1
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Reddy TS, Sidharthan VK. Three-fold expansion of the genetic diversity of blunerviruses through plant (meta)transcriptome data-mining. Virology 2024; 599:110210. [PMID: 39213990 DOI: 10.1016/j.virol.2024.110210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/04/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Kitaviruses are plant-infecting, non-systemic disease-causing viruses with multipartite single-stranded RNA genomes. Despite their importance, knowledge on kitaviruses is limited in comparison with other plant virus groups, mainly because of the lesser number of identified and characterized kitaviruses and their isolates. In the present study, we explored plant (meta)transcriptome data available in public domain and identified genome sequences of eighteen putative novel blunerviruses in eighteen plant species, including four gymnosperm and four monocot species. Four RNA segments (RNAs 1-4) of eleven identified viruses were recovered, whilst at least two RNA segments were recovered for the remaining viruses. Phylogenetic analysis grouped the identified viruses with known blunerviruses. Based on genome organization, sequence identities of encoded proteins with known blunerviruses and phylogeny, the identified viruses are regarded as new members of the genus Blunervirus. The study paves way for initiating further studies on understanding biological properties, economic importance and geographical distribution of identified blunerviruses.
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2
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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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3
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Koonin EV, Fischer MG, Kuhn JH, Krupovic M. The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy. Microbiol Mol Biol Rev 2024:e0008623. [PMID: 39023254 DOI: 10.1128/mmbr.00086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
SUMMARYPolintons are 15-20 kb-long self-synthesizing transposons that are widespread in eukaryotic, and in particular protist, genomes. Apart from a transposase and a protein-primed DNA polymerase, polintons encode homologs of major and minor jelly-roll capsid proteins, DNA-packaging ATPases, and proteases involved in capsid maturation of diverse eukaryotic viruses of kingdom Bamfordvirae. Given the conservation of these structural and morphogenetic proteins among polintons, these elements are predicted to alternate between transposon and viral lifestyles and, although virions have thus far not been detected, are classified as viruses (class Polintoviricetes) in the phylum Preplasmiviricota. Related to polintoviricetes are vertebrate adenovirids; unclassified polinton-like viruses (PLVs) identified in various environments or integrated into diverse protist genomes; virophages (Maveriviricetes), which are part of tripartite hyperparasitic systems including protist hosts and giant viruses; and capsid-less derivatives, such as cytoplasmic linear DNA plasmids of fungi and transpovirons. Phylogenomic analysis indicates that the polinton-like supergroup of viruses bridges bacterial tectivirids (preplasmiviricot class Tectiliviricetes) to the phylum Nucleocytoviricota that includes large and giant eukaryotic DNA viruses. Comparative structural analysis of proteins encoded by polinton-like viruses led to the discovery of previously undetected functional domains, such as terminal proteins and distinct proteases implicated in DNA polymerase processing, and clarified the evolutionary relationships within Polintoviricetes. Here, we leverage these insights into the evolution of the polinton-like supergroup to develop an amended megataxonomy that groups Polintoviricetes, PLVs (new class 'Aquintoviricetes'), and virophages (renamed class 'Virophaviricetes') together with Adenoviridae (new class 'Pharingeaviricetes') in a preplasmiviricot subphylum 'Polisuviricotina' sister to a subphylum including Tectiliviricetes ('Prepoliviricotina').
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthias G Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
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4
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Krupovic M, Kuhn JH, Fischer MG, Koonin EV. Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins. Proc Natl Acad Sci U S A 2024; 121:e2405771121. [PMID: 38805295 PMCID: PMC11161782 DOI: 10.1073/pnas.2405771121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
The phylum Preplasmiviricota (kingdom Bamfordvirae, realm Varidnaviria) is a broad assemblage of diverse viruses with comparatively short double-stranded DNA genomes (<50 kbp) that produce icosahedral capsids built from double jelly-roll major capsid proteins. Preplasmiviricots infect hosts from all cellular domains, testifying to their ancient origin, and, in particular, are associated with six of the seven supergroups of eukaryotes. Preplasmiviricots comprise four major groups of viruses, namely, polintons, polinton-like viruses (PLVs), virophages, and adenovirids. We used protein structure modeling and analysis to show that protein-primed DNA polymerases (pPolBs) of polintons, virophages, and cytoplasmic linear plasmids encompass an N-terminal domain homologous to the terminal proteins (TPs) of prokaryotic PRD1-like tectivirids and eukaryotic adenovirids that are involved in protein-primed replication initiation, followed by a viral ovarian tumor-like cysteine deubiquitinylase (vOTU) domain. The vOTU domain is likely responsible for the cleavage of the TP from the large pPolB polypeptide and is inactivated in adenovirids, in which TP is a separate protein. Many PLVs and transpovirons encode a distinct derivative of polinton-like pPolB that retains the TP, vOTU, and pPolB polymerization palm domains but lacks the exonuclease domain and instead contains a superfamily 1 helicase domain. Analysis of the presence/absence and inactivation of the vOTU domains and replacement of pPolB with other DNA polymerases in eukaryotic preplasmiviricots enabled us to outline a complete scenario for their origin and evolution.
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Affiliation(s)
- Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, Paris75015, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, NIH, Fort Detrick, Frederick, MD21702
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg69120, Germany
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
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5
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van Vliet VJE, De Silva A, Mark BL, Kikkert M. Viral deubiquitinating proteases and the promising strategies of their inhibition. Virus Res 2024; 344:199368. [PMID: 38588924 PMCID: PMC11025011 DOI: 10.1016/j.virusres.2024.199368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Several viruses are now known to code for deubiquitinating proteases in their genomes. Ubiquitination is an essential post-translational modification of cellular substrates involved in many processes in the cell, including in innate immune signalling. This post-translational modification is regulated by the ubiquitin conjugation machinery, as well as various host deubiquitinating enzymes. The conjugation of ubiquitin chains to several innate immune related factors is often needed to induce downstream signalling, shaping the antiviral response. Viral deubiquitinating proteins, besides often having a primary function in the viral replication cycle by cleaving the viral polyprotein, are also able to cleave ubiquitin chains from such host substrates, in that way exerting a function in innate immune evasion. The presence of viral deubiquitinating enzymes has been firmly established for numerous animal-infecting viruses, such as some well-researched and clinically important nidoviruses, and their presence has now been confirmed in several plant viruses as well. Viral proteases in general have long been highlighted as promising drug targets, with a current focus on small molecule inhibitors. In this review, we will discuss the range of viral deubiquitinating proteases known to date, summarise the various avenues explored to inhibit such proteases and discuss novel strategies and models intended to inhibit and study these specific viral enzymes.
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Affiliation(s)
- Vera J E van Vliet
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands; The Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands.
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6
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Li M. Innate immune response against vector-borne bunyavirus infection and viral countermeasures. Front Cell Infect Microbiol 2024; 14:1365221. [PMID: 38711929 PMCID: PMC11070517 DOI: 10.3389/fcimb.2024.1365221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
Bunyaviruses are a large group of important viral pathogens that cause significant diseases in humans and animals worldwide. Bunyaviruses are enveloped, single-stranded, negative-sense RNA viruses that infect a wide range of hosts. Upon entry into host cells, the components of viruses are recognized by host innate immune system, leading to the activation of downstream signaling cascades to induce interferons (IFNs) and other proinflammatory cytokines. IFNs bind to their receptors and upregulate the expression of hundreds of interferon-stimulated genes (ISGs). Many ISGs have antiviral activities and confer an antiviral state to host cells. For efficient replication and spread, viruses have evolved different strategies to antagonize IFN-mediated restriction. Here, we discuss recent advances in our understanding of the interactions between bunyaviruses and host innate immune response.
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Affiliation(s)
- Minghua Li
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States
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7
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Penunuri G, Wang P, Corbett-Detig R, Russell SL. A Structural Proteome Screen Identifies Protein Mimicry in Host-Microbe Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588793. [PMID: 38645127 PMCID: PMC11030372 DOI: 10.1101/2024.04.10.588793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Host-microbe systems are evolutionary niches that produce coevolved biological interactions and are a key component of global health. However, these systems have historically been a difficult field of biological research due to their experimental intractability. Impactful advances in global health will be obtained by leveraging in silico screens to identify genes involved in mediating interspecific interactions. These predictions will progress our understanding of these systems and lay the groundwork for future in vitro and in vivo experiments and bioengineering projects. A driver of host-manipulation and intracellular survival utilized by host-associated microbes is molecular mimicry, a critical mechanism that can occur at any level from DNA to protein structures. We applied protein structure prediction and alignment tools to explore host-associated bacterial structural proteomes for examples of protein structure mimicry. By leveraging the Legionella pneumophila proteome and its many known structural mimics, we developed and validated a screen that can be applied to virtually any host-microbe system to uncover signals of protein mimicry. These mimics represent candidate proteins that mediate host interactions in microbial proteomes. We successfully applied this screen to other microbes with demonstrated effects on global health, Helicobacter pylori and Wolbachia , identifying protein mimic candidates in each proteome. We discuss the roles these candidates may play in important Wolbachia -induced phenotypes and show that Wobachia infection can partially rescue the loss of one of these factors. This work demonstrates how a genome-wide screen for candidates of host-manipulation and intracellular survival offers an opportunity to identify functionally important genes in host-microbe systems.
