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Zhang X, Wu J, Baeza J, Gu K, Zheng Y, Chen S, Zhou Z. DeepTAP: An RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens. Comput Biol Med 2023; 164:107247. [PMID: 37454505 DOI: 10.1016/j.compbiomed.2023.107247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/31/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The transport of peptides from the cytoplasm to the endoplasmic reticulum (ER) by transporters associated with antigen processing (TAP) is a critical step in the intracellular presentation of cytotoxic T lymphocyte (CTL) epitopes. The development and application of computational methods, especially deep learning methods and new neural network strategies that can automatically learn feature representations with limited knowledge, provide an opportunity to develop fast and efficient methods to identify TAP-binding peptides. Herein, this study presents a comprehensive analysis of TAP-binding peptide sequences to derive TAP-binding motifs and preferences for N-terminal and C-terminal amino acids. A novel recurrent neural network (RNN)-based method called DeepTAP, using bidirectional gated recurrent unit (BiGRU), was developed for the accurate prediction of TAP-binding peptides. Our results demonstrated that DeepTAP achieves an optimal balance between prediction precision and false positives, outperforming other baseline models. Furthermore, DeepTAP significantly improves the prediction accuracy of high-confidence neoantigens, especially the top-ranked ones, making it a valuable tool for researchers studying antigen presentation processes and T-cell epitope screening. DeepTAP is freely available at https://github.com/zjupgx/deeptap and https://pgx.zju.edu.cn/deeptap.
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Affiliation(s)
- Xue Zhang
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jingcheng Wu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Joseph Baeza
- Biology Program, Iowa State University, Ames, IA, 50011, USA
| | - Katie Gu
- Biology Program, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Yichun Zheng
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China.
| | - Shuqing Chen
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Zhan Zhou
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China.
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2
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Cruz FM, Chan A, Rock KL. Pathways of MHC I cross-presentation of exogenous antigens. Semin Immunol 2023; 66:101729. [PMID: 36804685 PMCID: PMC10023513 DOI: 10.1016/j.smim.2023.101729] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Phagocytes, particularly dendritic cells (DCs), generate peptide-major histocompatibility complex (MHC) I complexes from antigens they have collected from cells in tissues and report this information to CD8 T cells in a process called cross-presentation. This process allows CD8 T cells to detect, respond and eliminate abnormal cells, such as cancers or cells infected with viruses or intracellular microbes. In some settings, cross-presentation can help tolerize CD8 T cells to self-antigens. One of the principal ways that DCs acquire tissue antigens is by ingesting this material through phagocytosis. The resulting phagosomes are key hubs in the cross-presentation (XPT) process and in fact experimentally conferring the ability to phagocytize antigens can be sufficient to allow non-professional antigen presenting cells (APCs) to cross-present. Once in phagosomes, exogenous antigens can be cross-presented (XPTed) through three distinct pathways. There is a vacuolar pathway in which peptides are generated and then bind to MHC I molecules within the confines of the vacuole. Ingested exogenous antigens can also be exported from phagosomes to the cytosol upon vesicular rupture and/or possibly transport. Once in the cytosol, the antigen is degraded by the proteasome and the resulting oligopeptides can be transported to MHC I molecule in the endoplasmic reticulum (ER) (a phagosome-to-cytosol (P2C) pathway) or in phagosomes (a phagosome-to-cytosol-to-phagosome (P2C2P) pathway). Here we review how phagosomes acquire the necessary molecular components that support these three mechanisms and the contribution of these pathways. We describe what is known as well as the gaps in our understanding of these processes.
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Affiliation(s)
- Freidrich M Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amanda Chan
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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3
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Characterization of Host Cell Potential Proteins Interacting with OsHV-1 Membrane Proteins. Viruses 2021; 13:v13122518. [PMID: 34960787 PMCID: PMC8705437 DOI: 10.3390/v13122518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
The interaction between viral membrane associate proteins and host cellular surface molecules should facilitate the attachment and entry of OsHV-1 into host cells. Thus, blocking the putative membrane proteins ORF25 and ORF72 of OsHV-1 with antibodies that have previously been reported to subdue OsHV-1 replication in host cells, especially ORF25. In this study, prey proteins in host hemocytes were screened by pull-down assay with recombinant baits ORF25 and ORF72, respectively. Gene Ontology (GO) analysis of these prey proteins revealed that most of them were mainly associated with binding, structural molecule activity and transport activity in the molecular function category. The protein–protein interaction (PPI) network of the prey proteins was constructed by STRING and clustered via K-means. For both ORF25 and ORF72, three clusters of these prey proteins were distinguished that were mainly associated with cytoskeleton assembly, energy metabolism and nucleic acid processing. ORF25 tended to function in synergy with actins, while ORF72 functioned mainly with tubulins. The above results suggest that these two putative membrane proteins, ORF25 and ORF72, might serve a role in the transport of viral particles with the aid of a cytoskeleton inside cells.
