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Vu GT, Awad V, Norberto MF, Bowman TV, Trompouki E. Nucleic acid-induced inflammation on hematopoietic stem cells. Exp Hematol 2024; 131:104148. [PMID: 38151171 PMCID: PMC11061806 DOI: 10.1016/j.exphem.2023.104148] [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: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Hematopoiesis, the process of generating blood cells, starts during development with the primitive, pro-definitive, and definitive hematopoietic waves. The first two waves will generate erythrocytes and myeloid cells, although the definitive wave will give rise to hematopoietic stem cells (HSCs) that are multipotent and can produce most of the blood cells in an adult. Although HSCs are highly proliferative during development, during adulthood they remain quiescent in the bone marrow. Inflammatory signaling in the form of interferons, interleukins, tumor necrosis factors, and others is well-established to influence both developmental and adult hematopoiesis. Here we discuss the role of specific inflammatory pathways that are induced by sensing nucleic acids. We discuss the role of RNA-sensing members of the Toll-like, Rig-I-like, nucleotide-binding oligomerization domain (NOD)-like, and AIM2-like protein kinase receptors and the DNA-sensing receptors, DEAD-Box helicase 41 (DDX41) and cGAS. The main downstream pathways of these receptors are discussed, as well as their influence on developmental and adult hematopoiesis, including hematopoietic pathologies.
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Affiliation(s)
- Giang To Vu
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France
| | - Valerie Awad
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Maria Feliz Norberto
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY.
| | - Eirini Trompouki
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France.
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2
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Bai Q, Sun D, Zeng Y, Zhu J, Zhang C, Zhang X, Chen L, Zhou X, Ye L, Tang Y, Liu Y, Morozova-Roche LA. Effect of Proinflammatory S100A9 Protein on Migration and Proliferation of Microglial Cells. J Mol Neurosci 2023; 73:983-995. [PMID: 37947991 DOI: 10.1007/s12031-023-02168-1] [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: 05/19/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial disease affecting aging population worldwide. Neuroinflammation became a focus of research as one of the major pathologic processes relating to the disease onset and progression. Proinflammatory S100A9 is the central culprit in the amyloid-neuroinflammatory cascade implicated in AD and other neurodegenerative diseases. We studied the effect of S100A9 on microglial BV-2 cell proliferation and migration. The responses of BV-2 cells to S100A9 stimulation were monitored in real-time using live cell microscopy, transcriptome sequencing, immunofluorescence staining, western blot analysis, and ELISA. We observed that a low dose of S100A9 promotes migration and proliferation of BV-2 cells. However, acute inflammatory condition (i.e., high S100A9 doses) causes diminished cell viability; it is uncovered that S100A9 activates TLR-4 and TLR-7 signaling pathways, leading to TNF-α and IL-6 expression, which affect BV-2 cell migration and proliferation in a concentration-dependent manner. Interestingly, the effects of S100A9 are not only inhibited by TNF-α and IL-6 antibodies. The addition of amyloid-β (Aβ) 1-40 peptide resumes the capacities of BV-2 cells to the level of low S100A9 concentrations. Based on these results, we conclude that in contrast to the beneficial effects of low S100A9 dose, high S100A9 concentration leads to impaired mobility and proliferation of immune cells, reflecting neurotoxicity at acute inflammatory conditions. However, the formation of Aβ plaques may be a natural mechanism that rescues cells from the proinflammatory and cytotoxic effects of S100A9, especially considering that inflammation is one of the primary causes of AD.
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Affiliation(s)
- Qiao Bai
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Dan Sun
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Yang Zeng
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jie Zhu
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Ce Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, Shaanxi, China
| | - Xiaoyin Zhang
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Li Chen
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Xin Zhou
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Liu Ye
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Yong Tang
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China
| | - Yonggang Liu
- Chongqing Medical University, 1 Medical College Road, Yu Zhong District, Chongqing, China.
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3
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Jain A, Begum T, Ahmad S. Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates. J Mol Biol 2023; 435:168208. [PMID: 37479078 DOI: 10.1016/j.jmb.2023.168208] [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: 02/27/2023] [Revised: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Identification of key sequence, expression and function related features of nucleic acid-sensing host proteins is of fundamental importance to understand the dynamics of pathogen-specific host responses. To meet this objective, we considered toll-like receptors (TLRs), a representative class of membrane-bound sensor proteins, from 17 vertebrate species covering mammals, birds, reptiles, amphibians, and fishes in this comparative study. We identified the molecular signatures of host TLRs that are responsible for sensing pathogen nucleic acids or other pathogen-associated molecular patterns (PAMPs), and potentially play important roles in host defence mechanism. Interestingly, our findings reveal that such host-specific features are directly related to the strand (single or double) specificity of nucleic acid from pathogens. However, during host-pathogen interactions, such features were unable to explain the pathogenic PAMP (i.e., DNA, RNA or other) selectivity, suggesting a more complex mechanism. Using these features, we developed a number of machine learning models, of which Random Forest achieved a high performance (94.57% accuracy) to predict strand specificity of TLRs from protein-derived features. We applied the trained model to propose strand specificity of some previously uncharacterized distinct fish-specific novel TLRs (TLR18, TLR23, TLR24, TLR25, TLR27).
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Affiliation(s)
- Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. https://twitter.com/@Anuja334
| | - Tina Begum
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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4
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Basharat Z, Asghar S, Yasmin A. Leveraging molecular docking to understand Congo red degradation by Staphylococcus caprae MB400. Arch Microbiol 2023; 205:250. [PMID: 37243783 DOI: 10.1007/s00203-023-03591-z] [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: 02/21/2023] [Revised: 04/11/2023] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
Congo red (CR) is a genotoxic, sulphonated azo dye and poses significant pollution problem. We hereby report its degradation by Staphylococcus caprae MB400. The bacterium initially propagated as a suspected contaminant upon CR dye supplemented nutrient agar plates, forming zones of clearance around its growth area. The bacterium was purified, gram stained and identified as Staphylococcus caprae via 16S rRNA gene sequencing. Dye decolourization was analysed in liquid culture, and Fourier-transform infrared spectroscopy (FTIR) was conducted for analysis of degraded product/metabolites. A decolourization of ~ 96.0% at 100 µg/ml concentration and pH 7 after 24 h of incubation was observed. Structure of the azoreductase enzyme, responsible for breakage of the bond in the dye and ultimately decolourization, was predicted, and molecular docking was harnessed for understanding the mechanism behind the reduction of azo bond (-N=N-) and conversion to metabolites. Our analysis revealed 12 residues critical for structural interaction of the azoreductase enzyme with this dye. Among these, protein backbone region surrounding four residues, i.e. Lys65, Phe122, Ile166 and Phe169, showed major displacement changes, upon binding with the dye. However, overall the conformational changes were not large.
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Affiliation(s)
- Zarrin Basharat
- Alpha Genomics (Private) Limited, Islamabad, 45710, Pakistan.
| | - Sehrish Asghar
- Environmental Science Program, College of Natural Resources, University of Idaho, Moscow, ID, 83843, USA
| | - Azra Yasmin
- Microbiology and Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.
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5
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Anes E, Pires D, Mandal M, Azevedo-Pereira JM. Spatial localization of cathepsins: Implications in immune activation and resolution during infections. Front Immunol 2022; 13:955407. [PMID: 35990632 PMCID: PMC9382241 DOI: 10.3389/fimmu.2022.955407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022] Open
Abstract
Cathepsins were first described, as endolysosomal proteolytic enzymes in reference to the organelles where they degrade the bulk of endogenous and exogenous substrates in a slightly acidic environment. These substrates include pathogens internalized via endocytosis and/or marked for destruction by autophagy. However, the role of cathepsins during infection far exceeds that of direct digestion of the pathogen. Cathepsins have been extensively investigated in the context of tumour associated immune cells and chronic inflammation. Several cathepsin-dependent immune responses develop in the endocytic pathway while others take place in the cytosol, the nucleus, or in the extracellular space. In this review we highlight the spatial localization of cathepsins and their implications in immune activation and resolution pathways during infection.
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6
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Gao L, Zheng S, Wang Y. The Evasion of Antiviral Innate Immunity by Chicken DNA Viruses. Front Microbiol 2021; 12:771292. [PMID: 34777325 PMCID: PMC8581555 DOI: 10.3389/fmicb.2021.771292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022] Open
Abstract
The innate immune system constitutes the first line of host defense. Viruses have evolved multiple mechanisms to escape host immune surveillance, which has been explored extensively for human DNA viruses. There is growing evidence showing the interaction between avian DNA viruses and the host innate immune system. In this review, we will survey the present knowledge of chicken DNA viruses, then describe the functions of DNA sensors in avian innate immunity, and finally discuss recent progresses in chicken DNA virus evasion from host innate immune responses.
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Affiliation(s)
- Li Gao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shijun Zheng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yongqiang Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
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7
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Wang Z, Gao Y, He L, Sun S, Xia T, Hu L, Yao L, Wang L, Li D, Shi H, Liao X. Structure-Based Design of Highly Potent Toll-like Receptor 7/8 Dual Agonists for Cancer Immunotherapy. J Med Chem 2021; 64:7507-7532. [PMID: 34048243 DOI: 10.1021/acs.jmedchem.1c00179] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Activation of the toll-like receptors 7 and 8 has emerged as a promising strategy for cancer immunotherapy. Herein, we report the design and synthesis of a series of pyrido[3,2-d]pyrimidine-based toll-like receptor 7/8 dual agonists that exhibited potent and near-equivalent agonistic activities toward TLR7 and TLR8. In vitro, compounds 24e and 25a significantly induced the secretion of IFN-α, IFN-γ, TNF-α, IL-1β, IL-12p40, and IP-10 in human peripheral blood mononuclear cell assays. In vivo, compounds 24e, 24m, and 25a significantly suppressed tumor growth in CT26 tumor-bearing mice by remodeling the tumor microenvironment. Additionally, compounds 24e, 24m, and 25a markedly improved the antitumor activity of PD-1/PD-L1 blockade. In particular, compound 24e combined with the anti-PD-L1 antibody led to complete tumor regression. These results demonstrated that TLR7/8 agonists (24e, 24m, and 25a) held great potential as single agents or in combination with PD-1/PD-L1 blockade for cancer immunotherapy.