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8
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Wang Q, Wang L, Botchway BOA, Zhang Y, Huang M, Liu X. OTULIN Can Improve Spinal Cord Injury by the NF-κB and Wnt/β-Catenin Signaling Pathways. Mol Neurobiol 2024:10.1007/s12035-024-04134-3. [PMID: 38561559 DOI: 10.1007/s12035-024-04134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Spinal cord injury (SCI) is a significant health concern, as it presently has no effective treatment in the clinical setting. Inflammation is a key player in the pathophysiological process of SCI, with a number of studies evidencing that the inhibition of the NF-κB signaling pathway may impede the inflammatory response and improve SCI. OTULIN, as a de-ubiquitination enzyme, the most notable is its anti-inflammatory effect. OTULIN can inhibit the NF-κB signaling pathway to suppress the inflammatory reaction via de-ubiquitination. In addition, OTULIN may promote vascular regeneration through the Wnt/β-catenin pathway in the wake of SCI. In this review, we analyze the structure and physiological function of OTULIN, along with both NF-κB and Wnt/β-catenin signaling pathways. Furthermore, we examine the significant role of OTULIN in SCI through its impairment of the NF-κB signaling pathway, which could open the possibility of it being a novel interventional target for the condition.
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Affiliation(s)
- Qianhui Wang
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Lvxia Wang
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Benson O A Botchway
- Bupa Cromwell Hospital, London, SW5 0TU, UK
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus
| | - Yong Zhang
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Min Huang
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Xuehong Liu
- Department of Histology and Embryology, School of Medicine, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China.
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9
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Krupovic M, Kuhn JH, Fischer MG, Koonin EV. Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585575. [PMID: 38712159 PMCID: PMC11071308 DOI: 10.1101/2024.03.18.585575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The phylum Preplasmiviricota (kingdom Bamfordvirae, realm Varidnaviria) is a broad assemblage of diverse viruses with comparatively short double-stranded DNA genomes (<50 kbp) that produce icosahedral capsids built from double jelly-roll major capsid proteins. Preplasmiviricots infect hosts from all cellular domains, testifying to their ancient origin and, in particular, are associated with six of the seven supergroups of eukaryotes. Preplasmiviricots comprise four major groups of viruses, namely, polintons, polinton-like viruses (PLVs), virophages, and adenovirids. We employed protein structure modeling and analysis to show that protein-primed DNA polymerases (pPolBs) of polintons, virophages, and cytoplasmic linear plasmids encompass an N-terminal domain homologous to the terminal proteins (TPs) of prokaryotic PRD1-like tectivirids and eukaryotic adenovirids that are involved in protein-primed replication initiation, followed by a viral ovarian tumor-like cysteine deubiquitinylase (vOTU) domain. The vOTU domain is likely responsible for the cleavage of the TP from the large pPolB polypeptide and is inactivated in adenovirids, in which TP is a separate protein. Many PLVs and transpovirons encode a distinct derivative of polinton-like pPolB that retains the TP, vOTU and pPolB polymerization palm domains but lacks the exonuclease domain and instead contains a supefamily 1 helicase domain. Analysis of the presence/absence and inactivation of the vOTU domains, and replacement of pPolB with other DNA polymerases in eukaryotic preplasmiviricots enabled us to outline a complete scenario for their origin and evolution.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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10
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Su CM, Kim J, Tang J, Hung YF, Zuckermann FA, Husmann R, Roady P, Kim J, Lee YM, Yoo D. A clinically attenuated double-mutant of porcine reproductive and respiratory syndrome virus-2 that does not prompt overexpression of proinflammatory cytokines during co-infection with a secondary pathogen. PLoS Pathog 2024; 20:e1012128. [PMID: 38547254 PMCID: PMC11003694 DOI: 10.1371/journal.ppat.1012128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/09/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is known to suppress the type I interferon (IFNs-α/β) response during infection. PRRSV also activates the NF-κB signaling pathway, leading to the production of proinflammatory cytokines during infection. In swine farms, co-infections of PRRSV and other secondary bacterial pathogens are common and exacerbate the production of proinflammatory cytokines, contributing to the porcine respiratory disease complex (PRDC) which is clinically a severe disease. Previous studies identified the non-structural protein 1β (nsp1β) of PRRSV-2 as an IFN antagonist and the nucleocapsid (N) protein as the NF-κB activator. Further studies showed the leucine at position 126 (L126) of nsp1β as the essential residue for IFN suppression and the region spanning the nuclear localization signal (NLS) of N as the NF-κB activation domain. In the present study, we generated a double-mutant PRRSV-2 that contained the L126A mutation in the nsp1β gene and the NLS mutation (ΔNLS) in the N gene using reverse genetics. The immunological phenotype of this mutant PRRSV-2 was examined in porcine alveolar macrophages (PAMs) in vitro and in young pigs in vivo. In PAMs, the double-mutant virus did not suppress IFN-β expression but decreased the NF-κB-dependent inflammatory cytokine productions compared to those for wild-type PRRSV-2. Co-infection of PAMs with the mutant PRRSV-2 and Streptococcus suis (S. suis) also reduced the production of NF-κB-directed inflammatory cytokines. To further examine the cytokine profiles and the disease severity by the mutant virus in natural host animals, 6 groups of pigs, 7 animals per group, were used for co-infection with the mutant PRRSV-2 and S. suis. The double-mutant PRRSV-2 was clinically attenuated, and the expressions of proinflammatory cytokines and chemokines were significantly reduced in pigs after bacterial co-infection. Compared to the wild-type PRRSV-2 and S. suis co-infection control, pigs coinfected with the double-mutant PRRSV-2 exhibited milder clinical signs, lower titers and shorter duration of viremia, and lower expression of proinflammatory cytokines. In conclusion, our study demonstrates that genetic modification of the type I IFN suppression and NF-κB activation functions of PRRSV-2 may allow us to design a novel vaccine candidate to alleviate the clinical severity of PRRS-2 and PRDC during bacterial co-infection.
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Affiliation(s)
- Chia-Ming Su
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jineui Kim
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Junyu Tang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yu Fan Hung
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Federico A. Zuckermann
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Robert Husmann
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Patrick Roady
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jiyoun Kim
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Dongwan Yoo
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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11
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Bastidas RJ, Kędzior M, Davidson RK, Walsh SC, Dolat L, Sixt BS, Pruneda JN, Coers J, Valdivia RH. The acetylase activity of Cdu1 regulates bacterial exit from infected cells by protecting Chlamydia effectors from degradation. eLife 2024; 12:RP87386. [PMID: 38358795 PMCID: PMC10942603 DOI: 10.7554/elife.87386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Many cellular processes are regulated by ubiquitin-mediated proteasomal degradation. Pathogens can regulate eukaryotic proteolysis through the delivery of proteins with de-ubiquitinating (DUB) activities. The obligate intracellular pathogen Chlamydia trachomatis secretes Cdu1 (ChlaDUB1), a dual deubiquitinase and Lys-acetyltransferase, that promotes Golgi remodeling and survival of infected host cells presumably by regulating the ubiquitination of host and bacterial proteins. Here, we determined that Cdu1's acetylase but not its DUB activity is important to protect Cdu1 from ubiquitin-mediated degradation. We further identified three C. trachomatis proteins on the pathogen-containing vacuole (InaC, IpaM, and CTL0480) that required Cdu1's acetylase activity for protection from degradation and determined that Cdu1 and these Cdu1-protected proteins are required for optimal egress of Chlamydia from host cells. These findings highlight a non-canonical mechanism of pathogen-mediated protection of virulence factors from degradation after their delivery into host cells and the coordinated regulation of secreted effector proteins.
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Affiliation(s)
- Robert J Bastidas
- Department of Integrative Immunobiology, Duke UniversityDurhamUnited States
| | - Mateusz Kędzior
- Department of Integrative Immunobiology, Duke UniversityDurhamUnited States
| | - Robert K Davidson
- Department of Molecular Genetics and Microbiology, Duke UniversityDukeUnited States
| | - Stephen C Walsh
- Department of Molecular Genetics and Microbiology, Duke UniversityDukeUnited States
| | - Lee Dolat
- Department of Integrative Immunobiology, Duke UniversityDurhamUnited States
| | - Barbara S Sixt
- Deparment of Molecular Biology, Umeå UniversityUmeåSweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå UniversityUmeåSweden
- Umeå Centre for Microbial Research (UCMR), Umeå UniversityUmeåSweden
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Jorn Coers
- Department of Integrative Immunobiology, Duke UniversityDurhamUnited States
- Department of Molecular Genetics and Microbiology, Duke UniversityDukeUnited States
| | - Raphael H Valdivia
- Department of Integrative Immunobiology, Duke UniversityDurhamUnited States
- Department of Molecular Genetics and Microbiology, Duke UniversityDukeUnited States
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12
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Xia J, Yang Y, Chen X, Song K, Ma G, Yang Y, Yao C, Du A. An apicoplast-localized deubiquitinase contributes to the cell growth and apicoplast homeostasis of Toxoplasma gondii. Vet Res 2024; 55:10. [PMID: 38233899 PMCID: PMC10795397 DOI: 10.1186/s13567-023-01261-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024] Open
Abstract
Toxoplasma gondii is among the most important parasites worldwide. The apicoplast is a unique organelle shared by all Apicomplexan protozoa. Increasing lines of evidence suggest that the apicoplast possesses its own ubiquitination system. Deubiquitination is a crucial step executed by deubiquitinase (DUB) during protein ubiquitination. While multiple components of ubiquitination have been identified in T. gondii, the deubiquitinases involved remain unknown. The aim of the current study was to delineate the localization of TgOTU7 and elucidate its functions. TgOTU7 was specifically localized at the apicoplast, and its expression was largely regulated during the cell cycle. Additionally, TgOTU7 efficiently breaks down ubiquitin chains, exhibits linkage-nonspecific deubiquitinating activity and is critical for the lytic cycle and apicoplast biogenesis, similar to the transcription of the apicoplast genome and the nuclear genes encoding apicoplast-targeted proteins. Taken together, the results indicate that the newly described deubiquitinase TgOTU7 specifically localizes to the apicoplast and affects the cell growth and apicoplast homeostasis of T. gondii.