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Bieczynski F, Painefilú JC, Venturino A, Luquet CM. Expression and Function of ABC Proteins in Fish Intestine. Front Physiol 2021; 12:791834. [PMID: 34955897 PMCID: PMC8696203 DOI: 10.3389/fphys.2021.791834] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
In fish, the intestine is fundamental for digestion, nutrient absorption, and other functions like osmoregulation, acid-base balance, and excretion of some metabolic products. These functions require a large exchange surface area, which, in turn, favors the absorption of natural and anthropogenic foreign substances (xenobiotics) either dissolved in water or contained in the food. According to their chemical nature, nutrients, ions, and water may cross the intestine epithelium cells' apical and basolateral membranes by passive diffusion or through a wide array of transport proteins and also through endocytosis and exocytosis. In the same way, xenobiotics can cross this barrier by passive diffusion or taking advantage of proteins that transport physiological substrates. The entry of toxic substances is counterbalanced by an active efflux transport mediated by diverse membrane proteins, including the ATP binding cassette (ABC) proteins. Recent advances in structure, molecular properties, and functional studies have shed light on the importance of these proteins in cellular and organismal homeostasis. There is abundant literature on mammalian ABC proteins, while the studies on ABC functions in fish have mainly focused on the liver and, to a minor degree, on the kidney and other organs. Despite their critical importance in normal physiology and as a barrier to prevent xenobiotics incorporation, fish intestine's ABC transporters have received much less attention. All the ABC subfamilies are present in the fish intestine, although their functionality is still scarcely studied. For example, there are few studies of ABC-mediated transport made with polarized intestinal preparations. Thus, only a few works discriminate apical from basolateral transport activity. We briefly describe the main functions of each ABC subfamily reported for mammals and other fish organs to help understand their roles in the fish intestine. Our study considers immunohistochemical, histological, biochemical, molecular, physiological, and toxicological aspects of fish intestinal ABC proteins. We focus on the most extensively studied fish ABC proteins (subfamilies ABCB, ABCC, and ABCG), considering their apical or basolateral location and distribution along the intestine. We also discuss the implication of fish intestinal ABC proteins in the transport of physiological substrates and aquatic pollutants, such as pesticides, cyanotoxins, metals, hydrocarbons, and pharmaceutical products.
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Affiliation(s)
- Flavia Bieczynski
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue – Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Julio C. Painefilú
- Instituto Patagónico de Tecnologías Biológicas y Geoambientales, Consejo Nacional de Investigaciones Científicas y Técnicas – Universidad Nacional del Comahue, Bariloche, Argentina
| | - Andrés Venturino
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue – Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Comahue, Neuquén, Argentina
| | - Carlos M. Luquet
- Laboratorio de Ecotoxicología Acuática, Subsede INIBIOMA-CEAN (CONICET – UNCo), Junín de los Andes, Argentina
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5
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Al‐Majdoub ZM, Achour B, Couto N, Howard M, Elmorsi Y, Scotcher D, Alrubia S, El‐Khateeb E, Vasilogianni A, Alohali N, Neuhoff S, Schmitt L, Rostami‐Hodjegan A, Barber J. Mass spectrometry-based abundance atlas of ABC transporters in human liver, gut, kidney, brain and skin. FEBS Lett 2020; 594:4134-4150. [PMID: 33128234 PMCID: PMC7756589 DOI: 10.1002/1873-3468.13982] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/24/2020] [Accepted: 10/15/2020] [Indexed: 12/31/2022]
Abstract
ABC transporters (ATP-binding cassette transporter) traffic drugs and their metabolites across membranes, making ABC transporter expression levels a key factor regulating local drug concentrations in different tissues and individuals. Yet, quantification of ABC transporters remains challenging because they are large and low-abundance transmembrane proteins. Here, we analysed 200 samples of crude and membrane-enriched fractions from human liver, kidney, intestine, brain microvessels and skin, by label-free quantitative mass spectrometry. We identified 32 (out of 48) ABC transporters: ABCD3 was the most abundant in liver, whereas ABCA8, ABCB2/TAP1 and ABCE1 were detected in all tissues. Interestingly, this atlas unveiled that ABCB2/TAP1 may have TAP2-independent functions in the brain and that biliary atresia (BA) and control livers have quite different ABC transporter profiles. We propose that meaningful biological information can be derived from a direct comparison of these data sets.
