNA replication and translesion synthesis. The β-clamp and its eukaryotic homolog, PCNA, share a C-terminal hydrophobic pocket where all the DNA polymerases bind. Here we report that cell penetrating peptides containing the PCNA-interacting motif APIM (APIM-peptides) inhibit bacterial growth at low concentrations in vitro, and in vivo in a bacterial skin infection model in mice. Surface plasmon resonance analysis and computer modeling suggest that APIM bind to the hydrophobic pocket on the β-clamp, and accordingly, we find that APIM-peptides inhibit bacterial DNA replication. Interestingly, at sub-lethal concentrations, APIM-peptides have anti-mutagenic activities, and this activity is increased after SOS induction. Our results show that although the sequence homology between the β-clamp and PCNA are modest, the presence of similar polymerase binding pockets in the DNA clamps allows for binding of the eukaryotic binding motif APIM to the bacterial β-clamp. Importantly, because APIM-peptides display both anti-mutagenic and growth inhibitory properties, they may have clinical potential both in combination with other antibiotics and as single agents.
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Affiliation(s)
- Aina Nedal
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Synnøve B Ræder
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Emily Helgesen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Rune J Forstrøm
- Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Kim Lindland
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Balagra K Sumabe
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Jacob H Martinsen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Kirsten Skarstad
- Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
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39
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Ahel J, Lehner A, Vogel A, Schleiffer A, Meinhart A, Haselbach D, Clausen T. Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism. eLife 2020; 9:e56185. [PMID: 32573437 PMCID: PMC7311170 DOI: 10.7554/elife.56185] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
RNF213 is the major susceptibility factor for Moyamoya disease, a progressive cerebrovascular disorder that often leads to brain stroke in adults and children. Characterization of disease-associated mutations has been complicated by the enormous size of RNF213. Here, we present the cryo-EM structure of mouse RNF213. The structure reveals the intricate fold of the 584 kDa protein, comprising an N-terminal stalk, a dynein-like core with six ATPase units, and a multidomain E3 module. Collaboration with UbcH7, a cysteine-reactive E2, points to an unexplored ubiquitin-transfer mechanism that proceeds in a RING-independent manner. Moreover, we show that pathologic MMD mutations cluster in the composite E3 domain, likely interfering with substrate ubiquitination. In conclusion, the structure of RNF213 uncovers a distinct type of an E3 enzyme, highlighting the growing mechanistic diversity in ubiquitination cascades. Our results also provide the molecular framework for investigating the emerging role of RNF213 in lipid metabolism, hypoxia, and angiogenesis.
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Affiliation(s)
- Juraj Ahel
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Anita Lehner
- Vienna BioCenter Core Facilities, Vienna BioCenter, Vienna, Austria
| | - Antonia Vogel
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
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40
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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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41
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N-benzylpiperidinol derivatives as novel USP7 inhibitors: Structure-activity relationships and X-ray crystallographic studies. Eur J Med Chem 2020; 199:112279. [PMID: 32497973 DOI: 10.1016/j.ejmech.2020.112279] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
USP7 as a deubiquitinase plays important roles in regulating the stability of some oncoproteins including MDM2 and DNMT1, and thus represents a potential anticancer target. Through comparative analysis of USP7 co-crystal structures in complex with the reported piperidinol inhibitors, we noticed that the USP7 Phe409 sub-site might have good adaptability to the ligands. Based on this observation, 55 N-aromatic and N-benzyl piperidinol derivatives were designed, synthesized and biologically evaluated, among which compound L55 was identified as a highly selective and potent USP7 inhibitor (IC50 = 40.8 nM, KD = 78.3 nM). X-ray crystallographic studies revealed that L55 bound to USP7 with a new pose that was very different from the previously reported inhibitors. The results of cellular assays showed that L55 had strong antitumor activity against LNCaP (IC50 = 29.6 nM) and RS4; 11 (IC50 = 41.6 nM) cells, probably through inducing cell death and restricting G0/G1 and S phases. Moreover, L55 dose-dependently reduced the protein levels of MDM2 and DNMT1 and increased the protein levels of p53 and p21. These findings could have valuable implications for designing novel structural classes of USP7 inhibitors.