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Affiliation(s)
- Zhisong Wang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China.,Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Gao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China.,Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Lei He
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Shuhao Sun
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Tingting Xia
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Lu Hu
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Licheng Yao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Liangliang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Dan Li
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Hui Shi
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China.,Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuebin Liao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China.,Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
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8
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Gadanec LK, McSweeney KR, Qaradakhi T, Ali B, Zulli A, Apostolopoulos V. Can SARS-CoV-2 Virus Use Multiple Receptors to Enter Host Cells? Int J Mol Sci 2021; 22:992. [PMID: 33498183 PMCID: PMC7863934 DOI: 10.3390/ijms22030992] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
The occurrence of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for coronavirus disease 2019 (COVD-19), represents a catastrophic threat to global health. Protruding from the viral surface is a densely glycosylated spike (S) protein, which engages angiotensin-converting enzyme 2 (ACE2) to mediate host cell entry. However, studies have reported viral susceptibility in intra- and extrapulmonary immune and non-immune cells lacking ACE2, suggesting that the S protein may exploit additional receptors for infection. Studies have demonstrated interactions between S protein and innate immune system, including C-lectin type receptors (CLR), toll-like receptors (TLR) and neuropilin-1 (NRP1), and the non-immune receptor glucose regulated protein 78 (GRP78). Recognition of carbohydrate moieties clustered on the surface of the S protein may drive receptor-dependent internalization, accentuate severe immunopathological inflammation, and allow for systemic spread of infection, independent of ACE2. Furthermore, targeting TLRs, CLRs, and other receptors (Ezrin and dipeptidyl peptidase-4) that do not directly engage SARS-CoV-2 S protein, but may contribute to augmented anti-viral immunity and viral clearance, may represent therapeutic targets against COVID-19.
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9
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Liu G, Zhang H, Zhao C, Zhang H. Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates. Genome Biol Evol 2020; 12:3615-3634. [PMID: 31800025 PMCID: PMC6946030 DOI: 10.1093/gbe/evz266] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2019] [Indexed: 12/13/2022] Open
Abstract
Adaptation to a wide range of pathogenic environments is a major aspect of the ecological adaptations of vertebrates during evolution. Toll-like receptors (TLRs) are ancient membrane-bound sensors in animals and are best known for their roles in detecting and defense against invading pathogenic microorganisms. To understand the evolutionary history of the vertebrate TLR gene family, we first traced the origin of single-cysteine cluster TLRs that share the same protein architecture with vertebrate TLRs in early-branching animals and then analyzed all members of the TLR family in over 200 species covering all major vertebrate clades. Our results indicate that although the emergence of single-cysteine cluster TLRs predates the separation of bilaterians and cnidarians, most vertebrate TLR members originated shortly after vertebrate emergence. Phylogenetic analyses divided 1,726 vertebrate TLRs into 8 subfamilies, and TLR3 may represent the most ancient subfamily that emerged before the branching of deuterostomes. Our analysis reveals that purifying selection predominated in the evolution of all vertebrate TLRs, with mean dN/dS (ω) values ranging from 0.082 for TLR21 in birds to 0.434 for TLR11 in mammals. However, we did observe patterns of positive selection acting on specific codons (527 of 60,294 codons across all vertebrate TLRs, 8.7‰), which are significantly concentrated in ligand-binding extracellular domains and suggest host–pathogen coevolutionary interactions. Additionally, we found stronger positive selection acting on nonviral compared with viral TLRs, indicating the more essential nonredundant function of viral TLRs in host immunity. Taken together, our findings provide comprehensive insight into the complex evolutionary processes of the vertebrate TLR gene family, involving gene duplication, pseudogenization, purification, and positive selection.
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Affiliation(s)
- Guangshuai Liu
- College of Life Science, Qufu Normal University, Shandong, China
| | - Huanxin Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Shandong, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Shandong, China
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10
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Torosin NS, Argibay H, Webster TH, Corneli PS, Knapp LA. Comparing the selective landscape of TLR7 and TLR8 across primates reveals unique sites under positive selection in Alouatta. Mol Phylogenet Evol 2020; 152:106920. [PMID: 32768453 DOI: 10.1016/j.ympev.2020.106920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/06/2020] [Accepted: 07/31/2020] [Indexed: 11/24/2022]
Abstract
Among primates, susceptibility to yellow fever (YFV), a single-stranded (ss) RNA virus, ranges from complete resistance to high susceptibility. Howler monkeys (genus Alouatta) are the most susceptible to YFV. In order to identify Alouatta-specific genetic factors that may be responsible for their susceptibility, we collected skin samples from howler monkey museum specimens of the species A. caraya and A. guariba clamitans. We compared the rate of nonsynonymous to synonymous (dN/dS) changes of Toll-like receptor (TLR) 7 and TLR8, the two genes responsible for detecting all ssRNA viruses, across the Primate order. Overall, we found that the TLR7 gene is under stronger purifying selection in howler monkeys compared to other New World and Old World primates, but TLR8 is under the same selective pressure. When we evaluated dN/dS at each codon, we found six codons under positive selection in Alouatta TLR8 and two codons under positive selection in TLR7. The changes in TLR7 are unique to A. guariba clamitans and are found in functionally important regions likely to affect detection of ssRNA viruses by TLR7/TLR8, as well as downstream signaling. These amino acid differences in A. guariba clamitans may play a role in YFV susceptibility. These results have implications for identifying genetic factors affecting YFV susceptibility in primates.
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Affiliation(s)
- Nicole S Torosin
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States.
| | - Hernan Argibay
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Intendente Güiraldes 2160 - Ciudad Universitaria (C1428EGA) Ciudad Autónoma de Buenos Aires, Argentina
| | - Timothy H Webster
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States
| | - Patrice Showers Corneli
- Department of Biology, University of Utah, 257 S. 1400 E., Salt Lake City, UT 84112, United States
| | - Leslie A Knapp
- Department of Anthropology, University of Utah, 260 S. Central Campus Dr., Salt Lake City, UT 84112, United States
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11
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Ghosh SK, Saha B, Banerjee R. Insight into the sequence-structure relationship of TLR cytoplasm's Toll/Interleukin-1 receptor domain towards understanding the conserved functionality of TLR 2 heterodimer in mammals. J Biomol Struct Dyn 2020; 39:5348-5357. [PMID: 32643540 DOI: 10.1080/07391102.2020.1786457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The signaling response of TLR2 to ligands has always been as a homodimer or in heterodimerization with TLR1/TLR6. The Toll/Interleukin-1 Receptor (TIR) domain of the TLR cytoplasmic region regulates the dimerization and interactions with adaptor molecules to build an active signaling complex. To understand the conservation of functionality of the TLR2-heterodimers between the distantly related species human(h) and mice(m), the pattern of TIR-TIR interaction in heterodimers has been studied through the sequence-structural point of view. Comparative analysis of primary sequence and structural pattern of TLRs(1/2/6) corroborates higher sequence homology between TLR1 and TLR6. Molecular docking analysis of TLR2-TLR1 and TLR2-TLR6 cytoplasmic dimers in both mouse and human have identified that for interaction the BB loop/near-BB loop residues of TLR2 are involved with the near-DD loop of TLR1 and DD loop residues of TLR6 within the TIR domains, which may cause to differential signaling. Molecular dynamics simulation of dimers for both human and mice species recognize stable interface between near-BB/BB loop region of TLR2 and discrete near-DD and DD loop region of TLR1 and TLR6 respectively. The observed dimerization pattern in both the species is further supported by Alanine scanning mutation study. However, Solvent Accessible Surface Area (SASA) of BB and DD loop regions of the cytoplasmic monomers and the heterodimers suggests that while TLR2 BB loop is actively associated as the dimer interface with its heterodimer partners in both the species, the DD loop acts as the active interfacing region in hTLR1 and mTLR6. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumya Kanti Ghosh
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, India
| | | | - Raja Banerjee
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, India
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12
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Torosin NS, Webster TH, Argibay H, Sanchez Fernandez C, Ferreyra H, Uhart M, Agostini I, Knapp LA. Positively selected variants in functionally important regions of TLR7 in Alouatta guariba clamitans with yellow fever virus exposure in Northern Argentina. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:50-60. [PMID: 32583896 DOI: 10.1002/ajpa.24086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 04/28/2020] [Accepted: 05/10/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND In 2007-2009, a major yellow fever virus (YFV) outbreak in Northern Argentina decimated the local howler monkey (Alouatta) population. AIMS To evaluate whether the surviving howler monkeys possess advantageous genetic variants inherited from monkeys alive prior to the YFV outbreak, we explored the relationship between Toll-like receptor (TLR) 7 and TLR8 gene variation and YFV susceptibility. METHODS We used samples from Alouatta individuals in Misiones, Argentina alive before the YFV outbreak, individuals that died during the outbreak, and individuals that survived the outbreak and are alive today. We measured genetic divergence between Alouatta YFV exposure groups and evaluated Alouatta-specific substitutions for functional consequences. RESULTS We did not find different allele frequencies in the post-YFV exposure Alouatta group compared to the pre-exposure group. We identified three nonsynonymous variants in TLR7 in Alouatta guariba clamitans. Two of these substitutions are under positive selection in functionally important regions of the gene. DISCUSSION AND CONCLUSIONS Our results did not indicate that surviving howler monkey spossess advantageous genetic variants at greater frequency than those alive before the YFV outbreak. However, the positively selected unique coding differences in A. guariba clamitans are in the region important in pathogen detection which may affect YFV resistance. Morework is necessary to fully explore this hypothesis.