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Affiliation(s)
- Zubida M. Al‐Majdoub
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
| | - Brahim Achour
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
| | - Narciso Couto
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
| | - Martyn Howard
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
| | - Yasmine Elmorsi
- Clinical Pharmacy DepartmentFaculty of PharmacyTanta UniversityEgypt
| | - Daniel Scotcher
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
| | - Sarah Alrubia
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
- Pharmaceutical Chemistry DepartmentCollege of PharmacyKing Saud UniversityRiyadhSaudi Arabia
| | - Eman El‐Khateeb
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
- Clinical Pharmacy DepartmentFaculty of PharmacyTanta UniversityEgypt
| | | | - Noura Alohali
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
- Pharmaceutical Practice DepartmentCollege of PharmacyPrincess Noura Bint Abdul Rahman UniversityRiyadhSaudi Arabia
| | | | - Lutz Schmitt
- Institute of BiochemistryHeinrich Heine University DüsseldorfGermany
| | - Amin Rostami‐Hodjegan
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
- Simcyp DivisionCertara UK LtdSheffieldUK
| | - Jill Barber
- Centre for Applied Pharmacokinetic ResearchSchool of Health SciencesUniversity of ManchesterUK
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6
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RNA Sequencing (RNA-Seq) Based Transcriptome Analysis in Immune Response of Holstein Cattle to Killed Vaccine against Bovine Viral Diarrhea Virus Type I. Animals (Basel) 2020; 10:ani10020344. [PMID: 32098229 PMCID: PMC7070844 DOI: 10.3390/ani10020344] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Due to the undeniable detrimental impact of bovine viral diarrhea virus (BVDV) on cattle worldwide, various preventive approaches are carried out to control the spread of this disease. Among the established preventive approaches, vaccination remains the most widely used cost-effective method of control. Hence, a deeper study into the host immune response to vaccines will further refine the efficacy of these vaccines; the identification of differentially expressed genes (DEGs) related to immune response might bring a long-lasting solution. Thus far, studies showing the genes related to the immune response of cattle to vaccines are still limited. Therefore, this study identified DEGs in animals with high and low sample to positive (S/P) ratio based on the BVDV antibody level, using RNA sequencing (RNA-seq) transcriptome analysis, and functional enrichment analysis in gene ontology (GO) annotations and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Results revealed that several upregulated and downregulated genes were significantly annotated to antigen processing and presentation (MHC class I), immune response, and interferon-gamma production, indicating the immune response of the animals related to possible shaping of their adaptive immunity against the BVDV type I. Moreover, significant enrichment to various KEGG pathways related to the development of adaptive immunity was observed. Abstract Immune response of 107 vaccinated Holstein cattle was initially obtained prior to the ELISA test. Five cattle with high and low bovine viral diarrhea virus (BVDV) type I antibody were identified as the final experimental animals. Blood samples from these animals were then utilized to determine significant differentially expressed genes (DEGs) using the RNA-seq transcriptome analysis and enrichment analysis. Our analysis identified 261 DEGs in cattle identified as experimental animals. Functional enrichment analysis in gene ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed the DEGs potentially induced by the inactivated BVDV type I vaccine, and might be responsible for the host immune responses. Our findings suggested that inactivated vaccine induced upregulation of genes involved in different GO annotations, including antigen processing and presentation of peptide antigen (via MHC class I), immune response, and positive regulation of interferon-gamma production. The observed downregulation of other genes involved in immune response might be due to inhibition of toll-like receptors (TLRs) by the upregulation of the Bcl-3 gene. Meanwhile, the result of KEGG pathways revealed that the majority of DEGs were upregulated and enriched to different pathways, including cytokine-cytokine receptor interaction, platelet activation, extracellular matrix (ECM) receptor interaction, hematopoietic cell lineage, and ATP-binding cassette (ABC) transporters. These significant pathways supported our initial findings and are known to play a vital role in shaping adaptive immunity against BVDV type 1. In addition, type 1 diabetes mellitus pathways tended to be significantly enriched. Thus, further studies are needed to investigate the prevalence of type 1 diabetes mellitus in cattle vaccinated with inactivated and live BVDV vaccine.
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7
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Kotsias F, Cebrian I, Alloatti A. Antigen processing and presentation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 348:69-121. [PMID: 31810556 DOI: 10.1016/bs.ircmb.2019.07.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dendritic cells are at the center of immune responses. They are defined by their ability to sense the environment, take up and process antigen, migrate to secondary lymphoid organs, where they present antigens to the adaptive immune system. In particular, they present lipids and proteins from pathogens, which they encountered in peripheral tissues, to T cells in order to induce a specific effector immune response. These complex antigens need to be broken down into peptides of a certain length in association with Major Histocompatibility Complex (MHC) molecules. Presentation of MHC/antigen complexes alongside costimulatory molecules and secretion of proinflammatory cytokines will induce an appropriate immune response. This interaction between dendritic cells and T cells takes place at defined locations within secondary lymphoid organs. In this review, we discuss the current knowledge and recent advances on the cellular and molecular mechanisms that underlie antigen processing and the subsequent presentation to T lymphocytes.
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Affiliation(s)
- Fiorella Kotsias
- Cátedra de Virología, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina; Instituto de Investigaciones en Producción Animal (INPA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Ignacio Cebrian
- Facultad de Ciencias Médicas, Instituto de Histología y Embriología de Mendoza (IHEM)-CONICET/Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Andrés Alloatti
- Facultad de Ciencias Médicas, Instituto de Inmunología Clínica y Experimental de Rosario (IDICER)-CONICET/Universidad Nacional de Rosario, Rosario, Argentina.