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Affiliation(s)
- Jie Xia
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yimin Yang
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xueqiu Chen
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kaiyue Song
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Guangxu Ma
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yi Yang
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, Saint Kitts and Nevis.
| | - Aifang Du
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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13
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Bailey-Elkin BA, Knaap RCM, De Silva A, Boekhoud IM, Mous S, van Vught N, Khajehpour M, van den Born E, Kikkert M, Mark BL. Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis. PLoS Pathog 2023; 19:e1011872. [PMID: 38096325 PMCID: PMC10754444 DOI: 10.1371/journal.ppat.1011872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/28/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Deubiquitination of cellular substrates by viral proteases is a mechanism used to interfere with host cellular signaling processes, shared between members of the coronavirus- and arterivirus families. In the case of Arteriviruses, deubiquitinating and polyprotein processing activities are accomplished by the virus-encoded papain-like protease 2 (PLP2). Several studies have implicated the deubiquitinating activity of the porcine reproductive and respiratory syndrome virus (PRRSV) PLP2 in the downregulation of cellular interferon production, however to date, the only arterivirus PLP2 structure described is that of equine arteritis virus (EAV), a distantly related virus. Here we describe the first crystal structure of the PRRSV PLP2 domain both in the presence and absence of its ubiquitin substrate, which reveals unique structural differences in this viral domain compared to PLP2 from EAV. To probe the role of PRRSV PLP2 deubiquitinating activity in host immune evasion, we selectively removed this activity from the domain by mutagenesis and found that the viral domain could no longer downregulate cellular interferon production. Interestingly, unlike EAV, and also unlike the situation for MERS-CoV, we found that recombinant PRRSV carrying PLP2 DUB-specific mutations faces significant selective pressure to revert to wild-type virus in MARC-145 cells, suggesting that the PLP2 DUB activity, which in PRRSV is present as three different versions of viral protein nsp2 expressed during infection, is critically important for PRRSV replication.
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Affiliation(s)
- Ben A. Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert C. M. Knaap
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ilse M. Boekhoud
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Mous
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Niek van Vught
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Mazdak Khajehpour
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Brian L. Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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14
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Rawal G, Almeida MN, Gauger PC, Zimmerman JJ, Ye F, Rademacher CJ, Armenta Leyva B, Munguia-Ramirez B, Tarasiuk G, Schumacher LL, Aljets EK, Thomas JT, Zhu JH, Trexel JB, Zhang J. In Vivo and In Vitro Characterization of the Recently Emergent PRRSV 1-4-4 L1C Variant (L1C.5) in Comparison with Other PRRSV-2 Lineage 1 Isolates. Viruses 2023; 15:2233. [PMID: 38005910 PMCID: PMC10674456 DOI: 10.3390/v15112233] [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: 10/04/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The recently emerged PRRSV 1-4-4 L1C variant (L1C.5) was in vivo and in vitro characterized in this study in comparison with three other contemporary 1-4-4 isolates (L1C.1, L1A, and L1H) and one 1-7-4 L1A isolate. Seventy-two 3-week-old PRRSV-naive pigs were divided into six groups with twelve pigs/group. Forty-eight pigs (eight/group) were for inoculation, and 24 pigs (four/group) served as contact pigs. Pigs in pen A of each room were inoculated with the corresponding virus or negative media. At two days post inoculation (DPI), contact pigs were added to pen B adjacent to pen A in each room. Pigs were necropsied at 10 and 28 DPI. Compared to other virus-inoculated groups, the L1C.5-inoculated pigs exhibited more severe anorexia and lethargy, higher mortality, a higher fraction of pigs with fever (>40 °C), higher average temperature at several DPIs, and higher viremia levels at 2 DPI. A higher percentage of the contact pigs in the L1C.5 group became viremic at two days post contact, implying the higher transmissibility of this virus strain. It was also found that some PRRSV isolates caused brain infection in inoculation pigs and/or contact pigs. The complete genome sequences and growth characteristics in ZMAC cells of five PRRSV-2 isolates were further compared. Collectively, this study confirms that the PRRSV 1-4-4 L1C variant (L1C.5) is highly virulent with potential higher transmissibility, but the genetic determinants of virulence remain to be elucidated.
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Affiliation(s)
- Gaurav Rawal
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Marcelo N. Almeida
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Phillip C. Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Jeffrey J. Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Fangshu Ye
- Department of Statistics, Iowa State University, Ames, IA 50011, USA;
| | - Christopher J. Rademacher
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Betsy Armenta Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Berenice Munguia-Ramirez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Grzegorz Tarasiuk
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Loni L. Schumacher
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Ethan K. Aljets
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Joseph T. Thomas
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Jin-Hui Zhu
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Jolie B. Trexel
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (M.N.A.); (P.C.G.); (J.J.Z.); (C.J.R.); (B.A.L.); (B.M.-R.); (G.T.); (L.L.S.); (E.K.A.); (J.T.T.); (J.-H.Z.); (J.B.T.)
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15
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Bastidas RJ, Kędzior M, Davidson RK, Walsh SC, Dolat L, Sixt BS, Pruneda JN, Coers J, Valdivia RH. The acetylase activity of Cdu1 regulates bacterial exit from infected cells by protecting Chlamydia effectors from degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530337. [PMID: 36909574 PMCID: PMC10002621 DOI: 10.1101/2023.02.28.530337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Many cellular processes are regulated by ubiquitin-mediated proteasomal degradation. Pathogens can regulate eukaryotic proteolysis through the delivery of proteins with de-ubiquitinating (DUB) activities. The obligate intracellular pathogen Chlamydia trachomatis secretes Cdu1 (ChlaDUB1), a dual deubiquitinase and Lys-acetyltransferase, that promotes Golgi remodeling and survival of infected host cells presumably by regulating the ubiquitination of host and bacterial proteins. Here we determined that Cdu1's acetylase but not its DUB activity is important to protect Cdu1 from ubiquitin-mediated degradation. We further identified three C. trachomatis proteins on the pathogen-containing vacuole (InaC, IpaM, and CTL0480) that required Cdu1's acetylase activity for protection from degradation and determined that Cdu1 and these Cdu1-protected proteins are required for optimal egress of Chlamydia from host cells. These findings highlight a non-canonical mechanism of pathogen-mediated protection of virulence factors from degradation after their delivery into host cells and the coordinated regulation of secreted effector proteins.
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Affiliation(s)
- Robert J. Bastidas
- Department of Integrative Immunobiology, Duke University, Durham, N.C 27708, USA
| | - Mateusz Kędzior
- Department of Integrative Immunobiology, Duke University, Durham, N.C 27708, USA
| | - Robert K. Davidson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, N.C 27708, USA
| | - Stephen C. Walsh
- Department of Molecular Genetics and Microbiology, Duke University, Durham, N.C 27708, USA
| | - Lee Dolat
- Department of Integrative Immunobiology, Duke University, Durham, N.C 27708, USA
| | - Barbara S. Sixt
- Deparment of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jörn Coers
- Department of Integrative Immunobiology, Duke University, Durham, N.C 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, N.C 27708, USA
| | - Raphael H. Valdivia
- Department of Integrative Immunobiology, Duke University, Durham, N.C 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, N.C 27708, USA
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16
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Klonisch T, Logue SE, Hombach-Klonisch S, Vriend J. DUBing Primary Tumors of the Central Nervous System: Regulatory Roles of Deubiquitinases. Biomolecules 2023; 13:1503. [PMID: 37892185 PMCID: PMC10605193 DOI: 10.3390/biom13101503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The ubiquitin proteasome system (UPS) utilizes an orchestrated enzymatic cascade of E1, E2, and E3 ligases to add single or multiple ubiquitin-like molecules as post-translational modification (PTM) to proteins. Ubiquitination can alter protein functions and/or mark ubiquitinated proteins for proteasomal degradation but deubiquitinases (DUBs) can reverse protein ubiquitination. While the importance of DUBs as regulatory factors in the UPS is undisputed, many questions remain on DUB selectivity for protein targeting, their mechanism of action, and the impact of DUBs on the regulation of diverse biological processes. Furthermore, little is known about the expression and role of DUBs in tumors of the human central nervous system (CNS). In this comprehensive review, we have used publicly available transcriptional datasets to determine the gene expression profiles of 99 deubiquitinases (DUBs) from five major DUB families in seven primary pediatric and adult CNS tumor entities. Our analysis identified selected DUBs as potential new functional players and biomarkers with prognostic value in specific subtypes of primary CNS tumors. Collectively, our analysis highlights an emerging role for DUBs in regulating CNS tumor cell biology and offers a rationale for future therapeutic targeting of DUBs in CNS tumors.
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Affiliation(s)
- Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Susan E. Logue
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Jerry Vriend
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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17
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Xu Q, He L, Zhang S, Di X, Jiang H. Deubiquitinase OTUD3: a double-edged sword in immunity and disease. Front Cell Dev Biol 2023; 11:1237530. [PMID: 37829187 PMCID: PMC10566363 DOI: 10.3389/fcell.2023.1237530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/28/2023] [Indexed: 10/14/2023] Open
Abstract
Deubiquitination is an important form of post-translational modification that regulates protein homeostasis. Ovarian tumor domain-containing proteins (OTUDs) subfamily member OTUD3 was identified as a deubiquitinating enzyme involved in the regulation of various physiological processes such as immunity and inflammation. Disturbances in these physiological processes trigger diseases in humans and animals, such as cancer, neurodegenerative diseases, diabetes, mastitis, etc. OTUD3 is aberrantly expressed in tumors and is a double-edged sword, exerting tumor-promoting or anti-tumor effects in different types of tumors affecting cancer cell proliferation, metastasis, and metabolism. OTUD3 is regulated at the transcriptional level by a number of MicroRNAs, such as miR-520h, miR-32, and miR101-3p. In addition, OTUD3 is regulated by a number of post-translational modifications, such as acetylation and ubiquitination. Therefore, understanding the regulatory mechanisms of OTUD3 expression can help provide insight into its function in human immunity and disease, offering the possibility of its use as a therapeutic target to diagnose or treat disease.