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42
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Berglund J, Gjondrekaj R, Verney E, Maupin-Furlow JA, Edelmann MJ. Modification of the host ubiquitome by bacterial enzymes. Microbiol Res 2020; 235:126429. [PMID: 32109687 PMCID: PMC7369425 DOI: 10.1016/j.micres.2020.126429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 12/14/2022]
Abstract
Attachment of ubiquitin molecules to protein substrates is a reversible post-translational modification (PTM), which occurs ubiquitously in eukaryotic cells and controls most cellular processes. As a consequence, ubiquitination is an attractive target of pathogen-encoded virulence factors. Pathogenic bacteria have evolved multiple mechanisms to hijack the host's ubiquitin system to their advantage. In this review, we discuss the bacteria-encoded E3 ligases and deubiquitinases translocated to the host for an addition or removal of eukaryotic ubiquitin modification, effectively hijacking the host's ubiquitination processes. We review bacterial enzymes homologous to host proteins in sequence and functions, as well as enzymes with novel mechanisms in ubiquitination, which have significant structural differences in comparison to the mammalian E3 ligases. Finally, we will also discuss examples of molecular "counter-weapons" - eukaryotic proteins, which counteract pathogen-encoded E3 ligases. The many examples of the pathogen effector molecules that catalyze eukaryotic ubiquitin modification bring to light the intricate pathways involved in the pathogenesis of some of the most virulent bacterial infections with human pathogens. The role of these effector molecules remains an essential determinant of bacterial virulence in terms of infection, invasion, and replication. A comprehensive understanding of the mechanisms dictating the mimicry employed by bacterial pathogens is of vital importance in developing new strategies for therapeutic approaches.
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Affiliation(s)
- Jennifer Berglund
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Rafaela Gjondrekaj
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Ellen Verney
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA.
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43
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Hausman JM, Kenny S, Iyer S, Babar A, Qiu J, Fu J, Luo ZQ, Das C. The Two Deubiquitinating Enzymes from Chlamydia trachomatis Have Distinct Ubiquitin Recognition Properties. Biochemistry 2020; 59:1604-1617. [PMID: 32275137 PMCID: PMC7700883 DOI: 10.1021/acs.biochem.9b01107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chlamydia trachomatis is the cause of several diseases such as sexually transmitted urogenital disease and ocular trachoma. The pathogen contains a small genome yet, upon infection, expresses two enzymes with deubiquitinating activity, termed ChlaDUB1 and ChlaDUB2, presumed to have redundant deubiquitinase (DUB) function because of the similarity of the primary structure of their catalytic domain. Previous studies have led to structural characterization of the enzymatic properties of ChlaDUB1; however, ChlaDUB2 has yet to be investigated thoroughly. In this study, we investigated the deubiquitinase properties of ChlaDUB2 and compared them to those of ChlaDUB1. This revealed a distinct difference in hydrolytic activity with regard to di- and polyubiquitin chains while showing similar ability to cleave a monoubiquitin-based substrate, ubiquitin aminomethylcoumarin (Ub-AMC). ChlaDUB2 was unable to cleave a diubiquitin substrate efficiently, whereas ChlaDUB1 could rapidly hydrolyze this substrate like a prototypical prokaryotic DUB, SdeA. With polyubiquitinated green fluorescent protein substrate (GFP-Ubn), whereas ChlaDUB1 efficiently disassembled the polyubiquitin chains into the monoubiquitin product, the deubiquitination activity of ChlaDUB2, while showing depletion of the substrate, did not produce appreciable levels of the monoubiquitin product. We report the structures of a catalytic construct of ChlaDUB2 and its complex with ubiquitin propargyl amide. These structures revealed differences in residues involved in substrate recognition between the two Chlamydia DUBs. On the basis of the structures, we conclude that the distal ubiquitin binding is equivalent between the two DUBs, consistent with the Ub-AMC activity result. Therefore, the difference in activity with longer ubiquitinated substrates may be due to the differential recognition of these substrates involving additional ubiquitin binding sites.
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Affiliation(s)
- John M. Hausman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Sebastian Kenny
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Shalini Iyer
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Aditya Babar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Xi’an Road 5333, Changchun, Jilin 130062, China
| | - Jiaqi Fu
- Department of Biology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhao-Qing Luo
- Department of Biology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States,Corresponding Author:
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44
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Liao J, Orsi RH, Carroll LM, Wiedmann M. Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica. Environ Microbiol 2020; 22:2811-2828. [PMID: 32337816 DOI: 10.1111/1462-2920.15014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/04/2020] [Accepted: 04/06/2020] [Indexed: 01/24/2023]
Abstract
Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host- and geographic-associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large-scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic-associated single-nucleotide polymorphisms (SNPs), rather than geographic-associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein-encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter-population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.,Graduate Field of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Renato Hohl Orsi
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
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45
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Mu Y, Wang Y, Huang Y, Li D, Han Y, Chang M, Fu J, Xie Y, Ren J, Wang H, Zhang Y, Luo ZQ, Feng Y. Structural insights into the mechanism and inhibition of transglutaminase-induced ubiquitination by the Legionella effector MavC. Nat Commun 2020; 11:1774. [PMID: 32286321 PMCID: PMC7156659 DOI: 10.1038/s41467-020-15645-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/20/2020] [Indexed: 01/09/2023] Open
Abstract
Protein ubiquitination is one of the most prevalent post-translational modifications, controlling virtually every process in eukaryotic cells. Recently, the Legionella effector MavC was found to mediate a unique ubiquitination through transglutamination, linking ubiquitin (Ub) to UBE2N through UbGln40 in a process that can be inhibited by another Legionella effector, Lpg2149. Here, we report the structures of MavC/UBE2N/Ub ternary complex, MavC/UBE2N-Ub (product) binary complex, and MavC/Lpg2149 binary complex. During the ubiquitination, the loop containing the modification site K92 of UBE2N undergoes marked conformational change, and Lpg2149 inhibits this ubiquitination through competing with Ub to bind MavC. Moreover, we found that MavC itself also exhibits weak deubiquitinase activity towards this non-canonical ubiquitination. Together, our study not only provides insights into the mechanism and inhibition of this transglutaminase-induced ubiquitination by MavC, but also sheds light on the future studies into UBE2N inhibition by this modification and deubiquitinases of this unique ubiquitination.