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8
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Saleh M, Kumar G, Abdel-Baki AAS, Dkhil MA, El-Matbouli M, Al-Quraishy S. Quantitative proteomic profiling of immune responses to Ichthyophthirius multifiliis in common carp skin mucus. FISH & SHELLFISH IMMUNOLOGY 2019; 84:834-842. [PMID: 30385245 DOI: 10.1016/j.fsi.2018.10.078] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/23/2018] [Accepted: 10/28/2018] [Indexed: 06/08/2023]
Abstract
Ichthyophthirius multifiliis, a ciliated protozoan parasite, causes ichthyophthiriasis and leads to considerable economic losses to the aquaculture industry. Understanding the fish immune response and host-parasite interactions could support developing novel strategies for better disease management and control. Fish skin mucus is the first line of defence against infections through the epidermis. Yet, the common carp, Cyprinus carpio, protein-based defence strategies against infection with I. multifiliis at this barrier remain elusive. The skin mucus proteome of common carp was investigated at 1 day and 9 days post-exposure with I. multifiliis. Using nano-LC ESI MS/MS and statistical analysis, the abundance of 19 immune related and signal transduction proteins was found to be differentially regulated in skin mucus of common carp in response to I. multifiliis. The analysis revealed increased abundance values of epithelial chloride channel protein, galactose-specific lectin nattection, high choriolytic enzyme 1 (nephrosin), lysozyme C, granulin and protein-glutamine gamma-glutamyltransferase 2 in I. multifiliis-exposed carp skin mucus. Multiple lectins and a diverse array of distinct serpins with protease inhibitor activity were identified likely implicated in lectin pathway activation and regulation of proteolysis, indicating that these proteins contribute to the carp innate immune system and the protective properties of skin mucus. The results obtained from this proteomic analysis enables a better understanding of fish host response to parasitic infection and gives insights into the key role skin mucus plays in protecting fish against deleterious effects of I. multifiliis.
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Affiliation(s)
- Mona Saleh
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria.
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Abdel-Azeem S Abdel-Baki
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia; Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Mohamed A Dkhil
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Zoology and Entomology, Faculty of Science, Helwan University, Cairo, Egypt
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
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9
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Abstract
The transport of specific molecules across lipid membranes is an essential function of all living organisms. The processes are usually mediated by specific transporters. One of the largest transporter families is the ATP-binding cassette (ABC) family. More than 40 ABC transporters have been identified in human, which are divided into 7 subfamilies (ABCA to ABCG) based on their gene structure, amino acid sequence, domain organization, and phylogenetic analysis. Of them, at least 11 ABC transporters including P-glycoprotein (P-GP/ABCB1), multidrug resistance-associated proteins (MRPs/ABCCs), and breast cancer resistance protein (BCRP/ABCG2) are involved in multidrug resistance (MDR) development. These ABC transporters are expressed in various tissues such as the liver, intestine, kidney, and brain, playing important roles in absorption, distribution, and excretion of drugs. Some ABC transporters are also involved in diverse cellular processes such as maintenance of osmotic homeostasis, antigen processing, cell division, immunity, cholesterol, and lipid trafficking. Several human diseases such as cystic fibrosis, sitosterolemia, Tangier disease, intrahepatic cholestasis, and retinal degeneration are associated with mutations in corresponding transporters. This chapter will describe function and expression of several ABC transporters (such as P-GP, BCRP, and MRPs), their substrates and inhibitors, as well as their clinical significance.
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Affiliation(s)
- Xiaodong Liu
- China Pharmaceutical University, Nanjing, China.
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10
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Abstract
Unlike B cells, CD8-positive and CD4-positive T cells of the adaptive immune system do not recognize intact foreign proteins but instead recognize polypeptide fragments of potential antigens. These antigenic peptides are expressed on the surface of antigen presenting cells bound to MHC class I and MHC class II proteins. Here, we review the basics of antigen acquisition by antigen presenting cells, antigen proteolysis into polypeptide fragments, antigenic peptide binding to MHC proteins, and surface display of both MHC class I-peptide and MHC class II-peptide complexes.
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Weng J, Gu S, Gao X, Huang X, Wang W. Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2. Phys Chem Chem Phys 2017; 19:9366-9373. [DOI: 10.1039/c6cp07943a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Maltose transporter MalFGK2is a type-I importer in the ATP-binding cassette (ABC) transporter superfamily.
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Affiliation(s)
- Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Department of Chemistry, and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Shuo Gu
- Department of Chemistry
- Institute for Advance Study and School of Science
- The Hong Kong University of Science and Technology
- Kowloon
- China
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division
- King Abdullah University of Science and Technology
- Thuwal
- Saudi Arabia
| | - Xuhui Huang
- Department of Chemistry
- Institute for Advance Study and School of Science
- The Hong Kong University of Science and Technology
- Kowloon
- China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Department of Chemistry, and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
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12
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Zhao N, Pan Y, Cheng Z, Liu H. Lasso peptide, a highly stable structure and designable multifunctional backbone. Amino Acids 2016; 48:1347-56. [PMID: 27074719 DOI: 10.1007/s00726-016-2228-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/01/2016] [Indexed: 12/18/2022]
Abstract
Lasso peptide belongs to a new class of natural product with highly compact and stable structure. It has varieties of biological activities, among which the most important one is its antibacterial efficacy. Novel lasso peptides have been constantly discovered and analyzed by advanced techniques, and the biosynthesis or even chemical synthesis of lasso peptide has been studied after learning its constituent amino acids and maturation process. Structural identification of lasso peptide provides information for elucidating the mechanisms of its antibacterial activity and basis for further modifications. Ring of lasso peptide is the key to both its highly compact and stable structure and its intrinsic antibacterial property. The loop has been considered as suitable modification region of lasso peptide, such as V11-S18 of MccJ25 being modifiable without disrupting the lasso structure in biosynthesis. The tail is the immunity protein that can export lasso peptide out of its produced strain and serve as a self-protection mechanism at the same time. Most of currently known lasso peptides are non-pathogenic, which implies that the modified lasso peptides are promising candidates for medical applications. Arginine, glycine, and aspartic acid as a ligands of cancer-specific receptor have been grafted to the loop of lasso peptide without losing its bioactivity, and many other targets are expected to be used for lasso peptide modification. Multi-molecular modification and large-scale production need to be studied and solved in future for designing and using multifunctional lasso peptide based on its extraordinary stable structure.