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Affiliation(s)
- Qiao Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lan He
- School of Biomedical Science, Hunan University, Changsha, Hunan, China
| | - Shubing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaotang Di
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hao Jiang
- Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, Hunan, China
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18
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Harumoto T. Self-stabilization mechanism encoded by a bacterial toxin facilitates reproductive parasitism. Curr Biol 2023; 33:4021-4029.e6. [PMID: 37673069 DOI: 10.1016/j.cub.2023.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/30/2023] [Accepted: 08/10/2023] [Indexed: 09/08/2023]
Abstract
A wide variety of maternally transmitted endosymbionts in insects are associated with reproductive parasitism, whereby they interfere with host reproduction to increase the ratio of infected females and spread within populations.1,2 Recent successes in identifying bacterial factors responsible for reproductive parasitism3,4,5,6,7 as well as further omics approaches8,9,10,11,12 have highlighted the common appearance of deubiquitinase domains, although their biological roles-in particular, how they link to distinct manipulative phenotypes-remain poorly defined. Spiroplasma poulsonii is a helical and motile bacterial endosymbiont of Drosophila,13,14 which selectively kills male progeny with a male-killing toxin Spaid (S. poulsonii androcidin), which encodes an ovarian tumor (OTU) deubiquitinase domain.6 Artificial expression of Spaid in flies reproduces male-killing-associated pathologies that include abnormal apoptosis and neural defects during embryogenesis6,15,16,17,18,19; moreover, it highly accumulates on the dosage-compensated male X chromosome,20 congruent with cellular defects such as the DNA damage/chromatin bridge breakage specifically induced upon that chromosome.6,21,22,23 Here, I show that without the function of OTU, Spaid is polyubiquitinated and degraded through the host ubiquitin-proteasome pathway, leading to the attenuation of male-killing activity as shown previously.6 Furthermore, I find that Spaid utilizes its OTU domain to deubiquitinate itself in an intermolecular manner. Collectively, the deubiquitinase domain of Spaid serves as a self-stabilization mechanism to facilitate male killing in flies, optimizing a molecular strategy of endosymbionts that enables the efficient manipulation of the host at a low energetic cost.
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Affiliation(s)
- Toshiyuki Harumoto
- Hakubi Center for Advanced Research, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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19
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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20
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Ozhelvaci F, Steczkiewicz K. Identification and Classification of Papain-like Cysteine Proteinases. J Biol Chem 2023:104801. [PMID: 37164157 DOI: 10.1016/j.jbc.2023.104801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Papain-like cysteine peptidases form a big and highly diverse superfamily of proteins involved in many important biological functions, such as protein turnover, deubiquitination, tissue remodeling, blood clotting, virulence, defense, and cell wall remodeling. High sequence and structure diversity observed within these proteins hinders their comprehensive classification as well as the identification of new representatives. Moreover, in general protein databases, many families already classified as papain-like lack details regarding their mechanism of action or biological function. Here, we use transitive remote homology searches and 3D modeling to newly classify 21 families to the papain-like cysteine peptidase superfamily. We attempt to predict their biological function, and provide structural chacterization of 89 protein clusters defined based on sequence similarity altogether spanning 106 papain-like families. Moreover, we systematically discuss observed diversity in sequences, structures, and catalytic sites. Eventually, we expand the list of human papain-related proteins by seven representatives, including dopamine receptor-interacting protein (DRIP1) as potential deubiquitinase, and centriole duplication regulating CEP76 as retaining catalytically active peptidase-like domain. The presented results not only provide structure-based rationales to already existing peptidase databases but also may inspire further experimental research focused on peptidase-related biological processes.
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Affiliation(s)
- Fatih Ozhelvaci
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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21
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Radjacommare R, Lin SY, Usharani R, Lin WD, Jauh GY, Schmidt W, Fu H. The Arabidopsis Deubiquitylase OTU5 Suppresses Flowering by Histone Modification-Mediated Activation of the Major Flowering Repressors FLC, MAF4, and MAF5. Int J Mol Sci 2023; 24:ijms24076176. [PMID: 37047144 PMCID: PMC10093928 DOI: 10.3390/ijms24076176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Distinct phylogeny and substrate specificities suggest that 12 Arabidopsis Ovarian Tumor domain-containing (OTU) deubiquitinases participate in conserved or plant-specific functions. The otu5-1 null mutant displayed a pleiotropic phenotype, including early flowering, mimicking that of mutants harboring defects in subunits (e.g., ARP6) of the SWR1 complex (SWR1c) involved in histone H2A.Z deposition. Transcriptome and RT-qPCR analyses suggest that downregulated FLC and MAF4-5 are responsible for the early flowering of otu5-1. qChIP analyses revealed a reduction and increase in activating and repressive histone marks, respectively, on FLC and MAF4-5 in otu5-1. Subcellular fractionation, GFP-fusion expression, and MNase treatment of chromatin showed that OTU5 is nucleus-enriched and chromatin-associated. Moreover, OTU5 was found to be associated with FLC and MAF4-5. The OTU5-associated protein complex(es) appears to be distinct from SWR1c, as the molecular weights of OTU5 complex(es) were unaltered in arp6-1 plants. Furthermore, the otu5-1 arp6-1 double mutant exhibited synergistic phenotypes, and H2A.Z levels on FLC/MAF4-5 were reduced in arp6-1 but not otu5-1. Our results support the proposition that Arabidopsis OTU5, acting independently of SWR1c, suppresses flowering by activating FLC and MAF4-5 through histone modification. Double-mutant analyses also indicate that OTU5 acts independently of the HUB1-mediated pathway, but it is partially required for FLC-mediated flowering suppression in autonomous pathway mutants and FRIGIDA-Col.
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Luo R, Yang K, Xiao W. Plant deubiquitinases: from structure and activity to biological functions. PLANT CELL REPORTS 2023; 42:469-486. [PMID: 36567335 DOI: 10.1007/s00299-022-02962-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.
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Affiliation(s)
- Runbang Luo
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Kun Yang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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Job F, Mai C, Villavicencio-Lorini P, Herfurth J, Neuhaus H, Hoffmann K, Pfirrmann T, Hollemann T. OTUD3: A Lys6 and Lys63 specific deubiquitinase in early vertebrate development. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194901. [PMID: 36503125 DOI: 10.1016/j.bbagrm.2022.194901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Ubiquitination and deubiquitylation regulate essential cellular processes and involve hundreds of sequentially acting enzymes, many of which are barely understood. OTUD3 is an evolutionarily highly conserved deubiquitinase involved in many aspects of cellular homeostasis. However, its biochemical properties and physiological role during development are poorly understood. Here, we report on the expression of OTUD3 in human tissue samples where it appears prominently in those of neuronal origin. In cells, OTUD3 is present in the cytoplasm where it can bind to microtubules. Interestingly, we found that OTUD3 cleaves preferentially at K6 and K63, i.e., poly-ubiquitin linkages that are not primarily involved in protein degradation. We employed Xenopus embryos to study the consequences of suppressing otud3 function during early neural development. We found that Otud3 deficiency led to impaired formation of cranial and particularly of cranial neural crest-derived structures as well as movement defects. Thus, OTUD3 appears as a neuronally enriched deubiquitinase that is involved in the proper development of the neural system.
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Affiliation(s)
- Florian Job
- Martin-Luther-University Halle-Wittenberg, Institute for Physiological Chemistry, 06114 Halle, Germany; Martin-Luther-University Halle-Wittenberg, Institute of Human Genetics, 06114 Halle, Germany
| | - Carolin Mai
- Martin-Luther-University Halle-Wittenberg, Institute for Physiological Chemistry, 06114 Halle, Germany
| | | | - Juliane Herfurth
- Martin-Luther-University Halle-Wittenberg, Institute for Physiological Chemistry, 06114 Halle, Germany
| | - Herbert Neuhaus
- Martin-Luther-University Halle-Wittenberg, Institute for Physiological Chemistry, 06114 Halle, Germany
| | - Katrin Hoffmann
- Martin-Luther-University Halle-Wittenberg, Institute of Human Genetics, 06114 Halle, Germany
| | - Thorsten Pfirrmann
- Martin-Luther-University Halle-Wittenberg, Institute for Physiological Chemistry, 06114 Halle, Germany; Department of Medicine, Health and Medical University, 14471 Potsdam, Germany
| | - Thomas Hollemann
- Martin-Luther-University Halle-Wittenberg, Institute for Physiological Chemistry, 06114 Halle, Germany.
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Oikawa D, Shimizu K, Tokunaga F. Pleiotropic Roles of a KEAP1-Associated Deubiquitinase, OTUD1. Antioxidants (Basel) 2023; 12:antiox12020350. [PMID: 36829909 PMCID: PMC9952104 DOI: 10.3390/antiox12020350] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Protein ubiquitination, which is catalyzed by ubiquitin-activating enzymes, ubiquitin-conjugating enzymes, and ubiquitin ligases, is a crucial post-translational modification to regulate numerous cellular functions in a spatio-temporal-specific manner. The human genome encodes ~100 deubiquitinating enzymes (DUBs), which antagonistically regulate the ubiquitin system. OTUD1, an ovarian tumor protease (OTU) family DUB, has an N-terminal-disordered alanine-, proline-, glycine-rich region (APGR), a catalytic OTU domain, and a ubiquitin-interacting motif (UIM). OTUD1 preferentially hydrolyzes lysine-63-linked ubiquitin chains in vitro; however, recent studies indicate that OTUD1 cleaves various ubiquitin linkages, and is involved in the regulation of multiple cellular functions. Thus, OTUD1 predominantly functions as a tumor suppressor by targeting p53, SMAD7, PTEN, AKT, IREB2, YAP, MCL1, and AIF. Furthermore, OTUD1 regulates antiviral signaling, innate and acquired immune responses, and cell death pathways. Similar to Nrf2, OTUD1 contains a KEAP1-binding ETGE motif in its APGR and regulates the reactive oxygen species (ROS)-mediated oxidative stress response and cell death. Importantly, in addition to its association with various cancers, including multiple myeloma, OTUD1 is involved in acute graft-versus-host disease and autoimmune diseases such as systemic lupus erythematosus, rheumatoid arthritis, and ulcerative colitis. Thus, OTUD1 is an important DUB as a therapeutic target for a variety of diseases.