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Affiliation(s)
- Yajuan Mu
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Yue Wang
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Yanfei Huang
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Dong Li
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Youyou Han
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Min Chang
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Jiaqi Fu
- 0000 0004 1937 2197grid.169077.ePurdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN USA
| | - Yongchao Xie
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Jie Ren
- 0000 0001 0526 1937grid.410727.7State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Hao Wang
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Yi Zhang
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
| | - Zhao-Qing Luo
- 0000 0004 1937 2197grid.169077.ePurdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN USA
| | - Yue Feng
- 0000 0000 9931 8406grid.48166.3dBeijing 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, 100029 Beijing, China
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Kliza K, Husnjak K. Resolving the Complexity of Ubiquitin Networks. Front Mol Biosci 2020; 7:21. [PMID: 32175328 PMCID: PMC7056813 DOI: 10.3389/fmolb.2020.00021] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/04/2020] [Indexed: 12/22/2022] Open
Abstract
Ubiquitination regulates nearly all cellular processes by coordinated activity of ubiquitin writers (E1, E2, and E3 enzymes), erasers (deubiquitinating enzymes) and readers (proteins that recognize ubiquitinated proteins by their ubiquitin-binding domains). By differentially modifying cellular proteome and by recognizing these ubiquitin modifications, ubiquitination machinery tightly regulates execution of specific cellular events in space and time. Dynamic and complex ubiquitin architecture, ranging from monoubiquitination, multiple monoubiquitination, eight different modes of homotypic and numerous types of heterogeneous polyubiquitin linkages, enables highly dynamic and complex regulation of cellular processes. We discuss available tools and approaches to study ubiquitin networks, including methods for the identification and quantification of ubiquitin-modified substrates, as well as approaches to quantify the length, abundance, linkage type and architecture of different ubiquitin chains. Furthermore, we also summarize the available approaches for the discovery of novel ubiquitin readers and ubiquitin-binding domains, as well as approaches to monitor and visualize activity of ubiquitin conjugation and deconjugation machineries. We also discuss benefits, drawbacks and limitations of available techniques, as well as what is still needed for detailed spatiotemporal dissection of cellular ubiquitination networks.
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Affiliation(s)
- Katarzyna Kliza
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
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47
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Margalit A, Kavanagh K, Carolan JC. Characterization of the Proteomic Response of A549 Cells Following Sequential Exposure to Aspergillus fumigatus and Pseudomonas aeruginosa. J Proteome Res 2020; 19:279-291. [PMID: 31693381 DOI: 10.1021/acs.jproteome.9b00520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aspergillus fumigatus and Pseudomonas aeruginosa are the most prevalent fungal and bacterial pathogens associated with cystic-fibrosis-related infections, respectively. P. aeruginosa eventually predominates as the primary pathogen, though it is unknown why this is the case. Label-free quantitative proteomics was employed to investigate the cellular response of the alveolar epithelial cell line, A549, to coexposure of A. fumigatus and P. aeruginosa. These studies revealed a significant increase in the rate of P. aeruginosa proliferation where A. fumigatus was present. Shotgun proteomics performed on A549 cells exposed to either A. fumigatus or P. aeruginosa or to A. fumigatus and P. aeruginosa sequentially revealed distinct changes to the host cell proteome in response to either or both pathogens. While key signatures of infection were retained among all pathogen-exposed groups, including changes in mitochondrial activity and energy output, the relative abundance of proteins associated with endocytosis, phagosomes, and lysosomes was decreased in sequentially exposed cells compared to cells exposed to either pathogen. Our findings indicate that A. fumigatus renders A549 cells unable to internalize bacteria, thus providing an environment in which P. aeruginosa can proliferate. This research provides novel insights into the whole-cell proteomic response of A549 cells to A. fumigatus and P. aeruginosa and highlights distinct differences in the proteome following sequential exposure to both pathogens, which may explain why P. aeruginosa can predominate.