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Affiliation(s)
- Nicole S Torosin
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Hernán Argibay
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET), Intendente Güiraldes 2160 - Ciudad Universitaria (C1428EGA), Buenos Aires, Argentina
| | - Candelaria Sanchez Fernandez
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Hebe Ferreyra
- Global Health Program, Wildlife Conservation Society, Buenos Aires, Argentina
| | - Marcela Uhart
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Ilaria Agostini
- Instituto de Biología Subtropical (IBS), Universidad Nacional de Misiones (UNaM), Consejo Nacional de Investigaciones Científcas y Técnicas (CONICET), Puerto Iguazú, Argentina
| | - Leslie A Knapp
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
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13
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RNA Signaling in Pulmonary Arterial Hypertension-A Double-Stranded Sword. Int J Mol Sci 2020; 21:ijms21093124. [PMID: 32354189 PMCID: PMC7247700 DOI: 10.3390/ijms21093124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Recognition of and response to pathogens and tissue injury is driven by the innate immune system via activation of pattern recognition receptors. One of the many patterns recognized is RNA and, while several receptors bind RNA, Toll-like receptor 3 (TLR3) is well placed for initial recognition of RNA molecules due to its localization within the endosome. There is a growing body of work describing a role for TLR3 in maintenance of vascular homeostasis. For example, TLR3 deficiency has been shown to play repair and remodeling roles in the systemic vasculature and in lung parenchyma. A hallmark of pulmonary arterial hypertension (PAH) is pulmonary vascular remodeling, yet drivers and triggers of this remodeling remain incompletely understood. Based on its role in the systemic vasculature, our group discovered reduced endothelial TLR3 expression in PAH and revealed a protective role for a TLR3 agonist in rodent models of pulmonary hypertension. This review will provide an overview of RNA signaling in the vasculature and how it relates to PAH pathobiology, including whether targeting double-stranded RNA signaling is a potential treatment option for PAH.
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14
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Świderská Z, Šmídová A, Buchtová L, Bryjová A, Fabiánová A, Munclinger P, Vinkler M. Avian Toll-like receptor allelic diversity far exceeds human polymorphism: an insight from domestic chicken breeds. Sci Rep 2018; 8:17878. [PMID: 30552359 PMCID: PMC6294777 DOI: 10.1038/s41598-018-36226-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023] Open
Abstract
Immune genes show remarkable levels of adaptive variation shaped by pathogen-mediated selection. Compared to humans, however, population polymorphism in animals has been understudied. To provide an insight into immunogenetic diversity in birds, we sequenced complete protein-coding regions of all Toll-like receptor (TLR) genes with direct orthology between mammals and birds (TLR3, TLR4, TLR5 and TLR7) in 110 domestic chickens from 25 breeds and compared their variability with a corresponding human dataset. Chicken TLRs (chTLRs) exhibit on average nine-times higher nucleotide diversity than human TLRs (hTLRs). Increased potentially functional non-synonymous variability is found in chTLR ligand-binding ectodomains. While we identified seven sites in chTLRs under positive selection and found evidence for convergence between alleles, no selection or convergence was detected in hTLRs. Up to six-times more alleles were identified in fowl (70 chTLR4 alleles vs. 11 hTLR4 alleles). In chTLRs, high numbers of alleles are shared between the breeds and the allelic frequencies are more equal than in hTLRs. These differences may have an important impact on infectious disease resistance and host-parasite co-evolution. Though adaptation through high genetic variation is typical for acquired immunity (e.g. MHC), our results show striking levels of intraspecific polymorphism also in poultry innate immune receptors.
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Grants
- 504214 Grantová Agentura, Univerzita Karlova (Charles University Grant Agency)
- 504214 Grantová Agentura, Univerzita Karlova (Charles University Grant Agency)
- 204069 Univerzita Karlova v Praze (Charles University)
- 204069 Univerzita Karlova v Praze (Charles University)
- PRIMUS/17/SCI/12 Univerzita Karlova v Praze (Charles University)
- SVV 260434/2018 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- INTER-COST LTC18060 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- SVV 260434/2018 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- P502/12/P179 Grantová Agentura České Republiky (Grant Agency of the Czech Republic)
- Grantová Agentura, Univerzita Karlova (Charles University Grant Agency)
- Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- Grantová Agentura České Republiky (Grant Agency of the Czech Republic)
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Affiliation(s)
- Zuzana Świderská
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
- Charles University, Faculty of Science, Department of Cell Biology, Viničná 7, Prague, 12843, Czech Republic
| | - Adéla Šmídová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Lucie Buchtová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Anna Bryjová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
- The Czech Academy of Sciences, Institute of Vertebrate Biology, v.v.i., Květná 8, Brno, 60365, Czech Republic
| | - Anežka Fabiánová
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Pavel Munclinger
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, Prague, 12843, Czech Republic.
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15
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Velová H, Gutowska-Ding MW, Burt DW, Vinkler M. Toll-Like Receptor Evolution in Birds: Gene Duplication, Pseudogenization, and Diversifying Selection. Mol Biol Evol 2018; 35:2170-2184. [PMID: 29893911 PMCID: PMC6107061 DOI: 10.1093/molbev/msy119] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Toll-like receptors (TLRs) are key sensor molecules in vertebrates triggering initial phases of immune responses to pathogens. The avian TLR family typically consists of ten receptors, each adapted to distinct ligands. To understand the complex evolutionary history of each avian TLR, we analyzed all members of the TLR family in the whole genome assemblies and target sequence data of 63 bird species covering all major avian clades. Our results indicate that gene duplication events most probably occurred in TLR1 before synapsids diversified from sauropsids. Unlike mammals, ssRNA-recognizing TLR7 has duplicated independently in several avian taxa, while flagellin-sensing TLR5 has pseudogenized multiple times in bird phylogeny. Our analysis revealed stronger positive, diversifying selection acting in TLR5 and the three-domain TLRs (TLR10 [TLR1A], TLR1 [TLR1B], TLR2A, TLR2B, TLR4) that face the extracellular space and bind complex ligands than in single-domain TLR15 and endosomal TLRs (TLR3, TLR7, TLR21). In total, 84 out of 306 positively selected sites were predicted to harbor substitutions dramatically changing the amino acid physicochemical properties. Furthermore, 105 positively selected sites were located in the known functionally relevant TLR regions. We found evidence for convergent evolution acting between birds and mammals at 54 of these sites. Our comparative study provides a comprehensive insight into the evolution of avian TLR genetic variability. Besides describing the history of avian TLR gene gain and gene loss, we also identified candidate positions in the receptors that have been likely shaped by direct molecular host-pathogen coevolutionary interactions and most probably play key functional roles in birds.
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Affiliation(s)
- Hana Velová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Maria W Gutowska-Ding
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Midlothian, United Kingdom
| | - David W Burt
- Office of DVC (Research), University of Queensland, St. Lucia, QLD, Australia
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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16
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Gentile F, Deriu MA, Barakat K, Danani A, Tuszynski J. A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study. Pharmaceuticals (Basel) 2018; 11:ph11010022. [PMID: 29462934 PMCID: PMC5874718 DOI: 10.3390/ph11010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/01/2018] [Accepted: 02/13/2018] [Indexed: 01/05/2023] Open
Abstract
The Toll-Like Receptor 7 (TLR7) is an endosomal membrane receptor involved in the innate immune system response. Its best-known small molecule activators are imidazoquinoline derivatives such as imiquimod (R-837) and resiquimod (R-848). Recently, an interaction between R-837 and the colchicine binding site of tubulin was reported. To investigate the possibility of an interaction between structural analogues of colchicine and the TLR7, a recent computational model for the dimeric form of the TLR7 receptor was used to determine a possible interaction with a colchicine derivative called CR42-24, active as a tubulin polymerization inhibitor. The estimated values of the binding energy of this molecule with respect to the TLR7 receptor were comparable to the energies of known binders as reported in a previous study. The binding to the TLR7 was further assessed by introducing genetic transformations in the TLR7 gene in cancer cell lines and exposing them to the compound. A negative shift of the IC50 value in terms of cell growth was observed in cell lines carrying the mutated TLR7 gene. The reported study suggests a possible interaction between TLR7 and a colchicine derivative, which can be explored for rational design of new drugs acting on this receptor by using a colchicine scaffold for additional modifications.
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Affiliation(s)
- Francesco Gentile
- Department of Physics, University of Alberta, AB T6G 2E1 Edmonton, Canada.
| | - Marco A Deriu
- Istituto Dalle Molle di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), CH-6928 Manno, Switzerland.
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, AB T6G 2H1 Edmonton, Canada.
| | - Andrea Danani
- Istituto Dalle Molle di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), CH-6928 Manno, Switzerland.
| | - Jack Tuszynski
- Department of Physics, University of Alberta, AB T6G 2E1 Edmonton, Canada.
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
- Department of Oncology, University of Alberta, AB T6G 1Z2 Edmonton, Canada.
