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Yuan Y, Li P, Li J, Zhao Q, Chang Y, He X. Protein lipidation in health and disease: molecular basis, physiological function and pathological implication. Signal Transduct Target Ther 2024; 9:60. [PMID: 38485938 PMCID: PMC10940682 DOI: 10.1038/s41392-024-01759-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 03/18/2024] Open
Abstract
Posttranslational modifications increase the complexity and functional diversity of proteins in response to complex external stimuli and internal changes. Among these, protein lipidations which refer to lipid attachment to proteins are prominent, which primarily encompassing five types including S-palmitoylation, N-myristoylation, S-prenylation, glycosylphosphatidylinositol (GPI) anchor and cholesterylation. Lipid attachment to proteins plays an essential role in the regulation of protein trafficking, localisation, stability, conformation, interactions and signal transduction by enhancing hydrophobicity. Accumulating evidence from genetic, structural, and biomedical studies has consistently shown that protein lipidation is pivotal in the regulation of broad physiological functions and is inextricably linked to a variety of diseases. Decades of dedicated research have driven the development of a wide range of drugs targeting protein lipidation, and several agents have been developed and tested in preclinical and clinical studies, some of which, such as asciminib and lonafarnib are FDA-approved for therapeutic use, indicating that targeting protein lipidations represents a promising therapeutic strategy. Here, we comprehensively review the known regulatory enzymes and catalytic mechanisms of various protein lipidation types, outline the impact of protein lipidations on physiology and disease, and highlight potential therapeutic targets and clinical research progress, aiming to provide a comprehensive reference for future protein lipidation research.
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Affiliation(s)
- Yuan Yuan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyuan Li
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianghui Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Xingxing He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
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Müller GA, Müller TD. Transfer of membrane(s) matter(s)-non-genetic inheritance of (metabolic) phenotypes? Front Mol Biosci 2024; 11:1347397. [PMID: 38516184 PMCID: PMC10955475 DOI: 10.3389/fmolb.2024.1347397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/26/2024] [Indexed: 03/23/2024] Open
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are anchored at the outer phospholipid layer of eukaryotic plasma membranes exclusively by a glycolipid. GPI-APs are not only released into extracellular compartments by lipolytic cleavage. In addition, certain GPI-APs with the glycosylphosphatidylinositol anchor including their fatty acids remaining coupled to the carboxy-terminus of their protein components are also detectable in body fluids, in response to certain stimuli, such as oxidative stress, radicals or high-fat diet. As a consequence, the fatty acid moieties of GPI-APs must be shielded from access of the aqueous environment by incorporation into membranes of extracellular vesicles or into micelle-like complexes together with (lyso)phospholipids and cholesterol. The GPI-APs released from somatic cells and tissues are transferred via those complexes or EVs to somatic as well as pluripotent stem cells with metabolic consequences, such as upregulation of glycogen and lipid synthesis. From these and additional findings, the following hypotheses are developed: i) Transfer of GPI-APs via EVs or micelle-like complexes leads to the induction of new phenotypes in the daughter cells or zygotes, which are presumably not restricted to metabolism. ii) The membrane topographies transferred by the concerted action of GPI-APs and interacting components are replicated by self-organization and self-templation and remain accessible to structural changes by environmental factors. iii) Transfer from mother cells and gametes to their daughter cells and zygotes, respectively, is not restricted to DNA and genes, but also encompasses non-genetic matter, such as GPI-APs and specific membrane constituents. iv) The intergenerational transfer of membrane matter between mammalian organisms is understood as an epigenetic mechanism for phenotypic plasticity, which does not rely on modifications of DNA and histones, but is regarded as molecular mechanism for the inheritance of acquired traits, such as complex metabolic diseases. v) The missing interest in research of non-genetic matter of inheritance, which may be interpreted in the sense of Darwin's "Gemmules" or Galton's "Stirps", should be addressed in future investigations of the philosophy of science and sociology of media.
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Affiliation(s)
- Günter A. Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), Oberschleissheim, Germany
- Department of Media Studies, Media, Culture and Society, Faculty of Arts and Humanities, University Paderborn, Paderborn, Germany
| | - Timo D. Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), Oberschleissheim, Germany
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Xu Y, Li T, Zhou Z, Hong J, Chao Y, Zhu Z, Zhang Y, Qu Q, Li D. Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis. Nat Commun 2023; 14:5520. [PMID: 37684232 PMCID: PMC10491789 DOI: 10.1038/s41467-023-41281-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Many eukaryotic receptors and enzymes rely on glycosylphosphatidylinositol (GPI) anchors for membrane localization and function. The transmembrane complex GPI-T recognizes diverse proproteins at a signal peptide region that lacks consensus sequence and replaces it with GPI via a transamidation reaction. How GPI-T maintains broad specificity while preventing unintentional cleavage is unclear. Here, substrates- and products-bound human GPI-T structures identify subsite features that enable broad proprotein specificity, inform catalytic mechanism, and reveal a multilevel safeguard mechanism against its promiscuity. In the absence of proproteins, the catalytic site is invaded by a locally stabilized loop. Activation requires energetically unfavorable rearrangements that transform the autoinhibitory loop into crucial catalytic cleft elements. Enzyme-proprotein binding in the transmembrane and luminal domains respectively powers the conformational rearrangement and induces a competent cleft. GPI-T thus integrates various weak specificity regions to form strong selectivity and prevent accidental activation. These findings provide important mechanistic insights into GPI-anchored protein biogenesis.
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Affiliation(s)
- Yidan Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS, Shanghai, China
| | - Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS, Shanghai, China
| | - Zixuan Zhou
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, China
| | - Jingjing Hong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS, Shanghai, China
| | - Yulin Chao
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, China
| | - Zhini Zhu
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, China
| | - Ying Zhang
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, China
| | - Qianhui Qu
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS, Shanghai, China.
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Müller GA, Müller TD. (Patho)Physiology of Glycosylphosphatidylinositol-Anchored Proteins II: Intercellular Transfer of Matter (Inheritance?) That Matters. Biomolecules 2023; 13:994. [PMID: 37371574 DOI: 10.3390/biom13060994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins (APs) are anchored at the outer leaflet of the plasma membrane (PM) bilayer by covalent linkage to a typical glycolipid and expressed in all eukaryotic organisms so far studied. Lipolytic release from PMs into extracellular compartments and intercellular transfer are regarded as the main (patho)physiological roles exerted by GPI-APs. The intercellular transfer of GPI-APs relies on the complete GPI anchor and is mediated by extracellular vesicles such as microvesicles and exosomes and lipid-free homo- or heteromeric aggregates, and lipoprotein-like particles such as prostasomes and surfactant-like particles, or lipid-containing micelle-like complexes. In mammalian organisms, non-vesicular transfer is controlled by the distance between donor and acceptor cells/tissues; intrinsic conditions such as age, metabolic state, and stress; extrinsic factors such as GPI-binding proteins; hormones such as insulin; and drugs such as anti-diabetic sulfonylureas. It proceeds either "directly" upon close neighborhood or contact of donor and acceptor cells or "indirectly" as a consequence of the induced lipolytic release of GPI-APs from PMs. Those displace from the serum GPI-binding proteins GPI-APs, which have retained the complete anchor, and become assembled in aggregates or micelle-like complexes. Importantly, intercellular transfer of GPI-APs has been shown to induce specific phenotypes such as stimulation of lipid and glycogen synthesis, in cultured human adipocytes, blood cells, and induced pluripotent stem cells. As a consequence, intercellular transfer of GPI-APs should be regarded as non-genetic inheritance of (acquired) features between somatic cells which is based on the biogenesis and transmission of matter such as GPI-APs and "membrane landscapes", rather than the replication and transmission of information such as DNA. Its operation in mammalian organisms remains to be clarified.