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Affiliation(s)
- Anatte Margalit
- Department of Biology , Maynooth University , Maynooth, Co. Kildare W23F2H6 , Ireland
| | - Kevin Kavanagh
- Department of Biology , Maynooth University , Maynooth, Co. Kildare W23F2H6 , Ireland
| | - James C Carolan
- Department of Biology , Maynooth University , Maynooth, Co. Kildare W23F2H6 , Ireland
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48
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Shin D, Mukherjee R, Liu Y, Gonzalez A, Bonn F, Liu Y, Rogov VV, Heinz M, Stolz A, Hummer G, Dötsch V, Luo ZQ, Bhogaraju S, Dikic I. Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Mol Cell 2020; 77:164-179.e6. [PMID: 31732457 PMCID: PMC6941232 DOI: 10.1016/j.molcel.2019.10.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/07/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
Abstract
The family of bacterial SidE enzymes catalyzes non-canonical phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophila. Here, we describe identification of two bacterial effectors that reverse PR ubiquitination and are thus named deubiquitinases for PR ubiquitination (DUPs; DupA and DupB). Structural analyses revealed that DupA and SidE ubiquitin ligases harbor a highly homologous catalytic phosphodiesterase (PDE) domain. However, unlike SidE ubiquitin ligases, DupA displays increased affinity to PR-ubiquitinated substrates, which allows DupA to cleave PR ubiquitin from substrates. Interfering with DupA-ubiquitin binding switches its activity toward SidE-type ligase. Given the high affinity of DupA to PR-ubiquitinated substrates, we exploited a catalytically inactive DupA mutant to trap and identify more than 180 PR-ubiquitinated host proteins in Legionella-infected cells. Proteins involved in endoplasmic reticulum (ER) fragmentation and membrane recruitment to Legionella-containing vacuoles (LCV) emerged as major SidE targets. The global map of PR-ubiquitinated substrates provides critical insights into host-pathogen interactions during Legionella infection.
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Affiliation(s)
- Donghyuk Shin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Yaobin Liu
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Alexis Gonzalez
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Yan Liu
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Marcel Heinz
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Zhao-Qing Luo
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Sagar Bhogaraju
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
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Lopez‐Barbosa N, Ludwicki MB, DeLisa MP. Proteome editing using engineered proteins that hijack cellular quality control machinery. AIChE J 2019. [DOI: 10.1002/aic.16854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Lopez‐Barbosa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Morgan B. Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Matthew P. DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
- Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University Ithaca New York
- Biochemistry, Molecular and Cell Biology Cornell University Ithaca New York
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50
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Anas M, Kumari V, Gupta N, Dube A, Kumar N. Protein quality control machinery in intracellular protozoan parasites: hopes and challenges for therapeutic targeting. Cell Stress Chaperones 2019; 24:891-904. [PMID: 31228085 PMCID: PMC6717229 DOI: 10.1007/s12192-019-01016-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/08/2019] [Accepted: 06/10/2019] [Indexed: 01/28/2023] Open
Abstract
Intracellular protozoan parasites have evolved an efficient protein quality control (PQC) network comprising protein folding and degradation machineries that protect the parasite's proteome from environmental perturbations and threats posed by host immune surveillance. Interestingly, the components of PQC machinery in parasites have acquired sequence insertions which may provide additional interaction interfaces and diversify the repertoire of their biological roles. However, the auxiliary functions of PQC machinery remain poorly explored in parasite. A comprehensive understanding of this critical machinery may help to identify robust biological targets for new drugs against acute or latent and drug-resistant infections. Here, we review the dynamic roles of PQC machinery in creating a safe haven for parasite survival in hostile environments, serving as a metabolic sensor to trigger transformation into phenotypically distinct stages, acting as a lynchpin for trafficking of parasite cargo across host membrane for immune evasion and serving as an evolutionary capacitor to buffer mutations and drug-induced proteotoxicity. Versatile roles of PQC machinery open avenues for exploration of new drug targets for anti-parasitic intervention and design of strategies for identification of potential biomarkers for point-of-care diagnosis.
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Affiliation(s)
- Mohammad Anas
- Department of Parasitology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Varsha Kumari
- Department of Parasitology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Niharika Gupta
- Department of Parasitology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Anuradha Dube
- Department of Parasitology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Niti Kumar
- Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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