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17
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Han C, Li Q, Zhang Z, Huang J. Characterization, expression, and evolutionary analysis of new TLR3 and TLR5M genes cloned from the spiny eel Mastacembelus armatus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:174-187. [PMID: 28821419 DOI: 10.1016/j.dci.2017.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/12/2017] [Accepted: 08/13/2017] [Indexed: 06/07/2023]
Abstract
Toll-like receptors (TLRs) play an important role in innate and adaptive immunity. Here, we identify two new TLRs from the spiny eel Mastacembelus armatus (TLR3 and membrane TLR5M). Both MaTLR3 and MaTLR5M were expressed in all tested tissues; expression was highest in liver and spleen, respectively. After infection with Vibrio parahaemolyticus, expression of both TLRs fluctuated and differed significantly from controls at several time points. The predicted three-dimensional model of the MaTLR3 and MaTLR5M proteins indicates that most sites under positive selection were located in the extracellular domains of TLRs. Evolutionary analysis detected positively selected sites in the ancestral lineages of vertebrates, amphibians and reptiles. Multiple ML methods recovered 10 positively selected sites in teleost TLR3 and 24 in TLR5M, and most sites were located in leucine-rich repeat domain, possibly related to an "arms-race" co-evolution with pathogens.
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Affiliation(s)
- Chong Han
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Qiang Li
- School of Life Sciences, Guangzhou University, Guangzhou, PR China
| | - Zhipeng Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Jianrong Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
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18
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Divergence of protein sensing (TLR 4, 5) and nucleic acid sensing (TLR 3, 7) within the reptilian lineage. Mol Phylogenet Evol 2017; 119:210-224. [PMID: 29196206 DOI: 10.1016/j.ympev.2017.11.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 10/22/2017] [Accepted: 11/27/2017] [Indexed: 11/21/2022]
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19
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Liu G, Zhang H, Sun G, Zhao C, Shang S, Gao X, Xia T, Yang X. Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus). BMC Genomics 2017; 18:584. [PMID: 28784091 PMCID: PMC5545864 DOI: 10.1186/s12864-017-3983-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/01/2017] [Indexed: 01/25/2023] Open
Abstract
Background The wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, because it is well adapted to various ecological niches and their corresponding pathogen environments. Immunological competence is a crucial factor involved in adapting to a changing environment and fighting pathogen infection in animals. In this study, the peripheral blood transcriptome of wolves was generated via RNA-seq to advance understanding of the wolf immunome, with a special focus on the major histocompatibility complex class I (MHC I) and toll-like receptor (TLR) gene families, which are involved in pathogen recognition and defense. Results The blood transcriptomic libraries of eight wolves originating from Tibet and Inner Mongolia were sequenced, and approximately 383 million reads were generated. Using a genome-guided assembly strategy, we obtained 123,851 unigenes, with a mean length of 845 bp and an N50 length of 1121 bp. On the basis of BLAST searches against the NCBI non-redundant protein database (Nr), a total of 36,192 (29.22%) unigenes were annotated. For functional classification, 24,663 unigenes were assigned to 13,016 Gene Ontology (GO) terms belonging to 51 sub-categories of the three main GO categories. Additionally, 7682 unigenes were classified into 6 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, in which the most represented functional sub-categories were signal transduction and the immune system, and 16,238 unigenes were functionally classified into 25 Eukaryotic Orthologous Groups (KOG) categories. We observed an overall higher ω (dN/dS) value at antigen-binding sites (ABSs) than at non-ABS regions as well as clear evidence of intergenic/intragenic recombination events at wolf MHC I loci. Additionally, our analysis revealed that carnivorous TLRs were dominated by purifying selection, with mean ω values at each TLR locus ranging from 0.173 to 0.527. However, we also found significant instances of positive selection that acted on several codons in pathogen recognition domains and were linked to species-specific differences in pathogen recognition. Conclusions This study represents the first attempt to characterize the blood transcriptome of the wolf and to highlight the value of investigating the immune system. Balancing selection and recombination have contributed to the historical evolution of wolf MHC I genes. Moreover, TLRs in carnivores have undergone adaptive evolution against the background of purifying selection, and a high level of adaptive evolution was detected in the wolf TLR system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3983-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangshuai Liu
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Honghai Zhang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China.
| | - Guolei Sun
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Chao Zhao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Shuai Shang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiaodong Gao
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Tian Xia
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
| | - Xiufeng Yang
- Qufu Normal University, Jingxuan Street No. 57, Qufu, Shandong province, China
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20
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Kubli-Garfias C, Vázquez-Ramírez R, Trejo-Muñoz C, Berber A. Insights on the mechanism of action of immunostimulants in relation to their pharmacological potency. The effects of imidazoquinolines on TLR8. PLoS One 2017; 12:e0178846. [PMID: 28582454 PMCID: PMC5459437 DOI: 10.1371/journal.pone.0178846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 05/19/2017] [Indexed: 11/18/2022] Open
Abstract
Imidazoquinolines are powerful immunostimulants (IMMS) that function through Toll-like receptors, particularly TLR7 and TLR8. In addition to enhancing the immune response, IMMS also function as antineoplastic drugs and vaccine adjuvants. These small compounds display almost the same molecular structure, except in some cases in which atom in position 1 varies and changes the imidazole characteristics. A variable acyclic side chain is also always attached at atom in position 2, while another chain may be attached at atom in position 1. These structural differences alter immune responses, such as the production of interferon regulatory factor and nuclear factor-κB (IRF-NFκB). In this work, quantum mechanics theory and computational chemistry methods were applied to study the physicochemical properties of the crystal binding site of TLR8 complexed with the following six IMMS molecules: Hybrid-2, XG1-236, DS802, CL075, CL097 and R848 (resiquimod). The PDB IDs of the crystals were: 4R6A, 4QC0, 4QBZ, 3W3K, 3W3J, and 3W3N respectively. Thus, were calculated, the total energy, solvation energy, interaction energy (instead of free energy) of the system and interaction energy of the polar region of the IMMS. Additionally, the dipole moment, electrostatic potential, polar surface, atomic charges, hydrogen bonds, and polar and hydrophobic interactions, among others, were assessed. Together, these properties revealed important differences among the six TLR8-immunostimulant complexes, reflected as different interaction energies and therefore different electrostatic environments and binding energies. Remarkably, the interaction energy of a defined polar region composed of the highly polarized N3, N5 atoms and the N11 amino group, acted as a polar pharmacophore that correlates directly with the reported immunopharmacological potency of the six complexed molecules. Based on these results, it was concluded that accurate physicochemical analysis of the crystal binding site could reveal the binding energy (measured as interaction energy) and associated molecular mechanism of action between IMMS and TLR8. These findings may facilitate the development and design of improved small molecules with IMMS properties that are targeted to the TLR system and have enhanced pharmacological effectiveness and reduced toxicity.
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Affiliation(s)
- Carlos Kubli-Garfias
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ricardo Vázquez-Ramírez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Cynthia Trejo-Muñoz
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo Berber
- Fundación para el Avance de la Ciencia, Ciudad de México, México
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21
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Martínez-Campos C, Burguete-García AI, Madrid-Marina V. Role of TLR9 in Oncogenic Virus-Produced Cancer. Viral Immunol 2017; 30:98-105. [DOI: 10.1089/vim.2016.0103] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Cecilia Martínez-Campos
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Ana I. Burguete-García
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Vicente Madrid-Marina
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
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22
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Chai HH, Lim D, Suk JE, Choi BH, Cho YM. Design of anti-BVDV drug based on common chemical features, their interaction, and scaffolds of TLR8 agonists. Int J Biol Macromol 2016; 92:1095-1112. [DOI: 10.1016/j.ijbiomac.2016.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 08/02/2016] [Accepted: 08/08/2016] [Indexed: 11/16/2022]
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23
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Gao D, Zeng J, Wang X, Liu Y, Li W, Hu Y, Gao N, Diao Y, Wang Z, Jiang W, Chen J, Jin G. Conjugation of weak ligands with weak antigens to activate TLR-7: A step toward better vaccine adjuvants. Eur J Med Chem 2016; 120:111-20. [DOI: 10.1016/j.ejmech.2016.04.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 12/20/2022]
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24
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Kettle JG, Alwan H, Bista M, Breed J, Davies NL, Eckersley K, Fillery S, Foote KM, Goodwin L, Jones DR, Käck H, Lau A, Nissink JWM, Read J, Scott JS, Taylor B, Walker G, Wissler L, Wylot M. Potent and Selective Inhibitors of MTH1 Probe Its Role in Cancer Cell Survival. J Med Chem 2016; 59:2346-61. [PMID: 26878898 DOI: 10.1021/acs.jmedchem.5b01760] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent literature has claimed that inhibition of the enzyme MTH1 can eradicate cancer. MTH1 is one of the "housekeeping" enzymes that are responsible for hydrolyzing damaged nucleotides in cells and thus prevent them from being incorporated into DNA. We have developed orthogonal and chemically distinct tool compounds to those published in the literature to allow us to test the hypothesis that inhibition of MTH1 has wide applicability in the treatment of cancer. Here we present the work that led to the discovery of three structurally different series of MTH1 inhibitors with excellent potency, selectivity, and proven target engagement in cells. None of these compounds elicited the reported cellular phenotype, and additional siRNA and CRISPR experiments further support these observations. Critically, the difference between the responses of our highly selective inhibitors and published tool compounds suggests that the effect reported for the latter may be due to off-target cytotoxic effects. As a result, we conclude that the role of MTH1 in carcinogenesis and utility of its inhibition is yet to be established.