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Zhang X, Liang Y, Zheng K, Wang Z, Dong Y, Liu Y, Ren L, Wang H, Han Y, McMinn A, Sung YY, Mok WJ, Wong LL, He J, Wang M. Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms. Front Microbiol 2023; 14:1161265. [PMID: 37213492 PMCID: PMC10196503 DOI: 10.3389/fmicb.2023.1161265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/05/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed. Methods Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method. Results and Discussion Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage-host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.
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Affiliation(s)
- Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Antarctic Great Wall Ecology National Observation and Research Station, MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- *Correspondence: Yantao Liang, ; Jianfeng He, ; Min Wang,
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziyue Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ying Han
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Jianfeng He
- Antarctic Great Wall Ecology National Observation and Research Station, MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
- *Correspondence: Yantao Liang, ; Jianfeng He, ; Min Wang,
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Key Lab of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Yantao Liang, ; Jianfeng He, ; Min Wang,
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Kumar P, Kumar P, Mandal D, Velayutham R. The emerging role of Deubiquitinases (DUBs) in parasites: A foresight review. Front Cell Infect Microbiol 2022; 12:985178. [PMID: 36237424 PMCID: PMC9552668 DOI: 10.3389/fcimb.2022.985178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Before the discovery of the proteasome complex, the lysosomes with acidic proteases and caspases in apoptotic pathways were thought to be the only pathways for the degradation of damaged, unfolded, and aged proteins. However, the discovery of 26S and 20S proteasome complexes in eukaryotes and microbes, respectively, established that the degradation of most proteins is a highly regulated ATP-dependent pathway that is significantly conserved across each domain of life. The proteasome is part of the ubiquitin-proteasome system (UPS), where the covalent tagging of a small molecule called ubiquitin (Ub) on the proteins marks its proteasomal degradation. The type and chain length of ubiquitination further determine whether a protein is designated for further roles in multi-cellular processes like DNA repair, trafficking, signal transduction, etc., or whether it will be degraded by the proteasome to recycle the peptides and amino acids. Deubiquitination, on the contrary, is the removal of ubiquitin from its substrate molecule or the conversion of polyubiquitin chains into monoubiquitin as a precursor to ubiquitin. Therefore, deubiquitylating enzymes (DUBs) can maintain the dynamic state of cellular ubiquitination by releasing conjugated ubiquitin from proteins and controlling many cellular pathways that are essential for their survival. Many DUBs are well characterized in the human system with potential drug targets in different cancers. Although, proteasome complex and UPS of parasites, like plasmodium and leishmania, were recently coined as multi-stage drug targets the role of DUBs is completely unexplored even though structural domains and functions of many of these parasite DUBs are conserved having high similarity even with its eukaryotic counterpart. This review summarizes the identification & characterization of different parasite DUBs based on in silico and a few functional studies among different phylogenetic classes of parasites including Metazoan (Schistosoma, Trichinella), Apicomplexan protozoans (Plasmodium, Toxoplasma, Eimeria, Cryptosporidium), Kinetoplastidie (Leishmania, Trypanosoma) and Microsporidia (Nosema). The identification of different homologs of parasite DUBs with structurally similar domains with eukaryotes, and the role of these DUBs alone or in combination with the 20S proteosome complex in regulating the parasite survival/death is further elaborated. We propose that small molecules/inhibitors of human DUBs can be potential antiparasitic agents due to their significant structural conservation.
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Affiliation(s)
- Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Pawan Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
- *Correspondence: Ravichandiran Velayutham, ; Debabrata Mandal,
| | - Ravichandiran Velayutham
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
- National Institute of Pharmaceutical Education and Research, Kolkata, India
- *Correspondence: Ravichandiran Velayutham, ; Debabrata Mandal,
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Cai T, Huang J, Ma X, Hu S, Zhu L, Zhu J, Feng Z. Case Report: Identification of Two Variants of ALG13 in Families With or Without Seizure and Binocular Strabismus: Phenotypic Spectrum Analysis. Front Genet 2022; 13:892940. [PMID: 35899201 PMCID: PMC9310169 DOI: 10.3389/fgene.2022.892940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Genetic causes in most affected children with intellectual disability and/or development delay remain unknown. Methods: To identify potential variants responsible for these disorders, we recruited 161 affected families and performed whole-exome sequencing and associated bioinformatics analysis. Results: In the present study, we report the identification of variants in the ALG13 gene in two of the families. In family 1, a known pathogenic missense variant (c.23T > C; p.V8A) of ALG13 was identified in a boy and his mother. In family 2, a novel missense variant (c.862C > G; p.L288V) of the same gene was identified in the affected boy and his phenotypically normal mother. Genotype-phenotype correlation analysis by comparing reported 28 different variants (HGMD) showed that three major phenotypes, including various seizures/epilepsy, intellectual disability, and development delay (such as growth, speech, motor, etc.), are present in most affected individuals. However, other phenotypes, such as strabismus and absence of seizure in our second patient, are not reported if any, which may represent a unique case of X-linked recessive nonsyndromic disorder caused by a mutation in ALG13. Conclusion: We identified two missense variants in ALG13 in a cohort of 161 families with affected individuals diagnosed as intellectual disability and/or development delay. A novel c.862C > G mutation may represent a case of X-linked recessive.
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Affiliation(s)
- Tao Cai
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Experimental Medicine Section, National Institutes of Health/National Institute of Dental and Craniofacial Research, Bethesda, MD, United States,*Correspondence: Tao Cai, ; Zhichun Feng,
| | - Jieting Huang
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Xiuwei Ma
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Siqi Hu
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,The National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
| | - Lina Zhu
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Jinwen Zhu
- Angen Gene Medicine Technology, Beijing, China
| | - Zhichun Feng
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China,The National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China,*Correspondence: Tao Cai, ; Zhichun Feng,
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28
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Cai X, Zhou Z, Zhu J, Liu X, Ouyang G, Wang J, Li Z, Li X, Zha H, Zhu C, Rong F, Tang J, Liao Q, Chen X, Xiao W. Opposing effects of deubiquitinase OTUD3 in innate immunity against RNA and DNA viruses. Cell Rep 2022; 39:110920. [PMID: 35675783 DOI: 10.1016/j.celrep.2022.110920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/29/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022] Open
Abstract
Retinoic acid-inducible-I (RIG-I), melanoma differentiation-associated gene 5 (MDA5), and cyclic GMP-AMP synthase (cGAS) genes encode essential cytosolic receptors mediating antiviral immunity against viruses. Here, we show that OTUD3 has opposing role in response to RNA and DNA virus infection by removing distinct types of RIG-I/MDA5 and cGAS polyubiquitination. OTUD3 binds to RIG-I and MDA5 and removes K63-linked ubiquitination. This serves to reduce the binding of RIG-I and MDA5 to viral RNA and the downstream adaptor MAVS, leading to the suppression of the RNA virus-triggered innate antiviral responses. Meanwhile, OTUD3 associates with cGAS and targets at Lys279 to deubiquitinate K48-linked ubiquitination, resulting in the enhancement of cGAS protein stability and DNA-binding ability. As a result, Otud3-deficient mice and zebrafish are more resistant to RNA virus infection but are more susceptible to DNA virus infection. These findings demonstrate that OTUD3 limits RNA virus-triggered innate immunity but promotes DNA virus-triggered innate immunity.
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Affiliation(s)
- Xiaolian Cai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P. R. China
| | - Ziwen Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Junji Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xing Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P. R. China
| | - Gang Ouyang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P. R. China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P. R. China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiong Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Huangyuan Zha
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China
| | - Chunchun Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fangjing Rong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jinghua Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qian Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaoyun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wuhan Xiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P. R. China; Hubei Hongshan Laboratory, Wuhan 430070, P. R. China.
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Soh SM, Kim YJ, Kim HH, Lee HR. Modulation of Ubiquitin Signaling in Innate Immune Response by Herpesviruses. Int J Mol Sci 2022; 23:ijms23010492. [PMID: 35008917 PMCID: PMC8745310 DOI: 10.3390/ijms23010492] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/16/2022] Open
Abstract
The ubiquitin proteasome system (UPS) is a protein degradation machinery that is crucial for cellular homeostasis in eukaryotes. Therefore, it is not surprising that the UPS coordinates almost all host cellular processes, including host-pathogen interactions. This protein degradation machinery acts predominantly by tagging substrate proteins designated for degradation with a ubiquitin molecule. These ubiquitin tags have been involved at various steps of the innate immune response. Hence, herpesviruses have evolved ways to antagonize the host defense mechanisms by targeting UPS components such as ubiquitin E3 ligases and deubiquitinases (DUBs) that establish a productive infection. This review delineates how herpesviruses usurp the critical roles of ubiquitin E3 ligases and DUBs in innate immune response to escape host-antiviral immune response, with particular focus on retinoic acid-inducible gene I (RIG-I)-like receptors (RLR), cyclic-GMP-AMP (cGAMP) synthase (cGAS), stimulator of interferon (IFN) genes (STING) pathways, and inflammasome signaling.