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Affiliation(s)
- Günter A Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) and German Center for Diabetes Research (DZD) at the Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) and German Center for Diabetes Research (DZD) at the Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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Müller GA, Müller TD. (Patho)Physiology of Glycosylphosphatidylinositol-Anchored Proteins I: Localization at Plasma Membranes and Extracellular Compartments. Biomolecules 2023; 13:biom13050855. [PMID: 37238725 DOI: 10.3390/biom13050855] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins (APs) are anchored at the outer leaflet of plasma membranes (PMs) of all eukaryotic organisms studied so far by covalent linkage to a highly conserved glycolipid rather than a transmembrane domain. Since their first description, experimental data have been accumulating for the capability of GPI-APs to be released from PMs into the surrounding milieu. It became evident that this release results in distinct arrangements of GPI-APs which are compatible with the aqueous milieu upon loss of their GPI anchor by (proteolytic or lipolytic) cleavage or in the course of shielding of the full-length GPI anchor by incorporation into extracellular vesicles, lipoprotein-like particles and (lyso)phospholipid- and cholesterol-harboring micelle-like complexes or by association with GPI-binding proteins or/and other full-length GPI-APs. In mammalian organisms, the (patho)physiological roles of the released GPI-APs in the extracellular environment, such as blood and tissue cells, depend on the molecular mechanisms of their release as well as the cell types and tissues involved, and are controlled by their removal from circulation. This is accomplished by endocytic uptake by liver cells and/or degradation by GPI-specific phospholipase D in order to bypass potential unwanted effects of the released GPI-APs or their transfer from the releasing donor to acceptor cells (which will be reviewed in a forthcoming manuscript).
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Affiliation(s)
- Günter A Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), 85764 Oberschleissheim, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), 85764 Oberschleissheim, Germany
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Sauer LM, Canovas R, Roche D, Shams-Eldin H, Ravel P, Colinge J, Schwarz RT, Ben Mamoun C, Rivals E, Cornillot E. FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species. Malar J 2023; 22:27. [PMID: 36698187 PMCID: PMC9876418 DOI: 10.1186/s12936-022-04430-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/23/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Protozoan parasites are known to attach specific and diverse group of proteins to their plasma membrane via a GPI anchor. In malaria parasites, GPI-anchored proteins (GPI-APs) have been shown to play an important role in host-pathogen interactions and a key function in host cell invasion and immune evasion. Because of their immunogenic properties, some of these proteins have been considered as malaria vaccine candidates. However, identification of all possible GPI-APs encoded by these parasites remains challenging due to their sequence diversity and limitations of the tools used for their characterization. METHODS The FT-GPI software was developed to detect GPI-APs based on the presence of a hydrophobic helix at both ends of the premature peptide. FT-GPI was implemented in C ++and applied to study the GPI-proteome of 46 isolates of the order Haemosporida. Using the GPI proteome of Plasmodium falciparum strain 3D7 and Plasmodium vivax strain Sal-1, a heuristic method was defined to select the most sensitive and specific FT-GPI software parameters. RESULTS FT-GPI enabled revision of the GPI-proteome of P. falciparum and P. vivax, including the identification of novel GPI-APs. Orthology- and synteny-based analyses showed that 19 of the 37 GPI-APs found in the order Haemosporida are conserved among Plasmodium species. Our analyses suggest that gene duplication and deletion events may have contributed significantly to the evolution of the GPI proteome, and its composition correlates with speciation. CONCLUSION FT-GPI-based prediction is a useful tool for mining GPI-APs and gaining further insights into their evolution and sequence diversity. This resource may also help identify new protein candidates for the development of vaccines for malaria and other parasitic diseases.
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Affiliation(s)
- Lena M. Sauer
- Institute for Virology, Hans-Meerwein-Straße, 35043 Marburg, Germany
- Computational Biology Institute, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
- Present Address: GRN-Klinik Sinsheim, Alte Waibstadter Straße 2a, 74889 Sinsheim, Germany
| | - Rodrigo Canovas
- Computational Biology Institute, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
- grid.121334.60000 0001 2097 0141LIRMM, CNRS, Université de Montpellier, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
| | - Daniel Roche
- Computational Biology Institute, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
- grid.121334.60000 0001 2097 0141LIRMM, CNRS, Université de Montpellier, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
| | - Hosam Shams-Eldin
- Institute for Virology, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Patrice Ravel
- grid.121334.60000 0001 2097 0141Institut de Recherche en Cancérologie de Montpellier INSERM U1094, ICM, Université de Montpellier, Campus Val d’Aurelle, 208 Avenue Des Apothicaires, 34298 Montpellier, France
| | - Jacques Colinge
- grid.121334.60000 0001 2097 0141Institut de Recherche en Cancérologie de Montpellier INSERM U1094, ICM, Université de Montpellier, Campus Val d’Aurelle, 208 Avenue Des Apothicaires, 34298 Montpellier, France
| | - Ralph T. Schwarz
- Institute for Virology, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Choukri Ben Mamoun
- grid.47100.320000000419368710Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520 USA
| | - Eric Rivals
- Computational Biology Institute, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
- grid.121334.60000 0001 2097 0141LIRMM, CNRS, Université de Montpellier, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
- grid.510302.5Institut Français de Bioinformatique, CNRS UAR 3601, 2, rue Gaston Crémieux, 91057 Évry, France
| | - Emmanuel Cornillot
- Computational Biology Institute, Campus Saint Priest, 161 Rue Ada, 34095 Montpellier, France
- grid.121334.60000 0001 2097 0141Institut de Recherche en Cancérologie de Montpellier INSERM U1094, ICM, Université de Montpellier, Campus Val d’Aurelle, 208 Avenue Des Apothicaires, 34298 Montpellier, France
- Wespran SAS, 13 Rue de Penthièvre, 75008 Paris, France
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Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol 2022; 12:1051487. [PMID: 36505834 PMCID: PMC9730332 DOI: 10.3389/fonc.2022.1051487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer-specific alternatively spliced events (ASE) play a role in cancer pathogenesis and can be targeted by immunotherapy, oligonucleotide therapy, and small molecule inhibition. However, identifying actionable ASE targets remains challenging due to the uncertainty of its protein product, structure impact, and proteoform (protein isoform) function. Here we argue that an integrated multi-omics profiling strategy can overcome these challenges, allowing us to mine this untapped source of targets for therapeutic development. In this review, we will provide an overview of current multi-omics strategies in characterizing ASEs by utilizing the transcriptome, proteome, and state-of-art algorithms for protein structure prediction. We will discuss limitations and knowledge gaps associated with each technology and informatics analytics. Finally, we will discuss future directions that will enable the full integration of multi-omics data for ASE target discovery.