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Affiliation(s)
- Jason G Kettle
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Husam Alwan
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Michal Bista
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Jason Breed
- Discovery Sciences, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Nichola L Davies
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Kay Eckersley
- Discovery Sciences, AstraZeneca , Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Shaun Fillery
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Kevin M Foote
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Louise Goodwin
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - David R Jones
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Helena Käck
- Discovery Sciences, AstraZeneca , Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Alan Lau
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - J Willem M Nissink
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Jon Read
- Discovery Sciences, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - James S Scott
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Ben Taylor
- Discovery Sciences, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Graeme Walker
- Discovery Sciences, AstraZeneca , Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Lisa Wissler
- Discovery Sciences, AstraZeneca , Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Marta Wylot
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
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25
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Escalera-Zamudio M, Zepeda-Mendoza ML, Loza-Rubio E, Rojas-Anaya E, Méndez-Ojeda ML, Arias CF, Greenwood AD. The evolution of bat nucleic acid-sensing Toll-like receptors. Mol Ecol 2015; 24:5899-909. [PMID: 26503258 DOI: 10.1111/mec.13431] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/05/2015] [Accepted: 10/20/2015] [Indexed: 11/29/2022]
Abstract
We characterized the nucleic acid-sensing Toll-like receptors (TLR) of a New World bat species, the common vampire bat (Desmodus rotundus), and through a comparative molecular evolutionary approach searched for general adaptation patterns among the nucleic acid-sensing TLRs of eight different bats species belonging to three families (Pteropodidae, Vespertilionidae and Phyllostomidae). We found that the bat TLRs are evolving slowly and mostly under purifying selection and that the divergence pattern of such receptors is overall congruent with the species tree, consistent with the evolution of many other mammalian nuclear genes. However, the chiropteran TLRs exhibited unique mutations fixed in ligand-binding sites, some of which involved nonconservative amino acid changes and/or targets of positive selection. Such changes could potentially modify protein function and ligand-binding properties, as some changes were predicted to alter nucleic acid binding motifs in TLR 9. Moreover, evidence for episodic diversifying selection acting specifically upon the bat lineage and sublineages was detected. Thus, the long-term adaptation of chiropterans to a wide variety of environments and ecological niches with different pathogen profiles is likely to have shaped the evolution of the bat TLRs in an order-specific manner. The observed evolutionary patterns provide evidence for potential functional differences between bat and other mammalian TLRs in terms of resistance to specific pathogens or recognition of nucleic acids in general.
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Affiliation(s)
- Marina Escalera-Zamudio
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - M Lisandra Zepeda-Mendoza
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, kM 15.5 carretera federal México-Toluca Col. Palo Alto, 05110, México City, Mexico
| | - Edith Rojas-Anaya
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, kM 15.5 carretera federal México-Toluca Col. Palo Alto, 05110, México City, Mexico
| | - Maria L Méndez-Ojeda
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Miguel Ángel de Quevedo Col. Unidad Veracruzana, 91710, Veracruz, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, 62210, Cuernavaca Morelos, Mexico
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Oertzenweg 19b, 14163, Berlin, Germany
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Berglund NA, Kargas V, Ortiz-Suarez ML, Bond PJ. The role of protein–protein interactions in Toll-like receptor function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:72-83. [DOI: 10.1016/j.pbiomolbio.2015.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/12/2022]
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Gupta CL, Akhtar S, Sayyed U, Pathak N, Bajpai P. In silicoanalysis of human Toll-like receptor 7 ligand binding domain. Biotechnol Appl Biochem 2015; 63:441-50. [DOI: 10.1002/bab.1377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/23/2015] [Indexed: 12/28/2022]
Affiliation(s)
| | - Salman Akhtar
- Department of Bioengineering; Integral University; Lucknow India
| | - Uzma Sayyed
- Department of Biosciences; Integral University; Lucknow India
| | - Neelam Pathak
- Department of Biosciences; Integral University; Lucknow India
| | - Preeti Bajpai
- Department of Biosciences; Integral University; Lucknow India
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Gentile F, Deriu MA, Licandro G, Prunotto A, Danani A, Tuszynski JA. Structure Based Modeling of Small Molecules Binding to the TLR7 by Atomistic Level Simulations. Molecules 2015; 20:8316-40. [PMID: 26007168 PMCID: PMC6272798 DOI: 10.3390/molecules20058316] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 04/17/2015] [Accepted: 04/30/2015] [Indexed: 12/15/2022] Open
Abstract
Toll-Like Receptors (TLR) are a large family of proteins involved in the immune system response. Both the activation and the inhibition of these receptors can have positive effects on several diseases, including viral pathologies and cancer, therefore prompting the development of new compounds. In order to provide new indications for the design of Toll-Like Receptor 7 (TLR7)-targeting drugs, the mechanism of interaction between the TLR7 and two important classes of agonists (imidazoquinoline and adenine derivatives) was investigated through docking and Molecular Dynamics simulations. To perform the computational analysis, a new model for the dimeric form of the receptors was necessary and therefore created. Qualitative and quantitative differences between agonists and inactive compounds were determined. The in silico results were compared with previous experimental observations and employed to define the ligand binding mechanism of TLR7.
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Affiliation(s)
- Francesco Gentile
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Marco A Deriu
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno CH-6928, Switzerland.
| | - Ginevra Licandro
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno CH-6928, Switzerland.
| | - Alessio Prunotto
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno CH-6928, Switzerland.
| | - Andrea Danani
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno CH-6928, Switzerland.
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
- Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
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Darfour-Oduro KA, Megens HJ, Roca AL, Groenen MAM, Schook LB. Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae. PLoS One 2015; 10:e0124069. [PMID: 25894218 PMCID: PMC4404360 DOI: 10.1371/journal.pone.0124069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/25/2015] [Indexed: 12/16/2022] Open
Abstract
Members of the family Suidae have diverged over extended evolutionary periods in diverse environments, suggesting that adaptation in response to endemic infectious agents may have occurred. Toll-like receptors (TLRs) comprise a multigene family that acts as the first line of defense against infectious microbes at the host-environment interface. We hypothesized that across the Suidae, positive selection mediated by infectious agents has contributed to the evolution of TLR diversity. Thus, we analyzed Sus scrofa, Sus barbatus, Sus verrucosus, Sus celebensis, Sus scebifrons, Babyrousa babyrussa, Potamochoerus larvatus, Potamochoerus porcus and Phacochoerus africanus genomes. Specifically, analyses were performed to identify evidence of positive selection using Maximum likelihood (ML) methods within a phylogenetic framework for bacterial and viral sensing Suidae TLR extracellular domains. Our analyses did not reveal evidence of positive selection for TLR3 and TLR7, suggesting strong functional conservation among these two genes for members of the Suidae. Positive selection was inferred for Suidae TLR1, TLR2, TLR6 and TLR8 evolution. ML methods identified amino acid sites of the bacterial sensing TLR1, TLR2, TLR6 and the viral sensing TLR8 to be under persistent positive selection. Some of these sites are in close proximity to functionally relevant sites, further strengthening the case for pathogen mediated selection for these sites. The branch leading to the genus Sus demonstrated evidence of episodic positive selection for TLR1, indicating selection mediated by infectious agents encountered within the specific geographic origin of the Sus. These results indicate that species of the Suidae have positively selected residues within functional domains of TLRs reflective of prior infections. Thus, TLR genes represent candidates for experimental validation to determine their functional role in antibacterial and antiviral activity within members of the Suidae.
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Affiliation(s)
- Kwame A. Darfour-Oduro
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Alfred L. Roca
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America
| | - Martien A. M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Lawrence B. Schook
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America
- * E-mail:
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Vinkler M, Bainová H, Bryjová A, Tomášek O, Albrecht T, Bryja J. Characterisation of Toll-like receptors 4, 5 and 7 and their genetic variation in the grey partridge. Genetica 2015; 143:101-12. [PMID: 25626717 DOI: 10.1007/s10709-015-9819-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 01/18/2015] [Indexed: 12/21/2022]
Abstract
Toll-like receptors (TLRs) are a cornerstone of vertebrate innate immunity. In this study, we identified orthologues of TLR4, TLR5 and TLR7 (representing both bacterial- and viral-sensing TLRs) in the grey partridge (Perdix perdix), a European Galliform game bird species. The phylogeny of all three TLR genes follows the known phylogeny of Galloanserae birds, placing grey partridge TLRs (PePeTLRs) in close proximity to their turkey and pheasant orthologues. The predicted proteins encoded by the PePeTLR genes were 843, 862-863 and 1,047 amino acids long, respectively, and clearly showed all TLR structural features. To verify functionality in these genes we mapped their tissue-expression profiles, revealing generally high PePeTLR4 and PePeTLR5 expression in the thymus and absence of PePeTLR4 and PePeTLR7 expression in the brain. Using 454 next-generation sequencing, we then assessed genetic variation within these genes for a wild grey partridge population in the Czech Republic, EU. We identified 11 nucleotide substitutions in PePeTLR4, eight in PePeTLR5 and six in PePeTLR7, resulting in four, four and three amino acid replacements, respectively. Given their locations and chemical features, most of these non-synonymous substitutions probably have a minor functional impact. As the intraspecific genetic variation of the three TLR genes was low, we assume that either negative selection or a bottleneck may have reduced TLR population variability in this species.