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Affiliation(s)
- Sandrine-M. Soh
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong 30019, Korea; (S.-M.S.); (Y.-J.K.); (H.-H.K.)
| | - Yeong-Jun Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong 30019, Korea; (S.-M.S.); (Y.-J.K.); (H.-H.K.)
| | - Hong-Hee Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong 30019, Korea; (S.-M.S.); (Y.-J.K.); (H.-H.K.)
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong 30019, Korea; (S.-M.S.); (Y.-J.K.); (H.-H.K.)
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 136-701, Korea
- Correspondence: ; Tel.: +82-44-860-1831
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Schoeffler AJ, Helgason E, Popovych N, Dueber EC. Diagnosing and mitigating method-based avidity artifacts that confound polyubiquitin-binding assays. BIOPHYSICAL REPORTS 2021; 1:100033. [PMID: 36425458 PMCID: PMC9680732 DOI: 10.1016/j.bpr.2021.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/09/2021] [Indexed: 06/16/2023]
Abstract
Polyubiquitination is a complex form of posttranslational modification responsible for the control of numerous cellular processes. Many ubiquitin-binding proteins recognize distinct polyubiquitin chain types, and these associations help drive ubiquitin-signaling pathways. There is considerable interest in understanding the specificity of ubiquitin-binding proteins; however, because of the multivalent nature of polyubiquitin, affinity measurements of these interactions that rely on affixing ubiquitin-binding proteins to a surface can display artifactual, method-dependent avidity, or "bridging." This artifact, which is distinct from biologically relevant, avid interactions with polyubiquitin, is commonplace in such polyubiquitin-binding measurements and can lead to dramatic overestimations of binding affinities for particular chain types, and thus, incorrect conclusions about specificity. Here, we use surface-based measurements of ubiquitin binding in three model systems to illustrate bridging and lay out practical ways of identifying and mitigating it. Specifically, we describe a simple fitting model that enables researchers to diagnose the severity of bridging artifacts, determine whether they can be minimized, and more accurately evaluate polyubiquitin-binding specificity.
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Affiliation(s)
- Allyn J. Schoeffler
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Elizabeth Helgason
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Nataliya Popovych
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Erin C. Dueber
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
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Jiang DJ, Hao XH, Zhang J, Tang H, Wang F. Reducing expression of TaOTUB1s decreases tiller number in wheat. PLANT SIGNALING & BEHAVIOR 2021; 16:2018217. [PMID: 34968411 PMCID: PMC9208779 DOI: 10.1080/15592324.2021.2018217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Tiller number is an important agronomic trait that affects crop yield. The roles of OTUB1 in regulating tiller numbers in rice have been reported. However, the roles of OTUB1 in wheat remain elusive. In this study, TaOTUB1s were identified in wheat. TaOTUB1 proteins were localized in the nucleus and cytoplasm. Compared with wild-type Fielder, TaOTUB1-RNAi transgenic wheat plants had fewer tillers. Similar to OTUB1 in rice, the yeast double hybrid indicated that the TaOTUB1-A protein could interact with TaSPL17 and TaUBC13 proteins. The results of quantitative real-time polymerase chain reaction revealed that the expression levels of TaOTUB1s decreased while those of TaSPL17 significantly improved in TaOTUB1-RNAi lines. These findings suggested that TaOTUB1s influenced tiller number in wheat.
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Affiliation(s)
- Deng Ji Jiang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Xiao Hua Hao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Heng Tang
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
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Bolus S, Braithwaite KS, Grinstead SC, Fuentes-Bueno I, Beiriger R, Falk BW, Mollov D. Completion of Maize Stripe Virus Genome Sequence and Analysis of Diverse Isolates. Front Microbiol 2021; 12:684599. [PMID: 34194416 PMCID: PMC8238005 DOI: 10.3389/fmicb.2021.684599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/26/2021] [Indexed: 01/25/2023] Open
Abstract
Maize stripe virus is a pathogen of corn and sorghum in subtropical and tropical regions worldwide. We used high-throughput sequencing to obtain the complete nucleotide sequence for the reference genome of maize stripe virus and to sequence the genomes of ten additional isolates collected from the United States or Papua New Guinea. Genetically, maize stripe virus is most closely related to rice stripe virus. We completed and characterized the RNA1 sequence for maize stripe virus, which revealed a large open reading frame encoding a putative protein with ovarian tumor-like cysteine protease, endonuclease, and RNA-dependent RNA polymerase domains. Phylogenetic and amino acid identity analyses among geographically diverse isolates revealed evidence for reassortment in RNA3 that was correlated with the absence of RNA5. This study yielded a complete and updated genetic description of the tenuivirus maize stripe virus and provided insight into potential mechanisms underpinning its diversity.
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Affiliation(s)
- Stephen Bolus
- National Germplasm Resources Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | | | - Samuel C Grinstead
- National Germplasm Resources Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Irazema Fuentes-Bueno
- National Germplasm Resources Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Robert Beiriger
- Institute of Food and Agricultural Sciences, University of Florida, Belle Glade, FL, United States
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Dimitre Mollov
- National Germplasm Resources Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
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Kitao T, Taguchi K, Seto S, Arasaki K, Ando H, Nagai H, Kubori T. Legionella Manipulates Non-canonical SNARE Pairing Using a Bacterial Deubiquitinase. Cell Rep 2021; 32:108107. [PMID: 32905772 DOI: 10.1016/j.celrep.2020.108107] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 05/30/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila uses many effector proteins delivered by the bacterial type IV secretion system (T4SS) to hijack the early secretory pathway to establish its replicative niche, known as the Legionella-containing vacuole (LCV). On LCV biogenesis, the endoplasmic reticulum (ER) vesicular soluble N-ethylmaleimide-sensitive factor attachment protein receptors (v-SNARE) Sec22b is recruited to the bacterial phagosome and forms non-canonical pairings with target membrane SNAREs (t-SNAREs) from the plasma membrane. Here, we identify a Legionella deubiquitinase (DUB), LotB, that can modulate the early secretory pathway by interacting with coatomer protein complex I (COPI) vesicles when ectopically expressed. We show that Sec22b is ubiquitinated upon L. pneumophila infection in a T4SS-dependent manner and that, subsequently, LotB deconjugates K63-linked ubiquitins from Sec22b. The DUB activity of LotB stimulates dissociation of the t-SNARE syntaxin 3 (Stx3) from Sec22b, which resides on the LCV. Our study highlights a bacterial strategy manipulating the dynamics of infection-induced SNARE pairing using a bacterial DUB.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Kyoichiro Taguchi
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; Laboratory of Veterinary Microbiology, Faculty of Applied Biological Science, Gifu University, Gifu, Gifu 501-1193, Japan
| | - Shintaro Seto
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo 204-8533, Japan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Hiroki Ando
- G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan; Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan.
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan.
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Schlüter D, Schulze-Niemand E, Stein M, Naumann M. Ovarian tumor domain proteases in pathogen infection. Trends Microbiol 2021; 30:22-33. [PMID: 34016513 DOI: 10.1016/j.tim.2021.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 01/06/2023]
Abstract
With the aim of overcoming host immune responses, and to permit persistence, numerous bacterial and viral pathogens have evolved effective strategies to control the activity of ovarian tumor domain proteases (OTUs), a group of deubiquitinylases crucial for regulating ubiquitin-modified proteins. Due to the important role of eukaryotic OTUs in cellular physiology, it is not surprising that pathogens have evolutionarily developed effector proteins which mimic host OTUs. Here, we focus on recent findings that illustrate how pathogen-encoded OTUs modulate eukaryotic host proteins and how they are implicated in cellular dysregulation. Further, we discuss the biological effects of OTUs in the context of structural features and pharmacological targeting. We point out the potentiality of selective OTU inhibitors, which shield ubiquitin-binding sites, as pharmacologic targets to treat harmful infections.
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Affiliation(s)
- Dirk Schlüter
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Eric Schulze-Niemand
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany; Molecular Simulations and Design Group, Max Planck Institute of Dynamic of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute of Dynamic of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany.
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Proulx J, Borgmann K, Park IW. Role of Virally-Encoded Deubiquitinating Enzymes in Regulation of the Virus Life Cycle. Int J Mol Sci 2021; 22:ijms22094438. [PMID: 33922750 PMCID: PMC8123002 DOI: 10.3390/ijms22094438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 01/21/2023] Open
Abstract
The ubiquitin (Ub) proteasome system (UPS) plays a pivotal role in regulation of numerous cellular processes, including innate and adaptive immune responses that are essential for restriction of the virus life cycle in the infected cells. Deubiquitination by the deubiquitinating enzyme, deubiquitinase (DUB), is a reversible molecular process to remove Ub or Ub chains from the target proteins. Deubiquitination is an integral strategy within the UPS in regulating survival and proliferation of the infecting virus and the virus-invaded cells. Many viruses in the infected cells are reported to encode viral DUB, and these vial DUBs actively disrupt cellular Ub-dependent processes to suppress host antiviral immune response, enhancing virus replication and thus proliferation. This review surveys the types of DUBs encoded by different viruses and their molecular processes for how the infecting viruses take advantage of the DUB system to evade the host immune response and expedite their replication.