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Affiliation(s)
- Ning Zhao
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang, 110000, China
| | - Yongxu Pan
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang, 110000, China
| | - Zhen Cheng
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Bio-X Program and Stanford Cancer Center, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Hongguang Liu
- Institute of Molecular Medicine, College of Life and Health Sciences, Northeastern University, Shenyang, 110000, China.
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13
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Gu RX, Corradi V, Singh G, Choudhury HG, Beis K, Tieleman DP. Conformational Changes of the Antibacterial Peptide ATP Binding Cassette Transporter McjD Revealed by Molecular Dynamics Simulations. Biochemistry 2015; 54:5989-98. [PMID: 26334959 DOI: 10.1021/acs.biochem.5b00753] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ATP binding cassette (ABC) transporters form one of the largest protein superfamilies. They use the energy of ATP hydrolysis to transport chemically diverse ligands across membranes. An alternating access mechanism in which the transporter switches between inward- and outward-facing conformations has been proposed to describe the translocation process. One of the main open questions in this process is the degree of opening of the transporter at different stages of the transport cycle, as crystal structures and biochemical data have suggested a wide range of distances between nucleotide binding domains. Recently, the crystal structure of McjD, an antibacterial peptide ABC transporter from Escherichia coli, revealed a new occluded intermediate state of the transport cycle. The transmembrane domain is closed on both sides of the membrane, forming a cavity that can accommodate its ligand, MccJ25, a lasso peptide of 21 amino acids. In this work, we investigate the degree of opening of the transmembrane cavity required for ligand translocation. By means of steered molecular dynamics simulations, the ligand was pulled from the internal cavity to the extracellular side. This resulted in an outward-facing state. Comparison with existing outward-facing crystal structures shows a smaller degree of opening in the simulations, suggesting that the large conformational changes in some crystal structures may not be necessary even for a large substrate like MccJ25.
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Affiliation(s)
- Ruo-Xu Gu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - Gurpreet Singh
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - Hassanul G Choudhury
- Department of Life Sciences, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom.,Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, United Kingdom.,Rutherford Appleton Laboratory , Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London , South Kensington, London SW7 2AZ, United Kingdom.,Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, OX11 0DE, United Kingdom.,Rutherford Appleton Laboratory , Research Complex at Harwell, Oxfordshire OX11 0DE, United Kingdom
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
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14
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Vinci MC, Piacentini L, Chiesa M, Saporiti F, Colombo GI, Pesce M. Inflammatory environment and oxidized LDL convert circulating human proangiogenic cells into functional antigen-presenting cells. J Leukoc Biol 2015; 98:409-21. [PMID: 25990243 DOI: 10.1189/jlb.3a0814-412rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/23/2015] [Indexed: 11/24/2022] Open
Abstract
The function of human circulating PACs has been described extensively. However, little focus has been placed on understanding how these cells differ in their functions in the presence of microenvironments mimicking vascular inflammation. We hypothesized that exposure to proinflammatory cytokines or the oxLDL, an autoantigen abundant in advanced atherosclerotic plaques, converts PACs into immune-modulating/proinflammatory cells. Hence, we examined the effect of oxLDL and inflammatory stimuli on their phenotype by use of a functional genomics model based on secretome and whole genome transcriptome profiling. PACs obtained from culturing a PBMC fraction in angiogenic medium were primed with DC differentiation cytokines and then exposed to proinflammatory cytokines or oxLDL. Under these conditions, PACs converted into APCs, expressed maturation markers CD80 and CD83, and showed an increased up-regulation of CD86. APCcy and APCox induced a robust T cell BrdU incorporation. Despite a similar ability to induce lymphocyte proliferation, APCcy and APCox differed for the secretory pathway and mRNA expression. Analysis of the differentially expressed genes identified 4 gene "clusters," showing reciprocal modulation in APCcy vs. APCox, justifying, according to functional genomics analyses, a different putative function of the cells in antigen processing. Together, these data show that treatment with inflammatory cytokines or oxLDL converts human PAC phenotypes and functions into that of APCs with similar lymphocyte-activating ability but distinct maturation degree and paracrine functions.