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Affiliation(s)
- Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague, Czech Republic, EU,
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Alfano F, Peletto S, Lucibelli MG, Borriello G, Urciuolo G, Maniaci MG, Desiato R, Tarantino M, Barone A, Pasquali P, Acutis PL, Galiero G. Identification of single nucleotide polymorphisms in Toll-like receptor candidate genes associated with tuberculosis infection in water buffalo (Bubalus bubalis). BMC Genet 2014; 15:139. [PMID: 25496717 PMCID: PMC4278265 DOI: 10.1186/s12863-014-0139-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 11/27/2014] [Indexed: 12/17/2022] Open
Abstract
Background Toll-like receptors play a key role in innate immunity by recognizing pathogens and activating appropriate responses. Pathogens express several signal molecules (pathogen-associated molecular patterns, PAMPs) essential for survival and pathogenicity. Recognition of PAMPs triggers an array of anti-microbial immune responses through the induction of various inflammatory cytokines. The objective of this work was to perform a case-control study to characterize the distribution of polymorphisms in three candidate genes (toll-like receptor 2, toll-like receptor 4, toll-like receptor 9) and to test their role as potential risk factors for tuberculosis infection in water buffalo (Bubalus bubalis). Results The case-control study included 184 subjects, 59 of which resulted positive to both intradermal TB test and Mycobacterium bovis isolation (cases) and 125 resulted negative to at least three consecutive intradermal TB tests. The statistical analysis indicated that two polymorphisms exhibited significant differences in allelic frequencies between cases and controls. Indeed, the TT genotype at TLR9 2340 C > T locus resulted significantly associated with susceptibility to bovine tuberculosis (P = 0.030, OR = 3.31, 95% CI = 1.05-10.40). One polymorphism resulted significantly associated with resistance to the disease, and included the CC genotype, at the TLR4 672 A > C locus (P = 0.01, OR = 0.26, 95% CI = 0.08-0.80). Haplotype reconstruction of the TLR2 gene revealed one haplotype (CTTACCAGCGGCCAGTCCC) associated with disease resistance (P = 0.04, OR = 0.51, 95% CI = 0.27–0.96), including the allelic variant associated with disease resistance. Conclusions The work describes novel mutations in bubaline TLR2, TLR4 and TLR9 genes and presents their association with M. bovis infection. These results will enhance our ability to determine the risk of developing the disease by improving the knowledge of the immune mechanisms involved in host response to mycobacterial infection, and will allow the creation of multiple layers of disease resistance in herds by selective breeding.
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Affiliation(s)
- Flora Alfano
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 80055, Portici, Italy.
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Via Bologna, 148, 10154, Torino, Italy.
| | | | - Giorgia Borriello
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 80055, Portici, Italy.
| | - Giovanna Urciuolo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 80055, Portici, Italy.
| | - Maria Grazia Maniaci
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Via Bologna, 148, 10154, Torino, Italy.
| | - Rosanna Desiato
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Via Bologna, 148, 10154, Torino, Italy.
| | - Michela Tarantino
- Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Viale Regina Elena, 299, 00161, Roma, Italy.
| | - Amalia Barone
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", Via Università 100, 80055, Portici, Italy.
| | - Paolo Pasquali
- Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Viale Regina Elena, 299, 00161, Roma, Italy.
| | - Pier Luigi Acutis
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Via Bologna, 148, 10154, Torino, Italy.
| | - Giorgio Galiero
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 80055, Portici, Italy.
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Vinkler M, Bainová H, Bryja J. Protein evolution of Toll-like receptors 4, 5 and 7 within Galloanserae birds. Genet Sel Evol 2014; 46:72. [PMID: 25387947 PMCID: PMC4228102 DOI: 10.1186/s12711-014-0072-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/10/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Toll-like receptors (TLR) are essential activators of the innate part of the vertebrate immune system. In this study, we analysed the interspecific variability of three TLR (bacterial-sensing TLR4 and TLR5 and viral-sensing TLR7) within the Galloanserae bird clade, investigated their phylogeny, assessed their structural conservation and estimated site-specific selection pressures. RESULTS Physiochemical properties varied according to the TLR analysed, mainly with regards to the surface electrostatic potential distribution. The predicted ligand-binding features (mainly in TLR4 and TLR5) differed between the avian proteins and their fish and mammalian counterparts, but also varied within the Galloanserae birds. We identified 20 positively selected sites in the three TLR, among which several are topologically close to ligand-binding sites reported for mammalian and fish TLR. We described 26, 28 and 25 evolutionarily non-conservative sites in TLR4, TLR5 and TLR7, respectively. Thirteen of these sites in TLR4, and ten in TLR5 were located in functionally relevant regions. The variability appears to be functionally more conserved for viral-sensing TLR7 than for the bacterial-sensing TLR. Amino-acid positions 268, 270, 343, 383, 444 and 471 in TLR4 and 180, 183, 209, 216, 264, 342 and 379 in TLR5 are key candidates for further functional research. CONCLUSIONS Host-pathogen co-evolution has a major effect on the features of host immune receptors. Our results suggest that avian and mammalian TLR may be differentially adapted to pathogen-derived ligand recognition. We have detected signatures of positive selection even within the Galloanserae lineage. To our knowledge, this is the first study to depict evolutionary pressures on Galloanserae TLR and to estimate the validity of current knowledge on TLR function (based on mammalian and chicken models) for non-model species of this clade.
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Affiliation(s)
- Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University in Prague, Praha, Czech Republic.
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RETRACTED ARTICLE: Variant Interleukin-1 Receptor-Associated Kinase-2 Mediates Increased NF-κB and p38 Activity Induced by Lipopolysaccharide. Inflammation 2014; 37:993. [DOI: 10.1007/s10753-014-9823-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Mancini RJ, Stutts L, Ryu KA, Tom JK, Esser-Kahn AP. Directing the immune system with chemical compounds. ACS Chem Biol 2014; 9:1075-85. [PMID: 24690004 PMCID: PMC5674983 DOI: 10.1021/cb500079s] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Agonists of immune cell receptors direct innate and adaptive immunity. These agonists range in size and complexity from small molecules to large macromolecules. Here, agonists of a class of immune cell receptors known as the Toll-like receptors (TLRs) are highlighted focusing on the distinctive molecular moieties that pertain to receptor binding and activation. How the structure and combined chemical signals translate into a variety of immune responses remain major questions in the field. In this structure-focused review, we outline potential areas where the tools of chemical biology could help decipher the emerging molecular codes that direct immune stimulation.
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Affiliation(s)
- Rock J Mancini
- Department of Chemistry, Chemical Engineering and Materials Science, and Biomedical Engineering, University of California Irvine , 1102 Natural Sciences 2, Irvine, California 92697-2025, United States
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Tseng CY, Gajewski M, Danani A, Tuszynski JA. Homology and Molecular Dynamics Models of Toll-Like Receptor 7 Protein and Its Dimerization. Chem Biol Drug Des 2014; 83:656-65. [DOI: 10.1111/cbdd.12278] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/12/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Chih-Yuan Tseng
- Department of Oncology; University of Alberta; 3-336 Cross Cancer Institute 11560 University Avenue Edmonton AB T6G 1Z2 Canada
| | - Melissa Gajewski
- DTI-Department of Innovative Technologies; PMET-Laboratory of Pharmaceutical and Medical Technologies SUPSI-University of Applied Sciences of Southern Switzerland; Lugano Switzerland
| | - Andrea Danani
- DTI-Department of Innovative Technologies; PMET-Laboratory of Pharmaceutical and Medical Technologies SUPSI-University of Applied Sciences of Southern Switzerland; Lugano Switzerland
| | - Jack A. Tuszynski
- Department of Oncology; University of Alberta; 3-336 Cross Cancer Institute 11560 University Avenue Edmonton AB T6G 1Z2 Canada
- DTI-Department of Innovative Technologies; PMET-Laboratory of Pharmaceutical and Medical Technologies SUPSI-University of Applied Sciences of Southern Switzerland; Lugano Switzerland
- Department of Physics; University of Alberta; Edmonton AB Canada
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Roche DB, Buenavista MT, McGuffin LJ. Assessing the quality of modelled 3D protein structures using the ModFOLD server. Methods Mol Biol 2014; 1137:83-103. [PMID: 24573476 DOI: 10.1007/978-1-4939-0366-5_7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.
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Affiliation(s)
- Daniel Barry Roche
- Genoscope, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France
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Gao H, Wu L, Sun JS, Geng XY, Pan BP. Molecular characterization and expression analysis of Toll-like receptor 21 cDNA from Paralichthys olivaceus. FISH & SHELLFISH IMMUNOLOGY 2013; 35:1138-1145. [PMID: 23880453 DOI: 10.1016/j.fsi.2013.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/30/2013] [Accepted: 07/14/2013] [Indexed: 06/02/2023]
Abstract
Toll-like receptor (TLR) is believed to play crucial role in host defense of pathogenic microbes in innate immune system. In the present study, the full-length cDNA of Paralichthys olivaceus Toll-like receptor 21 (Po-TLR21) was cloned by homology cloning and rapid amplification of cDNA ends (RACE) technique. The Po-TLR21 cDNA sequence was 3687 bp, containing an open reading frame of 2922 bp encoding 973 amino acids. TMHMM and SMART program analysis indicated that protein contained one transmembrane domain, eighteen leucine-rich repeats (LRRs), and one Toll/IL-1 receptor homology domain (TIR). Multiple alignment analysis of the Po-TLR21 protein-coding sequence with other known TLR21 from grouper, pufferfish, zebrafish, cod, catfish, carp and chicken showed the homology of 67%, 63%, 54%, 52%, 51%, 49%, and 39%, respectively. The Po-TLR21 mRNA expression patterns were measured by real-time PCR. The results revealed that TLR21 is widely expressed in various tested healthy tissues, and highly expressed in spleen and gill. In vivo immunostimulation experiments revealed that expression of TLR21 is modulated by Vibrio anguillarum (V. anguillarum), CpG oligodeoxynucleotides (CpG ODN) and poly I:C. Moreover, the inhibitor of homodimerization of myeloid differentiation factor 88 (MyD88) could significantly reduce the up-regulation of TLR21, MyD88, and tumor necrosis factor (TNF) expression in CpG ODN or poly I:C-treated head kidney cells in vitro. These results indicate that TLR21 may be involved in the pathogen recognition in the early innate immune.