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Affiliation(s)
- Jessica Proulx
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.P.); (K.B.)
| | - Kathleen Borgmann
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.P.); (K.B.)
| | - In-Woo Park
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Correspondence: ; Tel.: +1-(817)-735-5115; Fax: +1-(817)-735-2610
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Vozandychova V, Stojkova P, Hercik K, Rehulka P, Stulik J. The Ubiquitination System within Bacterial Host-Pathogen Interactions. Microorganisms 2021; 9:638. [PMID: 33808578 PMCID: PMC8003559 DOI: 10.3390/microorganisms9030638] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitination of proteins, like phosphorylation and acetylation, is an important regulatory aspect influencing numerous and various cell processes, such as immune response signaling and autophagy. The study of ubiquitination has become essential to learning about host-pathogen interactions, and a better understanding of the detailed mechanisms through which pathogens affect ubiquitination processes in host cell will contribute to vaccine development and effective treatment of diseases. Pathogenic bacteria (e.g., Salmonella enterica, Legionella pneumophila and Shigella flexneri) encode many effector proteins, such as deubiquitinating enzymes (DUBs), targeting the host ubiquitin machinery and thus disrupting pertinent ubiquitin-dependent anti-bacterial response. We focus here upon the host ubiquitination system as an integral unit, its interconnection with the regulation of inflammation and autophagy, and primarily while examining pathogens manipulating the host ubiquitination system. Many bacterial effector proteins have already been described as being translocated into the host cell, where they directly regulate host defense processes. Due to their importance in pathogenic bacteria progression within the host, they are regarded as virulence factors essential for bacterial evasion. However, in some cases (e.g., Francisella tularensis) the host ubiquitination system is influenced by bacterial infection, although the responsible bacterial effectors are still unknown.
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Affiliation(s)
- Vera Vozandychova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
| | - Pavla Stojkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
| | - Kamil Hercik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000 Prague, Czech Republic
| | - Pavel Rehulka
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
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Molecular Mechanisms of DUBs Regulation in Signaling and Disease. Int J Mol Sci 2021; 22:ijms22030986. [PMID: 33498168 PMCID: PMC7863924 DOI: 10.3390/ijms22030986] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
The large family of deubiquitinating enzymes (DUBs) are involved in the regulation of a plethora of processes carried out inside the cell by protein ubiquitination. Ubiquitination is a basic pathway responsible for the correct protein homeostasis in the cell, which could regulate the fate of proteins through the ubiquitin–proteasome system (UPS). In this review we will focus on recent advances on the molecular mechanisms and specificities found for some types of DUBs enzymes, highlighting illustrative examples in which the regulatory mechanism for DUBs has been understood in depth at the molecular level by structural biology. DUB proteases are responsible for cleavage and regulation of the multiple types of ubiquitin linkages that can be synthesized inside the cell, known as the ubiquitin-code, which are tightly connected to specific substrate functions. We will display some strategies carried out by members of different DUB families to provide specificity on the cleavage of particular ubiquitin linkages. Finally, we will also discuss recent progress made for the development of drug compounds targeting DUB proteases, which are usually correlated to the progress of many pathologies such as cancer and neurodegenerative diseases.
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38
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Meléndez-Hevia E, de Paz-Lugo P, Sánchez G. Glycine can prevent and fight virus invasiveness by reinforcing the extracellular matrix. J Funct Foods 2021. [DOI: 10.1016/j.jff.2020.104318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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39
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Zong Z, Zhang Z, Wu L, Zhang L, Zhou F. The Functional Deubiquitinating Enzymes in Control of Innate Antiviral Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002484. [PMID: 33511009 PMCID: PMC7816709 DOI: 10.1002/advs.202002484] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/09/2020] [Indexed: 05/11/2023]
Abstract
Innate antiviral immunity is the first line of host defense against invading viral pathogens. Immunity activation primarily relies on the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Viral proteins or nucleic acids mainly engage three classes of PRRs: Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), and DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS). These receptors initiate a series of signaling cascades that lead to the production of proinflammatory cytokines and type I interferon (IFN-I) in response to viral infection. This system requires precise regulation to avoid aberrant activation. Emerging evidence has unveiled the crucial roles that the ubiquitin system, especially deubiquitinating enzymes (DUBs), play in controlling immune responses. In this review, an overview of the most current findings on the function of DUBs in the innate antiviral immune pathways is provided. Insights into the role of viral DUBs in counteracting host immune responses are also provided. Furthermore, the prospects and challenges of utilizing DUBs as therapeutic targets for infectious diseases are discussed.
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Affiliation(s)
- Zhi Zong
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Zhengkui Zhang
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
| | - Liming Wu
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
| | - Long Zhang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Fangfang Zhou
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
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Driscoll TP, Verhoeve VI, Brockway C, Shrewsberry DL, Plumer M, Sevdalis SE, Beckmann JF, Krueger LM, Macaluso KR, Azad AF, Gillespie JJ. Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas. PeerJ 2020; 8:e10646. [PMID: 33362982 PMCID: PMC7750005 DOI: 10.7717/peerj.10646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.
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Affiliation(s)
| | - Victoria I Verhoeve
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | | | | | - Mariah Plumer
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Spiridon E Sevdalis
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - John F Beckmann
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Laura M Krueger
- Orange County Mosquito and Vector Control District, Garden Grove, CA, USA
| | - Kevin R Macaluso
- Microbiology and Immunology, University of South Alabama, Mobile, AL, USA
| | - Abdu F Azad
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Joseph J Gillespie
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
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The N-terminal cysteine protease domain of rice stripe tenuivirus Pc1 possesses deubiquitinating enzyme activity. Virus Genes 2020; 57:117-120. [PMID: 33146853 DOI: 10.1007/s11262-020-01807-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022]
Abstract
Virus encoded deubiquitinating enzyme (DUB) plays important roles in viral replication and the regulation of host innate immunity. Bioinformatics-based analysis revealed the presence of an ovarian tumor (OTU) protease domain in the N terminus of rice stripe tenuivirus (RSV) Pc1. Many viral OTU domains have been reported to possess DUB activity, which suggests that RSV OTU probably also have DUB activity. To confirm this prediction, we first expressed and purified RSV OTU domain (the N-terminal 200 amino acids of Pc1) and its three mutants (D42A, C45A and H148A) from Escherichia coli and analyzed its DUB activity in vitro. The purified RSV OTU hydrolyzed both K48-linked and K63-linked polyubiquitin chains, indicating RSV OTU domain has DUB enzyme activity in vitro. The mutations of the predicted catalytic sites (Asp42, Cys45 and His148) resulted in the loss of DUB activity, demonstrating these three residues were required for enzyme activity. Then, RSV OTU and its mutants were expressed in insect cells and assayed their DUB activities in vivo by co-transfection with HA-tagged ubiquitin. RSV OTU dramatically reduced ubiquitin-conjugated cellular proteins compared to control and the mutants, showing that RSV OTU also displays DUB activity in vivo. Characterization of RSV OTU DUB enzyme activity and its key catalytic residues will facilitate the development of novel antiviral reagents against RSV.
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Schubert AF, Nguyen JV, Franklin TG, Geurink PP, Roberts CG, Sanderson DJ, Miller LN, Ovaa H, Hofmann K, Pruneda JN, Komander D. Identification and characterization of diverse OTU deubiquitinases in bacteria. EMBO J 2020; 39:e105127. [PMID: 32567101 PMCID: PMC7396840 DOI: 10.15252/embj.2020105127] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Manipulation of host ubiquitin signaling is becoming an increasingly apparent evolutionary strategy among bacterial and viral pathogens. By removing host ubiquitin signals, for example, invading pathogens can inactivate immune response pathways and evade detection. The ovarian tumor (OTU) family of deubiquitinases regulates diverse ubiquitin signals in humans. Viral pathogens have also extensively co-opted the OTU fold to subvert host signaling, but the extent to which bacteria utilize the OTU fold was unknown. We have predicted and validated a set of OTU deubiquitinases encoded by several classes of pathogenic bacteria. Biochemical assays highlight the ubiquitin and polyubiquitin linkage specificities of these bacterial deubiquitinases. By determining the ubiquitin-bound structures of two examples, we demonstrate the novel strategies that have evolved to both thread an OTU fold and recognize a ubiquitin substrate. With these new examples, we perform the first cross-kingdom structural analysis of the OTU fold that highlights commonalities among distantly related OTU deubiquitinases.
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Affiliation(s)
- Alexander F Schubert
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of Structural BiologyGenentech Inc.South San FranciscoCAUSA
| | - Justine V Nguyen
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Paul P Geurink
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Daniel J Sanderson
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Lauren N Miller
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Kay Hofmann
- Institute for GeneticsUniversity of CologneCologneGermany
| | - Jonathan N Pruneda
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - David Komander
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
- Ubiquitin Signalling DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVICAustralia
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Guo L, Chen W, Tao L, Hu B, Qu G, Tu B, Yuan H, Ma B, Wang Y, Zhu X, Qin P, Li S. GWC1 is essential for high grain quality in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110497. [PMID: 32540015 DOI: 10.1016/j.plantsci.2020.110497] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/16/2020] [Accepted: 04/02/2020] [Indexed: 05/23/2023]
Abstract
Appearance quality is an important determinant of rice quality. Many genes that affect grain appearance quality have been identified, but the regulatory mechanisms that contribute to this trait remain unclear. Here, two grains with chalkiness (gwc1) mutants, gwc1-1 and gwc1-2, were identified from an EMS-mutagenized population of indica rice cultivar Shuhui498 (R498). The gwc1 mutants had poor grain appearance quality consistent with the measured values for the percentage of grains with chalkiness, square of chalky endosperm, the total starch, amylose and sucrose contents. Milling quality and grain size were also affected in the gwc1 mutants. The gwc1-1 and gwc1-2 were found to be loss-of-function allelic mutants. GWC1 was mapped to the long arm of rice chromosome 8 using the MutMap strategy and incorrectly annotated in the reference genome for Nipponbare (MSU). The GWC1 gene corresponds to the WTG1/OsOTUB1 gene, which encodes an otubain-like protease with deubiquitinating activity that is homologous to human OTUB1. GWC1 transcripts accumulated to high levels in early endosperm after fertilization and developing inflorescences, and GWC1-green fluorescent protein (GFP) signal was detected in the nucleus and cytoplasm. GWC1 is likely to regulate grain appearance quality through genes involved in sucrose metabolism and starch biosynthesis. Overall, the present findings reveal that GWC1 is important for grain quality and yield due to its effects on grain chalkiness and size.