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Affiliation(s)
- Timothy I. Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States,*Correspondence: Timothy I. Shaw,
| | - Bi Zhao
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Brandon Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Aleksandra Karolak
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
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Snelders E, Moyrand F, Sturny-Leclère A, Vernel-Pauillac F, Volant S, Janbon G, Alanio A. The role of glycosylphosphatidylinositol (gpi) anchored proteins in Cryptococcus neoformans. Microbes Infect 2022; 24:105016. [DOI: 10.1016/j.micinf.2022.105016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/25/2022] [Accepted: 05/20/2022] [Indexed: 10/31/2022]
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 PMCID: PMC8820976 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F. Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
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De Coninck T, Gistelinck K, Janse van Rensburg HC, Van den Ende W, Van Damme EJM. Sweet Modifications Modulate Plant Development. Biomolecules 2021; 11:756. [PMID: 34070047 PMCID: PMC8158104 DOI: 10.3390/biom11050756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
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Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Koen Gistelinck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Henry C. Janse van Rensburg
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Els J. M. Van Damme
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
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Gonçales RA, Salamanca AL, Júnior LR, E Silva KS, de Vasconcelos EJ, Dos Reis TF, Castro RC, C Ruy PD, Romagnoli B, Ruiz J, Pereira M, de A Soares CM, Coelho PS. In silico identification of glycosylphosphatidylinositol-anchored proteins in Paracoccidioides spp. Future Microbiol 2021; 16:589-606. [PMID: 33998266 DOI: 10.2217/fmb-2020-0282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To predict glycosylphosphatidylinositol (GPI)-anchored proteins in the genome of Paracoccidioides brasiliensis and Paracoccidioides lutzii. Materials & methods: Five different bioinformatics tools were used for predicting GPI-anchored proteins; we considered as GPI-anchored proteins those detected by at least two in silico analysis methods. We also performed the proteomic analysis of P. brasiliensis cell wall by mass spectrometry. Results: Hundred GPI-anchored proteins were predicted in P. brasiliensis and P. lutzii genomes. A series of 57 proteins were classified in functional categories and 43 conserved proteins were reported with unknown functions. Four proteins identified by in silico analyses were also identified in the cell wall proteome. Conclusion: The data obtained in this study are important resources for future research of GPI-anchored proteins in Paracoccidioides spp. to identify targets for new diagnostic tools, drugs and immunological tests.
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Affiliation(s)
- Relber A Gonçales
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal, ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ayda Lm Salamanca
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas II (ICB II), Universidade Federal de Goiás (UFG), Goiânia, Goiás, 74690-900, Brazil
| | - Luiz Rb Júnior
- Department of Cellular & Molecular Biology and Pathogenic Bioagents, Faculty of Medicine of Ribeirão Preto (FMRP), University of São Paulo (USP), Ribeirão Preto, 14049-900, Brazil
| | - Kleber Sf E Silva
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas II (ICB II), Universidade Federal de Goiás (UFG), Goiânia, Goiás, 74690-900, Brazil
| | - Elton Jr de Vasconcelos
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Thaila F Dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, 14040-900, Brazil
| | - Ricardo C Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, 14040-900, Brazil
| | - Patrícia de C Ruy
- Department of Cellular & Molecular Biology and Pathogenic Bioagents, Faculty of Medicine of Ribeirão Preto (FMRP), University of São Paulo (USP), Ribeirão Preto, 14049-900, Brazil
| | - Bárbara Romagnoli
- Department of Cellular & Molecular Biology and Pathogenic Bioagents, Faculty of Medicine of Ribeirão Preto (FMRP), University of São Paulo (USP), Ribeirão Preto, 14049-900, Brazil
| | - Jerônimo Ruiz
- Fundação Oswaldo Cruz, Instituto Rene Rachaou (IRR), Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Maristela Pereira
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas II (ICB II), Universidade Federal de Goiás (UFG), Goiânia, Goiás, 74690-900, Brazil
| | - Célia M de A Soares
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas II (ICB II), Universidade Federal de Goiás (UFG), Goiânia, Goiás, 74690-900, Brazil
| | - Paulo Sr Coelho
- Department of Cellular & Molecular Biology and Pathogenic Bioagents, Faculty of Medicine of Ribeirão Preto (FMRP), University of São Paulo (USP), Ribeirão Preto, 14049-900, Brazil
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13
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Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. Int J Mol Sci 2020; 21:ijms21186727. [PMID: 32937895 PMCID: PMC7556027 DOI: 10.3390/ijms21186727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of glycobiology, glycomics, and glycoproteomics technologies, a large amount of glycoscience data has been generated. Subsequently, a number of glycobiology databases covering glycan structure, the glycosylation sites, the protein scaffolds, and related glycogenes have been developed to store, analyze, and integrate these data. However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins. In this study, the representative databases of glycan structure, glycoprotein, glycan-protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics are reviewed. We hope this overview could assist readers in searching for information on glycoproteins of interest, and promote further clinical application of glycobiology.
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Vidal M. Exosomes and GPI-anchored proteins: Judicious pairs for investigating biomarkers from body fluids. Adv Drug Deliv Rev 2020; 161-162:110-123. [PMID: 32828789 DOI: 10.1016/j.addr.2020.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/27/2020] [Accepted: 08/14/2020] [Indexed: 12/16/2022]
Abstract
Exosomes are 50-100 nm membranous vesicles actively released by cells which can be indicative of a diseased cell status. They contain various kinds of molecule - proteins, mRNA, miRNA, lipids - that are actively being studied as potential biomarkers. Hereafter I put forward several arguments in favor of the potential use of glycosylphosphatidylinositol-anchored proteins (GPI-APs) as biomarkers especially of cancerous diseases. I will briefly update readers on the exosome field and review various features of GPI-APs, before further discussing the advantages of this class of proteins as potential exosomal biomarkers. I will finish with a few examples of exosomal GPI-APs that have already been demonstrated to be good prognostic markers, as well as innovative approaches developed to quantify these exosomal biomarkers.