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Affiliation(s)
- Hong Gao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, PR China.
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Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE). BMC Evol Biol 2013; 13:194. [PMID: 24028551 PMCID: PMC3848458 DOI: 10.1186/1471-2148-13-194] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs). RESULTS We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades. CONCLUSIONS In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands.
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Swathi A, Dhinakar Raj G, Raja A, Tirumurugaan KG. Homology modeling and structural comparison of leucine rich repeats of Toll like receptors 1-10 of ruminants. J Mol Model 2013; 19:3863-74. [PMID: 23812948 DOI: 10.1007/s00894-013-1871-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 04/30/2013] [Indexed: 01/04/2023]
Abstract
Toll-like receptors (TLRs) are transmembrane receptors composed of extra cellular leucine rich repeats (LRRs) that identify specific pathogen associated molecular patterns triggering a innate immune cascade. The LRR regions of TLR 1-10 proteins of goat (Capra hircus), sheep (Ovis aries), buffalo (Bubalus bubalis) and bovine (Bos taurus) were modeled using MODELLER 9v7 tool and validated. The similarities and variations of these 10 TLRs extracellular regions of each species were compared using online servers like FATCAT, SSM and SSAP. It was evident that the LRRs of TLRs like 1, 2, 3 and 6 showed structural convergence with <1 % RMSD deviation while TLRs like 5, 7, 8 and 9 had high divergence. Docking analysis showed that TLR 2, 3 and 7 of all the selected four ruminant species were able to bind with their corresponding ligands like Peptidoglycan (PGN), Poly I:C, Resiquimod (R-848) and Imiquimod. However, there were variations in the active site regions, interacting residues and the number of bonded interactions. Variations seen among TLR structures and their ligand binding characteristics is likely to be responsible for species and breed specific genetic resistance observed among species or breeds.
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Affiliation(s)
- Anandan Swathi
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, 600 007, Chennai, India
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Yu H, Jin H, Sun L, Zhang L, Sun G, Wang Z, Yu Y. Toll-like receptor 7 agonists: chemical feature based pharmacophore identification and molecular docking studies. PLoS One 2013; 8:e56514. [PMID: 23526932 PMCID: PMC3603940 DOI: 10.1371/journal.pone.0056514] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/10/2013] [Indexed: 12/19/2022] Open
Abstract
Chemical feature based pharmacophore models were generated for Toll-like receptors 7 (TLR7) agonists using HypoGen algorithm, which is implemented in the Discovery Studio software. Several methods tools used in validation of pharmacophore model were presented. The first hypothesis Hypo1 was considered to be the best pharmacophore model, which consists of four features: one hydrogen bond acceptor, one hydrogen bond donor, and two hydrophobic features. In addition, homology modeling and molecular docking studies were employed to probe the intermolecular interactions between TLR7 and its agonists. The results further confirmed the reliability of the pharmacophore model. The obtained pharmacophore model (Hypo1) was then employed as a query to screen the Traditional Chinese Medicine Database (TCMD) for other potential lead compounds. One hit was identified as a potent TLR7 agonist, which has antiviral activity against hepatitis virus in vitro. Therefore, our current work provides confidence for the utility of the selected chemical feature based pharmacophore model to design novel TLR7 agonists with desired biological activity.
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Affiliation(s)
- Hui Yu
- Department of Laboratory Centre, the Affiliated Tenth People's Hospital, Tongji University, Shanghai, China
- The Second Affiliated Hospital, Baotou Medical College, Baotou, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Lidan Sun
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Gang Sun
- The Second Affiliated Hospital, Baotou Medical College, Baotou, China
| | - Zhanli Wang
- The First Affiliated Hospital, Baotou Medical College, Baotou, China
- * E-mail: (ZW); (YY)
| | - Yongchun Yu
- Department of Laboratory Centre, the Affiliated Tenth People's Hospital, Tongji University, Shanghai, China
- * E-mail: (ZW); (YY)
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Hoque R, Farooq A, Malik A, Trawick BN, Berberich DW, McClurg JP, Galen KP, Mehal W. A novel small-molecule enantiomeric analogue of traditional (-)-morphinans has specific TLR9 antagonist properties and reduces sterile inflammation-induced organ damage. THE JOURNAL OF IMMUNOLOGY 2013; 190:4297-304. [PMID: 23509352 DOI: 10.4049/jimmunol.1202184] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
TLR9 is a key determinant of the innate immune responses in both infectious and sterile injury. Specific antagonism of TLR9 is of great clinical interest to reduce tissue damage in a wide range of pathologies, and has been approached by modification of nucleic acids, the recognized ligand for TLR9. Such oligonucleotide-derived pharmacotherapeutics have limitations in specificity for nucleic acid receptors, significant potential for immunologic recognition with generation of innate and adaptive immune responses, and limited bioavailability. We have identified enantiomeric analogues of traditional (-)-morphinans as having TLR9 antagonist properties on reporter cell lines. One of these analogues (COV08-0064) is demonstrated to be a novel small-molecule antagonist of TLR9 with greater specificity for TLR9 than oligo-based antagonists. COV08-0064 has wide bioavailability, including the s.c. and oral routes. It specifically inhibits the action of TLR9 antagonists on reporter cells lines and the production of cytokines by TLR9 agonists from primary cells. It also has efficacy in limiting TLR9-mediated sterile inflammation in in vivo models of acute liver injury and acute pancreatitis. The identification of a morphinan-based novel small-molecule structure with TLR9 antagonism is a significant step in expanding therapeutic strategies in the field of sterile inflammatory injury.
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Affiliation(s)
- Rafaz Hoque
- Section of Digestive Diseases, Yale University, New Haven, CT 06520, USA
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Suwarti S, Yamazaki T, Svetlana C, Hanagata N. Recognition of CpG oligodeoxynucleotides by human Toll-like receptor 9 and subsequent cytokine induction. Biochem Biophys Res Commun 2012; 430:1234-9. [PMID: 23266611 DOI: 10.1016/j.bbrc.2012.12.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 12/16/2012] [Indexed: 01/08/2023]
Abstract
Toll-like receptor 9 (TLR9) recognizes a synthetic ligand, oligodeoxynucleotide (ODN) containing cytosine-phosphate-guanine (CpG). Activation of TLR9 by CpG ODN induces a signal transduction cascade that plays a pivotal role in first-line immune defense in the human body. The three-dimensional structure of TLR9 has not yet been reported, and the ligand-binding mechanism of TLR9 is still poorly understood; therefore, the mechanism of human TLR9 (hTLR9) ligand binding needs to be elucidated. In this study, we constructed several hTLR9 mutants, including truncated mutants and single mutants in the predicted CpG ODN-binding site. We used these mutants to analyze the role of potential important regions of hTLR9 in receptor signaling induced by phosphorothioate (PTO)-modified CpG ODN and CpG ODNs only consist entirely of a phosphodiester (PD) backbone, CpG ODN2006x3-PD that we developed. We found truncated mutants of hTLR9 lost the signaling activity, indicating that both the C- and N-termini of the extracellular domain (ECD) are necessary for the function of hTLR9. We identified residues, His505, Gln510, His530, and Tyr554, in the C-terminal of hTLR9-ECD that are essential for hTLR9 activation. These residues might form positive charged clusters with which negatively charged CpG ODN could interact. Furthermore, we observed ODN-PD induced interleukin-6 (IL-6) through TLR9 in a CpG-sequence-dependent manner in human peripheral blood mononuclear cells and B cells, whereas ODN-PTO induced IL-6 in a CpG-sequence-independent manner. These finding are relevant for the mechanism of hTLR9 activation by CpG ODNs.
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Affiliation(s)
- Suwarti Suwarti
- Graduate School of Life Science, Hokkaido University, N10W8, Sapporo 060-0810, Japan
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Qi R, Singh D, Kao CC. Proteolytic processing regulates Toll-like receptor 3 stability and endosomal localization. J Biol Chem 2012; 287:32617-29. [PMID: 22865861 PMCID: PMC3463343 DOI: 10.1074/jbc.m112.387803] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/30/2012] [Indexed: 11/06/2022] Open
Abstract
Toll-like receptors (TLRs) 3, 7, and 9 are innate immune receptors that recognize nucleic acids from pathogens in endosomes and initiate signaling transductions that lead to cytokine production. Activation of TLR9 for signaling requires proteolytic processing within the ectodomain by endosome-associated proteases. Whether TLR3 requires similar proteolytic processing to become competent for signaling remains unclear. Herein we report that human TLR3 is proteolytically processed to form two fragments in endosomes. Unc93b1 is required for processing by transporting TLR3 through the Golgi complex and to the endosomes. Proteolytic cleavage requires the eight-amino acid Loop1 within leucine-rich repeat 12 of the TLR3 ectodomain. Proteolytic cleavage is not required for TLR3 signaling in response to poly(I:C), although processing could modulate the degree of response toward viral double-stranded RNAs, especially in mouse cells. Both the full-length and cleaved fragments of TLR3 can bind poly(I:C) and are present in endosomes. However, although the full-length TLR3 has a half-life in HEK293T cells of 3 h, the cleaved fragments have half-lives in excess of 7 h. Inhibition of TLR3 cleavage by either treatment with cathepsin inhibitor or by a mutation in Loop1 decreased the abundance of TLR3 in endosomes targeted for lysosomal degradation.
