1
|
Rao H, Tian H, Wang X, Huo C, Zhu L, Li Z, Li Y. Diversification of Toll-like receptor 1 in swamp eel (Monopterus albus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 157:105190. [PMID: 38697378 DOI: 10.1016/j.dci.2024.105190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Toll-like receptor 1 (TLR1) is a pattern recognition receptor that plays critical roles in triggering immune activation via detecting bacterial lipoproteins and lipopeptides. In this study, the genetic characteristic of TLR1 was studied for an important aquaculture fish, swamp eel Monopterus albus. The eel has been seriously threatened by infectious diseases. However, a low level of genetic heterogeneity in the fish that has resulted from a demographic bottleneck presents further challenges in breeding for disease resistance. A comparison with the homologue of closely related species M. javanensis revealed that amino acid replacement (nonsynonymous) but not silent (synonymous) differences have accumulated nonrandomly over the coding sequences of the receptors at the early stage of their phylogenetic split. The combined results from comparative analyses of nonsynonymous-to-synonymous polymorphisms showed that the receptor has undergone significant diversification in M. albus driven by adaptive selection likely after the genetic bottleneck. Some of the changes reported here have taken place in the structures mediating heterodimerization with co-receptor TLR2, ligand recognition, and/or formation of active signaling complex with adaptor, which highlighted key structural elements and strategies of TLR1 in arms race against exogenous challenges. The findings of this study will add to the knowledge base of genetic engineering and breeding for disease resistance in the eel.
Collapse
Affiliation(s)
- Han Rao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, PR China
| | - Xueting Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, PR China
| | - Caifei Huo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
| | - Lilan Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, PR China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, PR China.
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China.
| |
Collapse
|
2
|
Lushpa VA, Goncharuk MV, Talyzina IA, Arseniev AS, Bocharov EV, Mineev KS, Goncharuk SA. TIR domains of TLR family-from the cell culture to the protein sample for structural studies. PLoS One 2024; 19:e0304997. [PMID: 38968257 PMCID: PMC11226090 DOI: 10.1371/journal.pone.0304997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/14/2024] [Indexed: 07/07/2024] Open
Abstract
Toll-like receptors (TLRs) are key players in the innate immune system. Despite the great efforts in TLR structural biology, today we know the spatial structures of only four human TLR intracellular TIR domains. All of them belong to one of five subfamilies of receptors. One of the main bottlenecks is the high-level production of correctly folded proteins in soluble form. Here we used a rational approach to find the optimal parameters to produce TIR domains of all ten human TLR family members in soluble form in E. coli cells. We showed that dozens of milligrams of soluble His-tagged TLR2/3/6/7TIR and MBP-tagged TLR3/5/7/8TIR can be produced. We also developed the purification protocols and demonstrated by CD and NMR spectroscopy that purified TLR2/3/7TIR demonstrate a structural organization inherent to TIR domains. This illustrates the correct folding of produced proteins and their suitability for further structural and functional investigations.
Collapse
Affiliation(s)
- Vladislav A. Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Irina A. Talyzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
3
|
Neupane KR, Ramon GS, Harvey B, Chun B, Aryal SP, Masud AA, McCorkle JR, Kolesar JM, Kekenes-Huskey PM, Richards CI. Programming Cell-Derived Vesicles with Enhanced Immunomodulatory Properties. Adv Healthc Mater 2023; 12:e2301163. [PMID: 37377147 PMCID: PMC11070110 DOI: 10.1002/adhm.202301163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 06/29/2023]
Abstract
Tumor-associated macrophages are the predominant immune cells present in the tumor microenvironment and mostly exhibit a pro-tumoral M2-like phenotype. However, macrophage biology is reversible allowing them to acquire an anti-tumoral M1-like phenotype in response to external stimuli. A potential therapeutic strategy for treating cancer may be achieved by modulating macrophages from an M2 to an M1-like phenotype with the tumor microenvironment. Here, programmed nanovesicles are generated as an immunomodulatory therapeutic platform with the capability to re-polarize M2 macrophages toward a proinflammatory phenotype. Programmed nanovesicles are engineered from cellular membranes to have specific immunomodulatory properties including the capability to bidirectionally modulate immune cell polarization. These programmed nanovesicles decorated with specific membrane-bound ligands can be targeted toward specific cell types including immune cells. Macrophage-derived vesicles are engineered to enhance immune cell reprogramming toward a proinflammatory phenotype.