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Peled Y, Drake JL, Malik A, Almuly R, Lalzar M, Morgenstern D, Mass T. Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata. ACTA ACUST UNITED AC 2020; 2:8. [PMID: 32724895 PMCID: PMC7115838 DOI: 10.1186/s42833-020-00014-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Stony corals generate their calcium carbonate exoskeleton in a highly controlled biomineralization process mediated by a variety of macromolecules including proteins. Fully identifying and classifying these proteins is crucial to understanding their role in exoskeleton formation, yet no optimal method to purify and characterize the full suite of extracted coral skeletal proteins has been established and hence their complete composition remains obscure. Here, we tested four skeletal protein purification protocols using acetone precipitation and ultrafiltration dialysis filters to present a comprehensive scleractinian coral skeletal proteome. We identified a total of 60 proteins in the coral skeleton, 44 of which were not present in previously published stony coral skeletal proteomes. Extracted protein purification protocols carried out in this study revealed that no one method captures all proteins and each protocol revealed a unique set of method-exclusive proteins. To better understand the general mechanism of skeletal protein transportation, we further examined the proteins’ gene ontology, transmembrane domains, and signal peptides. We found that transmembrane domain proteins and signal peptide secretion pathways, by themselves, could not explain the transportation of proteins to the skeleton. We therefore propose that some proteins are transported to the skeleton via non-traditional secretion pathways.
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Affiliation(s)
- Yanai Peled
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Jeana L Drake
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Ricardo Almuly
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Core Unit, University of Haifa, Haifa, Israel
| | - David Morgenstern
- De Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Mass
- Marine Biology Department, University of Haifa, Haifa, Israel
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16
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Müller GA. Membrane insertion and intercellular transfer of glycosylphosphatidylinositol-anchored proteins: potential therapeutic applications. Arch Physiol Biochem 2020; 126:139-156. [PMID: 30445857 DOI: 10.1080/13813455.2018.1498904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Anchorage of a subset of cell surface proteins in eukaryotic cells is mediated by a glycosylphosphatidylinositol (GPI) moiety covalently attached to the carboxy-terminus of the protein moiety. Experimental evidence for the potential of GPI-anchored proteins (GPI-AP) of being released from cells into the extracellular environment has been accumulating, which involves either the loss or retention of the GPI anchor. Release of GPI-AP from donor cells may occur spontaneously or in response to endogenous or environmental signals. The experimental evidence for direct insertion of exogenous GPI-AP equipped with the complete anchor structure into the outer plasma membrane bilayer leaflets of acceptor cells is reviewed as well as the potential underlying molecular mechanisms. Furthermore, promiscuous transfer of certain GPI-AP between plasma membranes of different cells in vivo under certain (patho)physiological conditions has been reported. Engineering of target cell surfaces using chimeric GPI-AP with complete GPI anchor may be useful for therapeutic applications.
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Affiliation(s)
- Günter A Müller
- Helmholtz Diabetes Center (HDC) at the Helmholtz Center München, Institute for Diabetes and Obesity, Oberschleissheim, Germany
- Department Biology I, Genetics, Ludwig-Maximilians-University München, Planegg-Martinsried, Germany
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17
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Hernández-Goenaga J, López-Abán J, Protasio AV, Vicente Santiago B, del Olmo E, Vanegas M, Fernández-Soto P, Patarroyo MA, Muro A. Peptides Derived of Kunitz-Type Serine Protease Inhibitor as Potential Vaccine Against Experimental Schistosomiasis. Front Immunol 2019; 10:2498. [PMID: 31736947 PMCID: PMC6838133 DOI: 10.3389/fimmu.2019.02498] [Citation(s) in RCA: 20] [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: 05/03/2019] [Accepted: 10/07/2019] [Indexed: 12/27/2022] Open
Abstract
Schistosomiasis is a significant public health problem in sub-Saharan Africa, China, Southeast Asia, and regions of South and Central America affecting about 189 million people. Kunitz-type serine protease inhibitors have been identified as important players in the interaction of other flatworm parasites with their mammalian hosts. They are involved in host blood coagulation, fibrinolysis, inflammation, and ion channel blocking, all of them critical biological processes, which make them interesting targets to develop a vaccine. Here, we evaluate the protective efficacy of chemically synthesized T- and B-cell peptide epitopes derived from a kunitz protein from Schistosoma mansoni. Putative kunitz-type protease inhibitor proteins were identified in the S. mansoni genome, and their expression was analyzed by RNA-seq. Gene expression analyses showed that the kunitz protein Smp_147730 (Syn. Smp_311670) was dramatically and significantly up-regulated in schistosomula and adult worms when compared to the invading cercariae. T- and B-cell epitopes were predicted using bioinformatics tools, chemically synthesized, and formulated in the Adjuvant Adaptation (ADAD) vaccination system. BALB/c mice were vaccinated and challenged with S. mansoni cercariae. Kunitz peptides were highly protective in vaccinated BALB/c mice showing significant reductions in recovery of adult females (89-91%) and in the numbers of eggs trapped in the livers (77-81%) and guts (57-77%) of mice. Moreover, liver lesions were significantly reduced in vaccinated mice (64-65%) compared to infected control mice. The vaccination regime was well-tolerated with both peptides. We propose the use of these peptides, alone or in combination, as reliable candidates for vaccination against schistosomiasis.
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Affiliation(s)
- Juan Hernández-Goenaga
- Infectious and Tropical Diseases Group (e-INTRO), IBSAL-CIETUS (Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Julio López-Abán
- Infectious and Tropical Diseases Group (e-INTRO), IBSAL-CIETUS (Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Anna V. Protasio
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Belén Vicente Santiago
- Infectious and Tropical Diseases Group (e-INTRO), IBSAL-CIETUS (Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Esther del Olmo
- Department of Pharmaceutical Chemistry, IBSAL-CIETUS, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Magnolia Vanegas
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Group (e-INTRO), IBSAL-CIETUS (Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Manuel Alfonso Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Antonio Muro
- Infectious and Tropical Diseases Group (e-INTRO), IBSAL-CIETUS (Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
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18
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Wang M, Fu H, Shen X, Ruan R, Rokas A, Li H. Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata. MOLECULAR PLANT PATHOLOGY 2019; 20:1425-1438. [PMID: 31297970 PMCID: PMC6792136 DOI: 10.1111/mpp.12848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The tangerine pathotype of the ascomycete fungus Alternaria alternata is the causal agent of citrus brown spot, which can result in significant losses of both yield and marketability for tangerines worldwide. A conditionally dispensable chromosome (CDC), which harbours the host-selective ACT toxin gene cluster, is required for tangerine pathogenicity of A. alternata. To understand the genetic makeup and evolution of the tangerine pathotype CDC, we isolated and sequenced the CDCs of the A. alternata Z7 strain and analysed the function and evolution of their genes. The A. alternata Z7 strain has two CDCs (~1.1 and ~0.8 Mb, respectively), and the longer Z7 CDC contains all but one contig of the shorter one. Z7 CDCs contain 254 predicted protein-coding genes, which are enriched in functional categories associated with 'metabolic process' (55 genes, P = 0.037). Relatively few of the CDC genes can be classified as carbohydrate-active enzymes (CAZymes) (4) and transporters (19) and none as kinases. Evolutionary analysis of the 254 CDC proteins showed that their evolutionary conservation tends to be restricted within the genus Alternaria and that the CDC genes evolve faster than genes in the essential chromosomes, likely due to fewer selective constraints. Interestingly, phylogenetic analysis suggested that four of the 25 genes responsible for the ACT toxin production were likely transferred from Colletotrichum (Sordariomycetes). Functional experiments showed that two of them are essential for the virulence of the tangerine pathotype of A. alternata. These results provide new insights into the function and evolution of CDC genes in Alternaria.