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Affiliation(s)
- Maria Cristina Vinci
- *Unità di Ingegneria Tissutale Cardiovascolare and Unità di Immunologia e Genomica Funzionale, Centro Cardiologico Monzino, Istituto Di Ricovero e Cura a Carattere Scientifico, Milan, Italy
| | - Luca Piacentini
- *Unità di Ingegneria Tissutale Cardiovascolare and Unità di Immunologia e Genomica Funzionale, Centro Cardiologico Monzino, Istituto Di Ricovero e Cura a Carattere Scientifico, Milan, Italy
| | - Mattia Chiesa
- *Unità di Ingegneria Tissutale Cardiovascolare and Unità di Immunologia e Genomica Funzionale, Centro Cardiologico Monzino, Istituto Di Ricovero e Cura a Carattere Scientifico, Milan, Italy
| | - Federica Saporiti
- *Unità di Ingegneria Tissutale Cardiovascolare and Unità di Immunologia e Genomica Funzionale, Centro Cardiologico Monzino, Istituto Di Ricovero e Cura a Carattere Scientifico, Milan, Italy
| | - Gualtiero I Colombo
- *Unità di Ingegneria Tissutale Cardiovascolare and Unità di Immunologia e Genomica Funzionale, Centro Cardiologico Monzino, Istituto Di Ricovero e Cura a Carattere Scientifico, Milan, Italy
| | - Maurizio Pesce
- *Unità di Ingegneria Tissutale Cardiovascolare and Unità di Immunologia e Genomica Funzionale, Centro Cardiologico Monzino, Istituto Di Ricovero e Cura a Carattere Scientifico, Milan, Italy
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15
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Antigen Translocation Machineries in Adaptive Immunity and Viral Immune Evasion. J Mol Biol 2015; 427:1102-18. [DOI: 10.1016/j.jmb.2014.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 11/23/2022]
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16
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Greenberg RM. Schistosome ABC multidrug transporters: From pharmacology to physiology. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2014; 4:301-9. [PMID: 25516841 PMCID: PMC4266782 DOI: 10.1016/j.ijpddr.2014.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The genuine and hypothesized roles of schistosome ABC transporters are reviewed. Evidence suggesting a role for transporters in schistosome drug susceptibility is discussed. Potential roles of ABC transporters in normal schistosome biology are outlined.
Praziquantel (PZQ) is essentially the only drug currently available for treatment and control of schistosomiasis, a disease affecting hundreds of millions worldwide. Though highly effective overall, PZQ has limitations, most notably its significant lack of activity against immature schistosomes. Furthermore, the availability of only a single drug for a disease of this magnitude makes reports of PZQ-resistant isolates particularly troubling. ATP-binding cassette (ABC) multidrug transporters such as P-glycoprotein (Pgp; ABCB1) are efflux transporters that underlie multidrug resistance (MDR); changes in their expression or structure are also associated with drug resistance in parasites, including helminths. This review will discuss the role these transporters might play in modulating schistosome susceptibility to PZQ, and the implications for developing new or repurposed treatments that enhance the efficacy of PZQ. However, in addition to influencing drug susceptibility, ABC transporters play important roles in several critical physiological functions such as excretion and maintenance of permeability barriers. They also transport signaling molecules with high affinity, and several lines of evidence implicate mammalian transporters in a diverse array of physiological functions, including regulation of immune responses. Like their mammalian counterparts, schistosome ABC transporters appear to be involved in functions critical to the parasite, including excretory activity and reproduction, and we hypothesize that they underlie at least some aspects of parasite–host interactions. Thus, in addition to their potential as targets for enhancers of PZQ susceptibility, these transporters might also serve as candidate targets for agents that disrupt the parasite life cycle and act as antischistosomals on their own.
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Affiliation(s)
- Robert M Greenberg
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, PA 19104, USA
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17
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Sun L, Li M, Huang X, Xu J, Gao Z, Liu C. High-resolution genome-wide analysis identified recurrent genetic alterations in NK/T-cell lymphoma, nasal type, which are associated with disease progression. Med Oncol 2014; 31:71. [PMID: 24952511 PMCID: PMC4079938 DOI: 10.1007/s12032-014-0071-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 06/06/2014] [Indexed: 12/19/2022]
Abstract
Extranodal NK/T-cell lymphoma, nasal type, is an aggressive mature NK-cell/T-cell lymphoma. Using array-based comparative genomic hybridization (array CGH) assays, we screened genomic alterations and potential candidate genes implicated in pathogenesis, progression, and prognosis. Our array CGH analysis detected an average of 83 chromosomal aberrations in 13 cases, ranging from 0 to 387. There were 177 recurrent chromosomal gains and 35 recurrent losses. Eleven gains and 14 losses were detected in more than 30 % of the cases, including gains of 3q26.1, 7q34, and 8q24.3 and losses of 15q24.2, 19q13.32, 5p13.2, and 14q21.1. The most common losses were observed in the 15q24.2 and 19q13.32 regions (9 cases, 69.2 %, respectively). Loss of 8p11.23 was associated with significant poor survival (P = 0.024). Five out of six patients with the loss of 8p11.23 died within 8 months after initial diagnosis with a median survival of 6 months. Several candidate genes were identified in the regions with frequent chromosomal aberrations, including ADAM3A (8p11.23) and GSTT1 (22q11.23). In summary, our studies detected recurrent genetic alterations in NK/T-cell lymphoma, some of which are associated with adverse prognosis. Some candidate genes in these regions may be involved in the pathogenesis and disease progression.