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Affiliation(s)
- Rongsu Qi
- From the Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47401
| | - Divyendu Singh
- From the Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47401
| | - C. Cheng Kao
- From the Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47401
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Mikami T, Miyashita H, Takatsuka S, Kuroki Y, Matsushima N. Molecular evolution of vertebrate Toll-like receptors: Evolutionary rate difference between their leucine-rich repeats and their TIR domains. Gene 2012; 503:235-43. [DOI: 10.1016/j.gene.2012.04.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 04/03/2012] [Accepted: 04/06/2012] [Indexed: 11/30/2022]
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Leucine-Rich Repeat (LRR) Domains Containing Intervening Motifs in Plants. Biomolecules 2012; 2:288-311. [PMID: 24970139 PMCID: PMC4030839 DOI: 10.3390/biom2020288] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 01/05/2023] Open
Abstract
LRRs (leucine rich repeats) are present in over 14,000 proteins. Non-LRR, island regions (IRs) interrupting LRRs are widely distributed. The present article reviews 19 families of LRR proteins having non-LRR IRs (LRR@IR proteins) from various plant species. The LRR@IR proteins are LRR-containing receptor-like kinases (LRR-RLKs), LRR-containing receptor-like proteins (LRR-RLPs), TONSOKU/BRUSHY1, and MJK13.7; the LRR-RLKs are homologs of TMK1/Rhg4, BRI1, PSKR, PSYR1, Arabidopsis At1g74360, and RPK2, while the LRR-RLPs are those of Cf-9/Cf-4, Cf-2/Cf-5, Ve, HcrVf, RPP27, EIX1, clavata 2, fascinated ear2, RLP2, rice Os10g0479700, and putative soybean disease resistance protein. The LRRs are intersected by single, non-LRR IRs; only the RPK2 homologs have two IRs. In most of the LRR-RLKs and LRR-RLPs, the number of repeat units in the preceding LRR block (N1) is greater than the number of the following block (N2); N1 » N2 in which N1 is variable in the homologs of individual families, while N2 is highly conserved. The five families of the LRR-RLKs except for the RPK2 family show N1 = 8 − 18 and N2 = 3 − 5. The nine families of the LRR-RLPs show N1 = 12 − 33 and N2 = 4; while N1 = 6 and N2 = 4 for the rice Os10g0479700 family and the N1 = 4 − 28 and N2 = 4 for the soybean protein family. The rule of N1 » N2 might play a common, significant role in ligand interaction, dimerization, and/or signal transduction of the LRR-RLKs and the LRR-RLPs. The structure and evolution of the LRR domains with non-LRR IRs and their proteins are also discussed.
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Abstract
Besides their well known functions in storage and translation of information nucleic acids have emerged as a target of pattern recognition receptors that drive activation of innate immunity. Due to the paucity of building block monomers used in nucleic acids, discrimination of host and microbial nucleic acids as a means of self/foreign discrimination is a complicated task. Pattern recognition receptors rely on discrimination by sequence, structural features and spatial compartmentalization to differentiate microbial derived nucleic acids from host ones. Microbial nucleic acid detection is important for the sensing of infectious danger and initiating an immune response to microbial attack. Failures in the underlying recognitions systems can have severe consequences: thus, inefficient recognition of microbial nucleic acids may increase susceptibility to infectious diseases. On the other hand, excessive immune responses as a result of failed self/foreign discrimination are associated with autoimmune diseases. This review gives a general overview over the underlying concepts of nucleic acid sensing by Toll-like receptors. Within this general framework, we focus on bacterial RNA and synthetic RNA oligomers.
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Affiliation(s)
- Alexander Dalpke
- Heidelberg University, Department of Infectious Diseases - Medical Microbiology and Hygiene, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
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Areal H, Abrantes J, Esteves PJ. Signatures of positive selection in Toll-like receptor (TLR) genes in mammals. BMC Evol Biol 2011; 11:368. [PMID: 22185391 PMCID: PMC3276489 DOI: 10.1186/1471-2148-11-368] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 12/20/2011] [Indexed: 12/13/2022] Open
Abstract
Background Toll-like receptors (TLRs) are a major class of pattern recognition receptors (PRRs) expressed in the cell surface or membrane compartments of immune and non-immune cells. TLRs are encoded by a multigene family and represent the first line of defense against pathogens by detecting foreigner microbial molecular motifs, the pathogen-associated molecular patterns (PAMPs). TLRs are also important by triggering the adaptive immunity in vertebrates. They are characterized by the presence of leucine-rich repeats (LRRs) in the ectodomain, which are associated with the PAMPs recognition. The direct recognition of different pathogens by TLRs might result in different evolutionary adaptations important to understand the dynamics of the host-pathogen interplay. Ten mammal TLR genes, viral (TLR3, 7, 8, 9) and non-viral (TLR1-6, 10), were selected to identify signatures of positive selection that might have been imposed by interacting pathogens and to clarify if viral and non-viral TLRs might display different patterns of molecular evolution. Results By using Maximum Likelihood approaches, evidence of positive selection was found in all the TLRs studied. The number of positively selected codons (PSC) ranged between 2-26 codons (0.25%-2.65%) with the non-viral TLR4 as the receptor with higher percentage of positively selected codons (2.65%), followed by the viral TLR8 (2.50%). The results indicated that viral and non-viral TLRs are similarly under positive selection. Almost all TLRs have at least one PSC located in the LRR ectodomain which underlies the importance of the pathogen recognition by this region. Conclusions Our results are not in line with previous studies on primates and birds that identified more codons under positive selection in non-viral TLRs. This might be explained by the fact that both primates and birds are homogeneous groups probably being affected by only a restricted number of related viruses with equivalent motifs to be recognized. The analyses performed in this work encompassed a large number of species covering some of the most representative mammalian groups - Artiodactyla, Rodents, Carnivores, Lagomorphs and Primates - that are affected by different families of viruses. This might explain the role of adaptive evolution in shaping viral TLR genes.
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Affiliation(s)
- Helena Areal
- CIBIO-UP, Centro de Investigacao em Biodiversidade e Recursos Geneticos - Universidade do Porto, Campus Agrario de Vairao, Rua Padre Armando Quintas, nr,7, 4485-661 Vairao, Portugal
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Comparative analysis of species-specific ligand recognition in Toll-like receptor 8 signaling: a hypothesis. PLoS One 2011; 6:e25118. [PMID: 21949866 PMCID: PMC3176813 DOI: 10.1371/journal.pone.0025118] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Accepted: 08/25/2011] [Indexed: 12/31/2022] Open
Abstract
Toll-like receptors (TLRs) play a central role in the innate immune response by recognizing conserved structural patterns in a variety of microbes. TLRs are classified into six families, of which TLR7 family members include TLR7, 8, and 9, which are localized to endolysosomal compartments recognizing viral infection in the form of foreign nucleic acids. In our current study, we focused on TLR8, which has been shown to recognize different types of ligands such as viral or bacterial ssRNA as well as small synthetic molecules. The primary sequences of rodent and non-rodent TLR8s are similar, but the antiviral compound (R848) that activates the TLR8 pathway is species-specific. Moreover, the factors underlying the receptor's species-specificity remain unknown. To this end, comparative homology modeling, molecular dynamics simulations refinement, automated docking and computational mutagenesis studies were employed to probe the intermolecular interactions between this anti-viral compound and TLR8. Furthermore, comparative analyses of modeled TLR8 (rodent and non-rodent) structures have shown that the variation mainly occurs at LRR14-15 (undefined region); hence, we hypothesized that this variation may be the primary reason for the exhibited species-specificity. Our hypothesis was further bolstered by our docking studies, which clearly showed that this undefined region was in close proximity to the ligand-binding site and thus may play a key role in ligand recognition. In addition, the interface between the ligand and TLR8s varied depending upon the amino acid charges, free energy of binding, and interaction surface. Therefore, our current work provides a hypothesis for previous in vivo studies in the context of TLR signaling.
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Manavalan B, Basith S, Choi S. Similar Structures but Different Roles - An Updated Perspective on TLR Structures. Front Physiol 2011; 2:41. [PMID: 21845181 PMCID: PMC3146039 DOI: 10.3389/fphys.2011.00041] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 07/11/2011] [Indexed: 01/25/2023] Open
Abstract
Toll-like receptors (TLRs) are pattern recognition receptors that recognize conserved structures in pathogens, trigger innate immune responses, and prime antigen-specific adaptive immunity. Elucidation of crystal structures of TLRs interacting with their ligands such as TLR1-2 with triacylated lipopeptide, TLR2-6 with diacylated lipopeptide, TLR4-MD-2 with LPS, and TLR3 with double-stranded RNA (dsRNA) have enabled an understanding of the initiation of TLR signaling. Agonistic ligands such as LPS, dsRNA, and lipopeptides induce "m" shaped TLR dimers in which C-termini converge at the center. Such central convergence is necessary to bring the two intracellular receptor TIR domains closer together and promote their dimerization, which serves as an essential step in downstream signaling. In this review, we summarize TLR ECD structures that have been reported to date with special emphasis on ligand recognition and activation mechanism.
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McKelvey KJ, Highton J, Hessian PA. Cell-specific expression of TLR9 isoforms in inflammation. J Autoimmun 2011; 36:76-86. [DOI: 10.1016/j.jaut.2010.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 10/07/2010] [Accepted: 11/02/2010] [Indexed: 01/08/2023]
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