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Affiliation(s)
- Mingshuang Wang
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
- Department of Biological SciencesVanderbilt UniversityNashvilleTN37235USA
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Huilan Fu
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
| | - Xing‐Xing Shen
- Department of Biological SciencesVanderbilt UniversityNashvilleTN37235USA
| | - Ruoxin Ruan
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
- Hangzhou Academy of Agricultural SciencesHangzhou310024China
| | - Antonis Rokas
- Department of Biological SciencesVanderbilt UniversityNashvilleTN37235USA
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
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19
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Identification and evaluation of novel anchoring proteins for cell surface display on Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2019; 103:3085-3097. [PMID: 30737536 DOI: 10.1007/s00253-019-09667-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/11/2019] [Accepted: 01/20/2019] [Indexed: 12/11/2022]
Abstract
The development of arming yeast strains as whole-cell biocatalysts involves a selection of effective anchoring proteins to display enzymes and proteins on yeast cell surface. To screen for novel anchoring proteins with improved efficiency, a bioinformatics pipeline for the identification of glycosylphosphatidylinositol-anchored cell wall proteins (GPI-CWPs) suitable for attaching passenger proteins to the cell surface of Saccharomyces cerevisiae has been developed. Here, the C-terminal sequences (CTSs) of putative GPI-CWPs were selected based on the criteria that the sequence must contain a serine/threonine-rich (S/T) region of at least 30% S/T content, a total threonine content of at least 10%, a continuous S/T stretch of at least 130 amino acids in length, and a continuous T-rich region of at least 10 amino acids in length. Of the predicted 790 proteins, 37 putative GPI-CWPs were selected from different yeast and fungal species to be evaluated for their performance in displaying yeast-enhanced green fluorescent protein and β-glucosidase enzyme. This led to the identification of five novel anchoring proteins with higher performance compared to α-agglutinin used as benchmark. In particular, the CTS of uncharacterized protein in Kluyveromyces lactis, namely 6_Kl, is the most efficient anchoring protein of the group. The CTS of 6_Kl protein provided a β-glucosidase activity of up to 23.5 U/g cell dry weight, which is 2.8 times higher than that of the CTS of α-agglutinin. These identified CTSs could be potential novel anchoring protein candidates for construction of efficient arming yeasts for biotechnology applications in the future.
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20
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Nizam S, Qiang X, Wawra S, Nostadt R, Getzke F, Schwanke F, Dreyer I, Langen G, Zuccaro A. Serendipita indica E5'NT modulates extracellular nucleotide levels in the plant apoplast and affects fungal colonization. EMBO Rep 2019; 20:embr.201847430. [PMID: 30642845 PMCID: PMC6362346 DOI: 10.15252/embr.201847430] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
Extracellular adenosine 5′‐triphosphate (eATP) is an essential signaling molecule that mediates different cellular processes through its interaction with membrane‐associated receptor proteins in animals and plants. eATP regulates plant growth, development, and responses to biotic and abiotic stresses. Its accumulation in the apoplast induces ROS production and cytoplasmic calcium increase mediating a defense response to invading microbes. We show here that perception of extracellular nucleotides, such as eATP, is important in plant–fungus interactions and that during colonization by the beneficial root endophyte Serendipita indica eATP accumulates in the apoplast at early symbiotic stages. Using liquid chromatography–tandem mass spectrometry, and cytological and functional analysis, we show that S. indica secrets SiE5′NT, an enzymatically active ecto‐5′‐nucleotidase capable of hydrolyzing nucleotides in the apoplast. Arabidopsis thaliana lines producing extracellular SiE5′NT are significantly better colonized, have reduced eATP levels, and altered responses to biotic stresses, indicating that SiE5′NT functions as a compatibility factor. Our data suggest that extracellular bioactive nucleotides and their perception play an important role in fungus–root interactions and that fungal‐derived enzymes can modify apoplastic metabolites to promote fungal accommodation.
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Affiliation(s)
- Shadab Nizam
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Xiaoyu Qiang
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Stephan Wawra
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Robin Nostadt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Felix Getzke
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Florian Schwanke
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Ingo Dreyer
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, Talca, Chile
| | - Gregor Langen
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Alga Zuccaro
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany .,Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, Germany
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21
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Zhou K. Glycosylphosphatidylinositol-Anchored Proteins in Arabidopsis and One of Their Common Roles in Signaling Transduction. FRONTIERS IN PLANT SCIENCE 2019; 10:1022. [PMID: 31555307 PMCID: PMC6726743 DOI: 10.3389/fpls.2019.01022] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/22/2019] [Indexed: 05/17/2023]
Abstract
Diverse proteins are found modified with glycosylphosphatidylinositol (GPI) at their carboxyl terminus in eukaryotes, which allows them to associate with membrane lipid bilayers and anchor on the external surface of the plasma membrane. GPI-anchored proteins (GPI-APs) play crucial roles in various processes, and more and more GPI-APs have been identified and studied. In this review, previous genomic and proteomic predictions of GPI-APs in Arabidopsis have been updated, which reveal their high abundance and complexity. From studies of individual GPI-APs in Arabidopsis, certain GPI-APs have been found associated with partner receptor-like kinases (RLKs), targeting RLKs to their subcellular localization and helping to recognize extracellular signaling polypeptide ligands. Interestingly, the association might also be involved in ligand selection. The analyses suggest that GPI-APs are essential and widely involved in signal transduction through association with RLKs.
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22
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Zhou K. GPI-anchored SKS proteins regulate root development through controlling cell polar expansion and cell wall synthesis. Biochem Biophys Res Commun 2018; 509:119-124. [PMID: 30578078 DOI: 10.1016/j.bbrc.2018.12.081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
Glycosylphosphatidylinositol-anchored proteins were reported to be involved in many developmental progresses in Arabidopsis. Here I report that, a group of homologous glycosylphosphatidylinositol-anchored proteins from SKU5-Similar family regulate seedling root development of Arabidopsis through controlling cell polar expansion and cell wall synthesis. Due to the irregular expansion of root cells and the defective synthesis of cell walls, their knockout mutants generated shorter roots with irregularly shaped root cells, and thicker cell walls.