Collapse
Affiliation(s)
- Khaga R Neupane
- Department of Chemistry, University of Kentucky, 506 Library Drive, 125 Chemistry-Physics Building, Lexington, KY, 40506, USA
| | - Geraldine S Ramon
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, IL, USA
| | - Brock Harvey
- Department of Chemistry, University of Kentucky, 506 Library Drive, 125 Chemistry-Physics Building, Lexington, KY, 40506, USA
| | - Byeong Chun
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, IL, USA
| | - Surya P Aryal
- Department of Chemistry, University of Kentucky, 506 Library Drive, 125 Chemistry-Physics Building, Lexington, KY, 40506, USA
| | - Abdullah A Masud
- Department of Chemistry, University of Kentucky, 506 Library Drive, 125 Chemistry-Physics Building, Lexington, KY, 40506, USA
| | - J Robert McCorkle
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Kentucky, Lexington, KY, 40508, USA
| | - Jill M Kolesar
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Kentucky, Lexington, KY, 40508, USA
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, IL, USA
| | - Christopher I Richards
- Department of Chemistry, University of Kentucky, 506 Library Drive, 125 Chemistry-Physics Building, Lexington, KY, 40506, USA
| |
Collapse
|
4
|
Kornilov FD, Shabalkina AV, Lin C, Volynsky PE, Kot EF, Kayushin AL, Lushpa VA, Goncharuk MV, Arseniev AS, Goncharuk SA, Wang X, Mineev KS. The architecture of transmembrane and cytoplasmic juxtamembrane regions of Toll-like receptors. Nat Commun 2023; 14:1503. [PMID: 36932058 PMCID: PMC10023784 DOI: 10.1038/s41467-023-37042-6] [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: 08/24/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
Toll-like receptors (TLRs) are the important participants of the innate immune response. Their spatial organization is well studied for the ligand-binding domains, while a lot of questions remain unanswered for the membrane and cytoplasmic regions of the proteins. Here we use solution NMR spectroscopy and computer simulations to investigate the spatial structures of transmembrane and cytoplasmic juxtamembrane regions of TLR2, TLR3, TLR5, and TLR9. According to our data, all the proteins reveal the presence of a previously unreported structural element, the cytoplasmic hydrophobic juxtamembrane α-helix. As indicated by the functional tests in living cells and bioinformatic analysis, this helix is important for receptor activation and plays a role, more complicated than a linker, connecting the transmembrane and cytoplasmic parts of the proteins.
Collapse
Affiliation(s)
- F D Kornilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - A V Shabalkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Cong Lin
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, Jilin, China
| | - P E Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Institute of Cytology of Russian Academy of Sciences, Tikhoretsky 4, 194064, Saint Petersburg, Russia
| | - E F Kot
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - A L Kayushin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - V A Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - M V Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - S A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, Jilin, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 230026, Hefei, Anhui, China.
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
| |
Collapse
|
5
|
Zheng H, Wu P, Bonnet PA. Recent Advances on Small-Molecule Antagonists Targeting TLR7. Molecules 2023; 28:molecules28020634. [PMID: 36677692 PMCID: PMC9865772 DOI: 10.3390/molecules28020634] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
Toll-like receptor 7 (TLR7) is a class of pattern recognition receptors (PRRs) recognizing the pathogen-associated elements and damage and as such is a major player in the innate immune system. TLR7 triggers the release of pro-inflammatory cytokines or type-I interferons (IFN), which is essential for immunoregulation. Increasing reports also highlight that the abnormal activation of endosomal TLR7 is implicated in various immune-related diseases, carcinogenesis as well as the proliferation of human immunodeficiency virus (HIV). Hence, the design and development of potent and selective TLR7 antagonists based on small molecules or oligonucleotides may offer new tools for the prevention and management of such diseases. In this review, we offer an updated overview of the main structural features and therapeutic potential of small-molecule antagonists of TLR7. Various heterocyclic scaffolds targeting TLR7 binding sites are presented: pyrazoloquinoxaline, quinazoline, purine, imidazopyridine, pyridone, benzanilide, pyrazolopyrimidine/pyridine, benzoxazole, indazole, indole, and quinoline. Additionally, their structure-activity relationships (SAR) studies associated with biological activities and protein binding modes are introduced.