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Affiliation(s)
- Lin Sun
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, People's Republic of China
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18
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Ishida K, Sekizuka T, Hayashida K, Matsuo J, Takeuchi F, Kuroda M, Nakamura S, Yamazaki T, Yoshida M, Takahashi K, Nagai H, Sugimoto C, Yamaguchi H. Amoebal endosymbiont Neochlamydia genome sequence illuminates the bacterial role in the defense of the host amoebae against Legionella pneumophila. PLoS One 2014; 9:e95166. [PMID: 24747986 PMCID: PMC3991601 DOI: 10.1371/journal.pone.0095166] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 03/24/2014] [Indexed: 11/19/2022] Open
Abstract
Previous work has shown that the obligate intracellular amoebal endosymbiont Neochlamydia S13, an environmental chlamydia strain, has an amoebal infection rate of 100%, but does not cause amoebal lysis and lacks transferability to other host amoebae. The underlying mechanism for these observations remains unknown. In this study, we found that the host amoeba could completely evade Legionella infection. The draft genome sequence of Neochlamydia S13 revealed several defects in essential metabolic pathways, as well as unique molecules with leucine-rich repeats (LRRs) and ankyrin domains, responsible for protein-protein interaction. Neochlamydia S13 lacked an intact tricarboxylic acid cycle and had an incomplete respiratory chain. ADP/ATP translocases, ATP-binding cassette transporters, and secretion systems (types II and III) were well conserved, but no type IV secretion system was found. The number of outer membrane proteins (OmcB, PomS, 76-kDa protein, and OmpW) was limited. Interestingly, genes predicting unique proteins with LRRs (30 genes) or ankyrin domains (one gene) were identified. Furthermore, 33 transposases were found, possibly explaining the drastic genome modification. Taken together, the genomic features of Neochlamydia S13 explain the intimate interaction with the host amoeba to compensate for bacterial metabolic defects, and illuminate the role of the endosymbiont in the defense of the host amoebae against Legionella infection.
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Affiliation(s)
- Kasumi Ishida
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kyoko Hayashida
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Fumihiko Takeuchi
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomohiro Yamazaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mitsutaka Yoshida
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaori Takahashi
- Division of Ultrastructural Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hiroki Nagai
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Chihiro Sugimoto
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
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19
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Gupta RP, Kueppers P, Hanekop N, Schmitt L. Generating symmetry in the asymmetric ATP-binding cassette (ABC) transporter Pdr5 from Saccharomyces cerevisiae. J Biol Chem 2014; 289:15272-9. [PMID: 24733388 DOI: 10.1074/jbc.m114.553065] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pdr5 is a plasma membrane-bound ABC transporter from Saccharomyces cerevisiae and is involved in the phenomenon of resistance against xenobiotics, which are clinically relevant in bacteria, fungi, and humans. Many fungal ABC transporters such as Pdr5 display an inherent asymmetry in their nucleotide-binding sites (NBS) unlike most of their human counterparts. This degeneracy of the NBSs is very intriguing and needs explanation in terms of structural and functional relevance. In this study, we mutated nonconsensus amino acid residues in the NBSs to its consensus counterpart and studied its effect on the function of the protein and effect on yeast cells. The completely "regenerated" Pdr5 protein was severely impaired in its function of ATP hydrolysis and of rhodamine 6G transport. Moreover, we observe alternative compensatory mechanisms to counteract drug toxicity in some of the mutants. In essence, we describe here the first attempts to restore complete symmetry in an asymmetric ABC transporter and to study its effects, which might be relevant to the entire class of asymmetric ABC transporters.
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Affiliation(s)
- Rakeshkumar P Gupta
- From the Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Petra Kueppers
- From the Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Nils Hanekop
- From the Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lutz Schmitt
- From the Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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20
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The Maltose ABC Transporter: Where Structure Meets Function. SPRINGER SERIES IN BIOPHYSICS 2014. [DOI: 10.1007/978-3-642-53839-1_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Structural and mechanistic insights into prokaryotic energy-coupling factor transporters. Nat Rev Microbiol 2013; 12:79-87. [PMID: 24362466 DOI: 10.1038/nrmicro3175] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Energy-coupling factor (ECF) transporters belong to the ATP-binding cassette (ABC)-transporter family and mediate the uptake of essential micronutrients in many prokaryotic species. Two crystal structures of bacterial ECF transporters have recently been obtained and suggest that transport involves an unprecedented re-orientation of a membrane protein in the lipid bilayer during catalysis. In this Progress article, I present the new structural insights, discuss a testable model for the transport mechanism and consider the more general implications of these findings for our understanding of membrane transporters.
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22
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Co-operative function and mutual stabilization of the half ATP-binding cassette transporters HAF-4 and HAF-9 in Caenorhabditis elegans. Biochem J 2013; 452:467-75. [PMID: 23458156 DOI: 10.1042/bj20130115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Caenorhabditis elegans HAF-4 and HAF-9 are half ABC (ATP-binding-cassette) transporters that are highly homologous to the human lysosomal peptide transporter TAPL [TAP (transporter associated with antigen processing)-like; ABCB9]. We reported previously that both HAF-4 and HAF-9 localize to the membrane of a subset of intestinal organelles, and are required for the formation of these organelles and other physiological aspects. In the present paper, we report the genetic and physical interactions between HAF-4 and HAF-9. Overexpression of HAF-4 and HAF-9 did not rescue the intestinal organelle defect of the haf-9 and haf-4 deletion mutants respectively, indicating that they cannot substitute for each other. Double haf-4 and haf-9 mutants do not exhibit more severe phenotypes than the single mutants, suggesting their co-operative function. Immunoprecipitation experiments demonstrated their physical interaction. The results of the present study suggest that HAF-4 and HAF-9 form a heterodimer. Furthermore, Western blot analysis of the deletion mutants and RNAi (RNA interference) knockdown experiments in GFP (green fluorescent protein)-tagged HAF-4 or HAF-9 transgenic worms suggest that HAF-4-HAF-9 heterodimer formation is required for their stabilization. The findings provide a clue as to how ABC transporters adopt a stable functional form.