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Affiliation(s)
- Ke Zhou
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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23
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Pei J, Kinch LN, Grishin NV. FlyXCDB—A Resource for Drosophila Cell Surface and Secreted Proteins and Their Extracellular Domains. J Mol Biol 2018; 430:3353-3411. [DOI: 10.1016/j.jmb.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 02/06/2023]
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Kolenda R, Burdukiewicz M, Schiebel J, Rödiger S, Sauer L, Szabo I, Orłowska A, Weinreich J, Nitschke J, Böhm A, Gerber U, Roggenbuck D, Schierack P. Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation. Front Microbiol 2018; 9:1905. [PMID: 30186250 PMCID: PMC6113376 DOI: 10.3389/fmicb.2018.01905] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/30/2018] [Indexed: 12/25/2022] Open
Abstract
Bacterial host tropism is a primary determinant of the range of host organisms they can infect. Salmonella serotypes are differentiated into host-restricted and host-adapted specialists, and host-unrestricted generalists. In order to elucidate the underlying molecular mechanisms of host specificity in Salmonella infection, we investigated the role of the intestinal host cell receptor zymogen granule membrane glycoprotein 2 (GP2), which is recognized by FimH adhesin of type 1 fimbriae found in Enterobacteriaceae. We compared four human and two porcine GP2 isoforms. Isoforms were expressed in Sf9 cells as well as in one human (HEp-2) and one porcine (IPEC-J2) cell line. FimH genes of 128 Salmonella isolates were sequenced and the 10 identified FimH variants were compared regarding adhesion (static adhesion assay) and infection (cell line assay) using an isogenic model. We expressed and characterized two functional porcine GP2 isoforms differing in their amino acid sequence to human isoforms by approximately 25%. By comparing all isoforms in the static adhesion assay, FimH variants were assigned to high, low or no-binding phenotypes. This FimH variant-dependent binding was neither specific for one GP2 isoform nor for GP2 in general. However, cell line infection assays revealed fundamental differences: using HEp-2 cells, infection was also FimH variant-specific but mainly independent of human GP2. In contrast, this FimH variant dependency was not obvious using IPEC-J2 cells. Here, we propose an alternative GP2 adhesion/infection mechanism whereby porcine GP2 is not a receptor that determined host-specificity of Salmonella. Salmonella specialists as well as generalists demonstrated similar binding to GP2. Future studies should focus on spatial distribution of GP2 isoforms in the human and porcine intestine, especially comparing health and disease.
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Affiliation(s)
- Rafał Kolenda
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Department of Biochemistry and Molecular Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Juliane Schiebel
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Lysann Sauer
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Istvan Szabo
- National Salmonella Reference Laboratory, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Aleksandra Orłowska
- Department of Biochemistry and Molecular Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jörg Weinreich
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Jörg Nitschke
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Alexander Böhm
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Ulrike Gerber
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- GA Generic Assays GmbH, Berlin, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
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Yeats TH, Bacic A, Johnson KL. Plant glycosylphosphatidylinositol anchored proteins at the plasma membrane-cell wall nexus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:649-669. [PMID: 29667761 DOI: 10.1111/jipb.12659] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/16/2018] [Indexed: 05/17/2023]
Abstract
Approximately 1% of plant proteins are predicted to be post-translationally modified with a glycosylphosphatidylinositol (GPI) anchor that tethers the polypeptide to the outer leaflet of the plasma membrane. Whereas the synthesis and structure of GPI anchors is largely conserved across eukaryotes, the repertoire of functional domains present in the GPI-anchored proteome has diverged substantially. In plants, this includes a large fraction of the GPI-anchored proteome being further modified with plant-specific arabinogalactan (AG) O-glycans. The importance of the GPI-anchored proteome to plant development is underscored by the fact that GPI biosynthetic null mutants exhibit embryo lethality. Mutations in genes encoding specific GPI-anchored proteins (GAPs) further supports their contribution to diverse biological processes, occurring at the interface of the plasma membrane and cell wall, including signaling, cell wall metabolism, cell wall polymer cross-linking, and plasmodesmatal transport. Here, we review the literature concerning plant GPI-anchored proteins, in the context of their potential to act as molecular hubs that mediate interactions between the plasma membrane and the cell wall, and their potential to transduce the signal into the protoplast and, thereby, activate signal transduction pathways.
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Affiliation(s)
- Trevor H Yeats
- School of Integrated Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Kim L Johnson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
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Awuoche EO, Weiss BL, Mireji PO, Vigneron A, Nyambega B, Murilla G, Aksoy S. Expression profiling of Trypanosoma congolense genes during development in the tsetse fly vector Glossina morsitans morsitans. Parasit Vectors 2018; 11:380. [PMID: 29970164 PMCID: PMC6029126 DOI: 10.1186/s13071-018-2964-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
Background The tsetse transmitted parasitic flagellate Trypanosoma congolense causes animal African trypanosomosis (AAT) across sub-Saharan Africa. AAT negatively impacts agricultural, economic, nutritional and subsequently, health status of the affected populace. The molecular mechanisms that underlie T. congolense’s developmental program within tsetse are largely unknown due to considerable challenges with obtaining sufficient parasite cells to perform molecular studies. Methods In this study, we used RNA-seq to profile T. congolense gene expression during development in two distinct tsetse tissues, the cardia and proboscis. Indirect immunofluorescent antibody test (IFA) and confocal laser scanning microscope was used to localize the expression of a putative protein encoded by the hypothetical protein (TcIL3000_0_02370). Results Consistent with current knowledge, genes coding several variant surface glycoproteins (including metacyclic specific VSGs), and the surface coat protein, congolense epimastigote specific protein, were upregulated in parasites in the proboscis (PB-parasites). Additionally, our results indicate that parasites in tsetse’s cardia (C-parasites) and PB employ oxidative phosphorylation and amino acid metabolism for energy. Several genes upregulated in C-parasites encoded receptor-type adenylate cyclases, surface carboxylate transporter family proteins (or PADs), transport proteins, RNA-binding proteins and procyclin isoforms. Gene ontology analysis of products of genes upregulated in C-parasites showed enrichment of terms broadly associated with nucleotides, microtubules, cell membrane and its components, cell signaling, quorum sensing and several transport activities, suggesting that the parasites colonizing the cardia may monitor their environment and regulate their density and movement in this tissue. Additionally, cell surface protein (CSP) encoding genes associated with the Fam50 ‘GARP’, ‘iii’ and ‘i’ subfamilies were also significantly upregulated in C-parasites, suggesting that they are important for the long non-dividing trypomastigotes to colonize tsetse’s cardia. The putative products of genes that were upregulated in PB-parasites were linked to nucleosomes, cytoplasm and membrane-bound organelles, which suggest that parasites in this niche undergo cell division in line with prior findings. Most of the CSPs upregulated in PB-parasites were hypothetical, thus requiring further functional characterization. Expression of one such hypothetical protein (TcIL3000_0_02370) was analyzed using immunofluorescence and confocal laser scanning microscopy, which together revealed preferential expression of this protein on the entire surface coat of T. congolense parasite stages that colonize G. m. morsitans’ proboscis. Conclusion Collectively, our results provide insight into T. congolense gene expression profiles in distinct niches within the tsetse vector. Our results show that the hypothetical protein TcIL3000_0_02370, is expressed on the entire surface of the trypanosomes inhabiting tsetse’s proboscis. We discuss our results in terms of their relevance to disease transmission processes. Electronic supplementary material The online version of this article (10.1186/s13071-018-2964-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erick O Awuoche
- Department of Biochemistry, Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya. .,Department of Biomedical Science and Technology, School of Public Health and Community Development, Maseno University, Private Bag, Maseno, Kenya. .,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. .,Department of Agriculture, School of Agriculture and Food Science, Meru University of Science and Technology, Meru, Kenya.