Collapse
Affiliation(s)
- Haoyang Zheng
- Faculty of Pharmacy, Montpellier University, 34093 Montpellier, France
| | - Peiyang Wu
- School of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Pierre-Antoine Bonnet
- Institut des Biomolécules Max Mousseron IBMM, Ecole Nationale Supérieure de Chimie de Montpellier ENSCM, Montpellier University, Centre National de La Recherche Scientifique CNRS, 34093 Montpellier, France
- Correspondence:
| |
Collapse
|
6
|
Manan A, Pirzada RH, Haseeb M, Choi S. Toll-like Receptor Mediation in SARS-CoV-2: A Therapeutic Approach. Int J Mol Sci 2022; 23:ijms231810716. [PMID: 36142620 PMCID: PMC9502216 DOI: 10.3390/ijms231810716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
The innate immune system facilitates defense mechanisms against pathogen invasion and cell damage. Toll-like receptors (TLRs) assist in the activation of the innate immune system by binding to pathogenic ligands. This leads to the generation of intracellular signaling cascades including the biosynthesis of molecular mediators. TLRs on cell membranes are adept at recognizing viral components. Viruses can modulate the innate immune response with the help of proteins and RNAs that downregulate or upregulate the expression of various TLRs. In the case of COVID-19, molecular modulators such as type 1 interferons interfere with signaling pathways in the host cells, leading to an inflammatory response. Coronaviruses are responsible for an enhanced immune signature of inflammatory chemokines and cytokines. TLRs have been employed as therapeutic agents in viral infections as numerous antiviral Food and Drug Administration-approved drugs are TLR agonists. This review highlights the therapeutic approaches associated with SARS-CoV-2 and the TLRs involved in COVID-19 infection.
Collapse
Affiliation(s)
- Abdul Manan
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | | | - Muhammad Haseeb
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
- Correspondence:
| |
Collapse
|
7
|
Lee E, Redzic JS, Nemkov T, Saviola AJ, Dzieciatkowska M, Hansen KC, D’Alessandro A, Dinarello C, Eisenmesser EZ. Human and Bacterial Toll-Interleukin Receptor Domains Exhibit Distinct Dynamic Features and Functions. Molecules 2022; 27:4494. [PMID: 35889366 PMCID: PMC9318647 DOI: 10.3390/molecules27144494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Toll-interleukin receptor (TIR) domains have emerged as critical players involved in innate immune signaling in humans but are also expressed as potential virulence factors within multiple pathogenic bacteria. However, there has been a shortage of structural studies aimed at elucidating atomic resolution details with respect to their interactions, potentially owing to their dynamic nature. Here, we used a combination of biophysical and biochemical studies to reveal the dynamic behavior and functional interactions of a panel of both bacterial TIR-containing proteins and mammalian receptor TIR domains. Regarding dynamics, all three bacterial TIR domains studied here exhibited an inherent exchange that led to severe resonance line-broadening, revealing their intrinsic dynamic nature on the intermediate NMR timescale. In contrast, the three mammalian TIR domains studied here exhibited a range in terms of their dynamic exchange that spans multiple timescales. Functionally, only the bacterial TIR domains were catalytic towards the cleavage of NAD+, despite the conservation of the catalytic nucleophile on human TIR domains. Our development of NMR-based catalytic assays allowed us to further identify differences in product formation for gram-positive versus gram-negative bacterial TIR domains. Differences in oligomeric interactions were also revealed, whereby bacterial TIR domains self-associated solely through their attached coil-coil domains, in contrast to the mammalian TIR domains that formed homodimers and heterodimers through reactive cysteines. Finally, we provide the first atomic-resolution studies of a bacterial coil-coil domain and provide the first atomic model of the TIR domain from a human anti-inflammatory IL-1R8 protein that undergoes a slow inherent exchange.
Collapse
Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Charles Dinarello
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA;
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Elan Z. Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| |
Collapse
|