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Affiliation(s)
- Lianan Guo
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weilan Chen
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lei Tao
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Binhua Hu
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China; Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Guoli Qu
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tu
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hua Yuan
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bingtian Ma
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuping Wang
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaobo Zhu
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Qin
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Shigui Li
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China.
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Molecular and Cellular Mechanisms for PRRSV Pathogenesis and Host Response to Infection. Virus Res 2020; 286:197980. [PMID: 32311386 PMCID: PMC7165118 DOI: 10.1016/j.virusres.2020.197980] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
PRRSV has evolved to arm with various strategies to modify host antiviral response. Viral modulation of homeostatic cellular processes provides favorable conditions for PRRSV survival during infection. PRRSV modulation of cellular processes includes pathways for interferons, apoptosis, microRNAs, cytokines, autophagy, and viral genome recombination.
Porcine reproductive and respiratory syndrome virus (PRRSV) has caused tremendous amounts of economic losses to the swine industry for more than three decades, but its control is still unsatisfactory. A significant amount of information is available for host cell-virus interactions during infection, and it is evident that PRRSV has evolved to equip various strategies to disrupt the host antiviral system and provide favorable conditions for survival. The current study reviews viral strategies for modulations of cellular processes including innate immunity, apoptosis, microRNAs, inflammatory cytokines, and other cellular pathways.
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45
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Bacterial DUBs: deubiquitination beyond the seven classes. Biochem Soc Trans 2020; 47:1857-1866. [PMID: 31845741 DOI: 10.1042/bst20190526] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022]
Abstract
Protein ubiquitination is a posttranslational modification that regulates many aspects of cellular life, including proteostasis, vesicular trafficking, DNA repair and NF-κB activation. By directly targeting intracellular bacteria or bacteria-containing vacuoles to the lysosome, ubiquitination is also an important component of cell-autonomous immunity. Not surprisingly, several pathogenic bacteria encode deubiquitinases (DUBs) and use them as secreted effectors that prevent ubiquitination of bacterial components. A systematic overview of known bacterial DUBs, including their cleavage specificities and biological roles, suggests multiple independent acquisition events from host-encoded DUBs and other proteases. The widely used classification of DUBs into seven well-defined families should only be applied to eukaryotic DUBs, since several bacterial DUBs do not follow this classification.
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Kumari R, Kumar R, Kumar S, Singh AK, Hanpude P, Jangir D, Maiti TK. Amyloid aggregates of the deubiquitinase OTUB1 are neurotoxic, suggesting that they contribute to the development of Parkinson's disease. J Biol Chem 2020; 295:3466-3484. [PMID: 32005664 DOI: 10.1074/jbc.ra119.009546] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 01/18/2020] [Indexed: 01/10/2023] Open
Abstract
Parkinson's disease (PD) is a multifactorial malady and the second most common neurodegenerative disorder, characterized by loss of dopaminergic neurons in the midbrain. A hallmark of PD pathology is the formation of intracellular protein inclusions, termed Lewy bodies (LBs). Recent MS studies have shown that OTU deubiquitinase ubiquitin aldehyde-binding 1 (OTUB1), a deubiquitinating enzyme of the OTU family, is enriched together with α-synuclein in LBs from individuals with PD and is also present in amyloid plaques associated with Alzheimer's disease. In the present study, using mammalian cell cultures and a PD mouse model, along with CD spectroscopy, atomic force microscopy, immunofluorescence-based imaging, and various biochemical assays, we demonstrate that after heat-induced protein aggregation, OTUB1 reacts strongly with both anti-A11 and anti-osteocalcin antibodies, detecting oligomeric, prefibrillar structures or fibrillar species of amyloidogenic proteins, respectively. Further, recombinant OTUB1 exhibited high thioflavin-T and Congo red binding and increased β-sheet formation upon heat induction. The oligomeric OTUB1 aggregates were highly cytotoxic, characteristic of many amyloid proteins. OTUB1 formed inclusions in neuronal cells and co-localized with thioflavin S and with α-synuclein during rotenone-induced stress. It also co-localized with the disease-associated variant pS129-α-synuclein in rotenone-exposed mouse brains. Interestingly, OTUB1 aggregates were also associated with severe cytoskeleton damage, rapid internalization inside the neuronal cells, and mitochondrial damage, all of which contribute to neurotoxicity. In conclusion, the results of our study indicate that OTUB1 may contribute to LB pathology through its amyloidogenic properties.
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Affiliation(s)
- Raniki Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India; Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha 751024, India
| | - Roshan Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sanjay Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Abhishek Kumar Singh
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India
| | - Pranita Hanpude
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India
| | - Deepak Jangir
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India.
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47
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The function and regulation of OTU deubiquitinases. Front Med 2019; 14:542-563. [PMID: 31884527 DOI: 10.1007/s11684-019-0734-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including cell division, immune responses, and apoptosis. Ubiquitin-mediated control over these processes can be reversed by deubiquitinases (DUBs), which remove ubiquitin from target proteins and depolymerize polyubiquitin chains. Recently, much progress has been made in the DUBs. In humans, the ovarian tumor protease (OTU) subfamily of DUBs includes 16 members, most of which mediate cell signaling cascades. These OTUs show great variation in structure and function, which display a series of mechanistic features. In this review, we provide a comprehensive analysis of current progress in character, structure and function of OTUs, such as the substrate specificity and catalytic activity regulation. Then we discuss the relationship between some diseases and OTUs. Finally, we summarize the structure of viral OTUs and their function in immune escape and viral survival. Despite the challenges, OTUs might provide new therapeutic targets, due to their involvement in key regulatory processes.
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48
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Frank S, Hollmann J, Mulisch M, Matros A, Carrión CC, Mock HP, Hensel G, Krupinska K. Barley cysteine protease PAP14 plays a role in degradation of chloroplast proteins. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6057-6069. [PMID: 31403664 PMCID: PMC6859807 DOI: 10.1093/jxb/erz356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/31/2019] [Indexed: 05/18/2023]
Abstract
Chloroplast protein degradation is known to occur both inside chloroplasts and in the vacuole. Genes encoding cysteine proteases have been found to be highly expressed during leaf senescence. However, it remains unclear where they participate in chloroplast protein degradation. In this study HvPAP14, which belongs to the C1A family of cysteine proteases, was identified in senescing barley (Hordeum vulgare L.) leaves by affinity enrichment using the mechanism-based probe DCG-04 targeting cysteine proteases and subsequent mass spectrometry. Biochemical analyses and expression of a HvPAP14:RFP fusion construct in barley protoplasts was used to identify the subcellular localization and putative substrates of HvPAP14. The HvPAP14:RFP fusion protein was detected in the endoplasmic reticulum and in vesicular bodies. Immunological studies showed that HvPAP14 was mainly located in chloroplasts, where it was found in tight association with thylakoid membranes. The recombinant enzyme was activated by low pH, in accordance with the detection of HvPAP14 in the thylakoid lumen. Overexpression of HvPAP14 in barley revealed that the protease can cleave LHCB proteins and PSBO as well as the large subunit of Rubisco. HvPAP14 is involved in the normal turnover of chloroplast proteins and may have a function in bulk protein degradation during leaf senescence.
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Affiliation(s)
- Susann Frank
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Julien Hollmann
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
- Solana Research, Eichenallee 9, Windeby, Germany
| | - Maria Mulisch
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
- Central Microscopy, Christian-Albrechts-University of Kiel, Olshausenstraße 40, Kiel, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, Germany
| | - Cristian C Carrión
- Instituto de Fisiología Vegetal, INFIVE, CONICET-UNLP, cc 327, 1900 La Plata, Argentina
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, Germany
| | - Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
- Correspondence:
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49
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Grewal JS, Catta-Preta CM, Brown E, Anand J, Mottram JC. Evaluation of clan CD C11 peptidase PNT1 and other Leishmania mexicana cysteine peptidases as potential drug targets. Biochimie 2019; 166:150-160. [DOI: 10.1016/j.biochi.2019.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/26/2019] [Indexed: 10/26/2022]
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Deng J, Hou G, Fang Z, Liu J, Lv XD. Distinct expression and prognostic value of OTU domain-containing proteins in non-small-cell lung cancer. Oncol Lett 2019; 18:5417-5427. [PMID: 31612050 PMCID: PMC6781715 DOI: 10.3892/ol.2019.10883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-proteasome pathway is an important protein degradation regulatory system in cells. This pathway is also a reversible process that is strictly regulated, and the regulation of deubiquitinating enzymes (DUBs) represents an important facet of the process. Ovarian tumor-associated proteases domain-containing proteins (OTUDs), as a subfamily within the DUB family, serve an important role in regulatory mechanisms of several biological processes, through the regulation of gene transcription, cell cycle, immune response, inflammation and tumor growth processes, and may be important in the diagnosis of various diseases and constitute novel drug targets. However, the role of OTUDs in non-small-cell lung cancer (NSCLC) has not been fully elucidated. In the present study, the Oncomine database was used to examine gene expression in NSCLC, and the prognostic value of each gene was analyzed by Kaplan-Meier analysis. The results indicated that high mRNA expression levels of OTUD1, OTUD3, OTUD4 and putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 were associated with improved prognosis in all NSCLC and adenocarcinoma, but not in squamous cell carcinoma. By contrast, high expression levels of OTUD2 mRNA were associated with poorer overall survival in patients with NSCLC. These data suggested that these OTUD isozymes may be a potential drug target for NSCLC.
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Affiliation(s)
- Jingjing Deng
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Gouxin Hou
- Department of Oncology, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Zhixian Fang
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Jialiang Liu
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Xiao-Dong Lv
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
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