| | - Brian L Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Paul O Mireji
- Department of Biochemistry, Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Aurélien Vigneron
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Benson Nyambega
- Department of Medical Biochemistry, School of Medicine, Maseno University, Private Bag, Maseno, Kenya
| | - Grace Murilla
- Department of Biochemistry, Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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Ray A, Jatana N, Thukral L. Lipidated proteins: Spotlight on protein-membrane binding interfaces. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:74-84. [DOI: 10.1016/j.pbiomolbio.2017.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 01/21/2023]
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Moreno-Pérez DA, Baquero LA, Chitiva-Ardila DM, Patarroyo MA. Characterising PvRBSA: an exclusive protein from Plasmodium species infecting reticulocytes. Parasit Vectors 2017; 10:243. [PMID: 28521840 PMCID: PMC5437689 DOI: 10.1186/s13071-017-2185-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/10/2017] [Indexed: 11/30/2022] Open
Abstract
Background Plasmodium vivax uses multiple ligand-receptor interactions for preferential invasion of human reticulocytes. Several of these ligands have been identified by in silico approaches based on the role displayed by their orthologs in other Plasmodium species during initial adhesion or invasion. However, the cell adhesion role of proteins that are exclusive to species that specifically invade reticulocytes (as P. vivax and P. cynomolgi) has not been evaluated to date. This study aimed to characterise an antigen shared between Plasmodium species that preferentially infect reticulocytes with a focus on assessing its binding activity to target cells. Results An in silico analysis was performed using P. vivax proteome data to identify and characterise one antigen shared between P. vivax and P. cynomolgi. This led to identification of the pvrbsa gene present in the P. vivax VCG-I strain genome. This gene is transcribed in mature schizonts and encodes a protein located on the parasite surface. rPvRBSA was antigenic and capable of binding to a population of reticulocytes with a different Duffy phenotype. Interestingly, the molecule showed a higher percentage of binding to immature human reticulocytes (CD71hi). Conclusions This study describes for the first time, a molecule involved in host cell binding that is exclusive in reticulocyte-infecting Plasmodium species. This suggest that PvRBSA is an antigenic adhesin that plays a role in parasite binding to target cells. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2185-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Darwin A Moreno-Pérez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, D.C., Colombia.,Programme in Biomedical and Biological Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá, D.C., Colombia
| | - Luis A Baquero
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, D.C., Colombia
| | - Diana M Chitiva-Ardila
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, D.C., Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, D.C., Colombia. .,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá, D.C., Colombia.
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Kessler RL, Contreras VT, Marliére NP, Aparecida Guarneri A, Villamizar Silva LH, Mazzarotto GACA, Batista M, Soccol VT, Krieger MA, Probst CM. Recently differentiated epimastigotes fromTrypanosoma cruziare infective to the mammalian host. Mol Microbiol 2017; 104:712-736. [DOI: 10.1111/mmi.13653] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Víctor Tulio Contreras
- Laboratorio de Protozoología, Centro de Biología Molecular de Parásitos, Facultad Ciencias de la Salud; Universidad de Carabobo; Valencia Venezuela
| | - Newmar Pinto Marliére
- Vector Behavior and Pathogen Interaction Group; Centro de Pesquisas René Rachou, Fiocruz; Belo Horizonte Minas Gerais Brazil
| | - Alessandra Aparecida Guarneri
- Vector Behavior and Pathogen Interaction Group; Centro de Pesquisas René Rachou, Fiocruz; Belo Horizonte Minas Gerais Brazil
| | | | | | | | - Vanete Thomaz Soccol
- Programa de Pós-Graduação em Processos Biotecnológicos e Biotecnologia, Centro Politécnico; Universidade Federal do Paraná; Curitiba PR Brazil
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30
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Oeser B, Kind S, Schurack S, Schmutzer T, Tudzynski P, Hinsch J. Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale. BMC Genomics 2017; 18:273. [PMID: 28372538 PMCID: PMC5379732 DOI: 10.1186/s12864-017-3619-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/10/2017] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The economically important Ergot fungus Claviceps purpurea is an interesting biotrophic model system because of its strict organ specificity (grass ovaries) and the lack of any detectable plant defense reactions. Though several virulence factors were identified, the exact infection mechanisms are unknown, e.g. how the fungus masks its attack and if the host detects the infection at all. RESULTS We present a first dual transcriptome analysis using an RNA-Seq approach. We studied both, fungal and plant gene expression in young ovaries infected by the wild-type and two virulence-attenuated mutants. We can show that the plant recognizes the fungus, since defense related genes are upregulated, especially several phytohormone genes. We present a survey of in planta expressed fungal genes, among them several confirmed virulence genes. Interestingly, the set of most highly expressed genes includes a high proportion of genes encoding putative effectors, small secreted proteins which might be involved in masking the fungal attack or interfering with host defense reactions. As known from several other phytopathogens, the C. purpurea genome contains more than 400 of such genes, many of them clustered and probably highly redundant. Since the lack of effective defense reactions in spite of recognition of the fungus could very well be achieved by effectors, we started a functional analysis of some of the most highly expressed candidates. However, the redundancy of the system made the identification of a drastic effect of a single gene most unlikely. We can show that at least one candidate accumulates in the plant apoplast. Deletion of some candidates led to a reduced virulence of C. purpurea on rye, indicating a role of the respective proteins during the infection process. CONCLUSIONS We show for the first time that- despite the absence of effective plant defense reactions- the biotrophic pathogen C. purpurea is detected by its host. This points to a role of effectors in modulation of the effective plant response. Indeed, several putative effector genes are among the highest expressed genes in planta.
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Affiliation(s)
- Birgitt Oeser
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Sabine Kind
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Selma Schurack
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Paul Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Janine Hinsch
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
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31
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Hernández-Pasos J, Valentín-Tirado G, García-Arrarás JE. Melanotransferrin: New Homolog Genes and Their Differential Expression during Intestinal Regeneration in the Sea Cucumber Holothuria glaberrima. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:259-274. [PMID: 28229527 DOI: 10.1002/jez.b.22731] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/15/2016] [Accepted: 01/17/2017] [Indexed: 11/09/2022]
Abstract
Melanotransferrin (MTf) is a protein associated with oncogenetic, developmental, and immune processes which function remains unclear. The MTf gene has been reported in numerous vertebrate and invertebrate species, including echinoderms. We now report the finding of four different MTfs in the transcriptome of the sea cucumber Holothuria glaberrima. Sequence studies and phylogenetic analyses were done to ascertain the similarities among the putative proteins and their relationship with other transferrin family members. The genes were shown to be differentially expressed in various holothurian organs and to respond differently when the animals were challenged with the immune system activator lipopolysaccharide (LPS). Moreover, the four genes were found to be highly overexpressed during the early stages of intestinal regeneration. The finding of four different genes in the holothurian is particularly surprising, because only one MTf gene has been reported in all other animal species sequenced to date. This finding, combined with the increase expression during intestinal regeneration, suggests a new possible function of MTf in organ regenerative processes.