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23
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Genome-wide identification, characterization and phylogenetic analysis of 50 catfish ATP-binding cassette (ABC) transporter genes. PLoS One 2013; 8:e63895. [PMID: 23696857 PMCID: PMC3655950 DOI: 10.1371/journal.pone.0063895] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/09/2013] [Indexed: 12/23/2022] Open
Abstract
Background Although a large set of full-length transcripts was recently assembled in catfish, annotation of large gene families, especially those with duplications, is still a great challenge. Most often, complexities in annotation cause mis-identification and thereby much confusion in the scientific literature. As such, detailed phylogenetic analysis and/or orthology analysis are required for annotation of genes involved in gene families. The ATP-binding cassette (ABC) transporter gene superfamily is a large gene family that encodes membrane proteins that transport a diverse set of substrates across membranes, playing important roles in protecting organisms from diverse environment. Methodology/Principal Findings In this work, we identified a set of 50 ABC transporters in catfish genome. Phylogenetic analysis allowed their identification and annotation into seven subfamilies, including 9 ABCA genes, 12 ABCB genes, 12 ABCC genes, 5 ABCD genes, 2 ABCE genes, 4 ABCF genes and 6 ABCG genes. Most ABC transporters are conserved among vertebrates, though cases of recent gene duplications and gene losses do exist. Gene duplications in catfish were found for ABCA1, ABCB3, ABCB6, ABCC5, ABCD3, ABCE1, ABCF2 and ABCG2. Conclusion/Significance The whole set of catfish ABC transporters provide the essential genomic resources for future biochemical, toxicological and physiological studies of ABC drug efflux transporters. The establishment of orthologies should allow functional inferences with the information from model species, though the function of lineage-specific genes can be distinct because of specific living environment with different selection pressure.
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24
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Wiesinger C, Kunze M, Regelsberger G, Forss-Petter S, Berger J. Impaired very long-chain acyl-CoA β-oxidation in human X-linked adrenoleukodystrophy fibroblasts is a direct consequence of ABCD1 transporter dysfunction. J Biol Chem 2013; 288:19269-79. [PMID: 23671276 DOI: 10.1074/jbc.m112.445445] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
X-linked adrenoleukodystrophy (X-ALD), an inherited peroxisomal disorder, is caused by mutations in the ABCD1 gene encoding the peroxisomal ATP-binding cassette (ABC) transporter ABCD1 (adrenoleukodystrophy protein, ALDP). Biochemically, X-ALD is characterized by an accumulation of very long-chain fatty acids and partially impaired peroxisomal β-oxidation. In this study, we used primary human fibroblasts from X-ALD and Zellweger syndrome patients to investigate the peroxisomal β-oxidation defect. Our results show that the degradation of C26:0-CoA esters is as severely impaired as degradation of unesterified very long-chain fatty acids in X-ALD and is abolished in Zellweger syndrome. Interestingly, the β-oxidation rates for both C26:0-CoA and C22:0-CoA were similarly affected, although C22:0 does not accumulate in patient fibroblasts. Furthermore, we show that the β-oxidation defect in X-ALD is directly caused by ABCD1 dysfunction as blocking ABCD1 function with a specific antibody reduced β-oxidation to levels observed in X-ALD fibroblasts. By quantification of mRNA and protein levels of the peroxisomal ABC transporters and by blocking with specific antibodies, we found that residual β-oxidation activity toward C26:0-CoA in X-ALD fibroblasts is mediated by ABCD3, although the efficacy of ABCD3 appeared to be much lower than that of ABCD1. Finally, using isolated peroxisomes, we show that β-oxidation of C26:0-CoA is independent of additional CoA but requires a cytosolic factor of >10-kDa molecular mass that is resistant to N-ethylmaleimide and heat inactivation. In conclusion, our findings in human cells suggest that, in contrast to yeast cells, very long-chain acyl-CoA esters are transported into peroxisomes by ABCD1 independently of additional synthetase activity.
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Affiliation(s)
- Christoph Wiesinger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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Abstract
T cell recognition of antigen-presenting cells depends on their expression of a spectrum of peptides bound to major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules. Conversion of antigens from pathogens or transformed cells into MHC-I- and MHC-II-bound peptides is critical for mounting protective T cell responses, and similar processing of self proteins is necessary to establish and maintain tolerance. Cells use a variety of mechanisms to acquire protein antigens, from translation in the cytosol to variations on the theme of endocytosis, and to degrade them once acquired. In this review, we highlight the aspects of MHC-I and MHC-II biosynthesis and assembly that have evolved to intersect these pathways and sample the peptides that are produced.
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Affiliation(s)
- Janice S Blum
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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