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Affiliation(s)
- Josué Hernández-Pasos
- Department of Biology, University of Puerto Rico-Río Piedras Campus, San Juan, Puerto Rico.,School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | | | - José E García-Arrarás
- Department of Biology, University of Puerto Rico-Río Piedras Campus, San Juan, Puerto Rico
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32
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Queiroz RML, Ricart CAO, Machado MO, Bastos IMD, de Santana JM, de Sousa MV, Roepstorff P, Charneau S. Insight into the Exoproteome of the Tissue-Derived Trypomastigote form of Trypanosoma cruzi. Front Chem 2016; 4:42. [PMID: 27872839 PMCID: PMC5097913 DOI: 10.3389/fchem.2016.00042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/19/2016] [Indexed: 01/07/2023] Open
Abstract
The protozoan parasite Trypanosoma cruzi causes Chagas disease, one of the major neglected infectious diseases. It has the potential to infect any nucleated mammalian cell. The secreted/excreted protein repertoire released by T. cruzi trypomastigotes is crucial in host-pathogen interactions. In this study, mammalian tissue culture-derived trypomastigotes (Y strain) were used to characterize the exoproteome of the infective bloodstream life form. Proteins released into the serum-free culture medium after 3 h of incubation were harvested and digested with trypsin. NanoLC-MS/MS analysis resulted in the identification of 540 proteins, the largest set of released proteins identified to date in Trypanosoma spp. Bioinformatic analysis predicted most identified proteins as secreted, predominantly by non-classical pathways, and involved in host-cell infection. Some proteins possess predicted GPI-anchor signals, these being mostly trans-sialidases, mucin associated surface proteins and surface glycoproteins. Moreover, we enriched phosphopeptides and glycopeptides from tryptic digests. The majority of identified glycoproteins are trans-sialidases and surface glycoproteins involved in host-parasite interaction. Conversely, most identified phosphoproteins have no Gene Ontology classification. The existence of various proteins related to similar functions in the exoproteome likely reflects this parasite's enhanced mechanisms for adhesion, invasion, and internalization of different host-cell types, and escape from immune defenses.
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Affiliation(s)
- Rayner M L Queiroz
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia, Brasilia, Brazil; Department of Biochemistry and Molecular Biology, University of Southern DenmarkOdense, Denmark
| | - Carlos A O Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Mara O Machado
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Izabela M D Bastos
- Laboratory of Host-Pathogen Interaction, Department of Cell Biology, University of Brasilia Brasilia, Brazil
| | - Jaime M de Santana
- Laboratory of Host-Pathogen Interaction, Department of Cell Biology, University of Brasilia Brasilia, Brazil
| | - Marcelo V de Sousa
- Laboratory of Host-Pathogen Interaction, Department of Cell Biology, University of Brasilia Brasilia, Brazil
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense, Denmark
| | - Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
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Ifeonu OO, Simon R, Tennant SM, Sheoran AS, Daly MC, Felix V, Kissinger JC, Widmer G, Levine MM, Tzipori S, Silva JC. Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw137. [PMID: 28095366 PMCID: PMC5070614 DOI: 10.1093/database/baw137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 01/19/2023]
Abstract
Human cryptosporidiosis, caused primarily by Cryptosporidium hominis and a subset of Cryptosporidium parvum, is a major cause of moderate-to-severe diarrhea in children under 5 years of age in developing countries and can lead to nutritional stunting and death. Cryptosporidiosis is particularly severe and potentially lethal in immunocompromised hosts. Biological and technical challenges have impeded traditional vaccinology approaches to identify novel targets for the development of vaccines against C. hominis, the predominant species associated with human disease. We deemed that the existence of genomic resources for multiple species in the genus, including a much-improved genome assembly and annotation for C. hominis, makes a reverse vaccinology approach feasible. To this end, we sought to generate a searchable online resource, termed C. hominis gene catalog, which registers all C. hominis genes and their properties relevant for the identification and prioritization of candidate vaccine antigens, including physical attributes, properties related to antigenic potential and expression data. Using bioinformatic approaches, we identified ∼400 C. hominis genes containing properties typical of surface-exposed antigens, such as predicted glycosylphosphatidylinositol (GPI)-anchor motifs, multiple transmembrane motifs and/or signal peptides targeting the encoded protein to the secretory pathway. This set can be narrowed further, e.g. by focusing on potential GPI-anchored proteins lacking homologs in the human genome, but with homologs in the other Cryptosporidium species for which genomic data are available, and with low amino acid polymorphism. Additional selection criteria related to recombinant expression and purification include minimizing predicted post-translation modifications and potential disulfide bonds. Forty proteins satisfying these criteria were selected from 3745 proteins in the updated C. hominis annotation. The immunogenic potential of a few of these is currently being tested. Database URL:http://cryptogc.igs.umaryland.edu
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Affiliation(s)
- Olukemi O Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA.,School of Systems Biology, George Mason University, 10900 University Boulevard, Manassas, VA 20110, USA
| | - Raphael Simon
- Center for Vaccine Development, Institute for Global Health, and Department of Medicine, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201, USA
| | - Sharon M Tennant
- Center for Vaccine Development, Institute for Global Health, and Department of Medicine, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201, USA
| | - Abhineet S Sheoran
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA 01536, USA
| | - Maria C Daly
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA
| | - Victor Felix
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA
| | - Jessica C Kissinger
- Department of Genetics, Institute of Bioinformatics and Center for Topical and Emerging Global Diseases, University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA and
| | - Giovanni Widmer
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA 01536, USA
| | - Myron M Levine
- Center for Vaccine Development, Institute for Global Health, and Department of Medicine, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA 01536, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA .,School of Systems Biology, George Mason University, 10900 University Boulevard, Manassas, VA 20110, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201, USA
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Mukai Y, Takahashi D, Inoue K, Sugita H, Kikegawa T, Etchuya K. Secondary Structure of GPI Attachment Signal Region Monitored by Circular Dichroism. CHEM LETT 2016. [DOI: 10.1246/cl.160551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Takahashi D, Kawamura Y, Uemura M. Cold acclimation is accompanied by complex responses of glycosylphosphatidylinositol (GPI)-anchored proteins in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5203-15. [PMID: 27471282 PMCID: PMC5014161 DOI: 10.1093/jxb/erw279] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cold acclimation results in changes of the plasma membrane (PM) composition. The PM is considered to contain specific lipid/protein-enriched microdomains which can be extracted as detergent-resistant plasma membrane (DRM). Previous studies in animal cells have demonstrated that glycosylphosphatidylinositol-anchored proteins (GPI-APs) can be targeted to microdomains and/or the apoplast. However, the functional significance of GPI-APs during cold acclimation in plants is not yet fully understood. In this study, we aimed to investigate the responsiveness of GPI-APs to cold acclimation treatment in Arabidopsis We isolated the PM, DRM, and apoplast fractions separately and, in addition, GPI-AP-enriched fractions were prepared from the PM preparation. Label-free quantitative shotgun proteomics identified a number of GPI-APs (163 proteins). Among them, some GPI-APs such as fasciclin-like arabinogalactan proteins and glycerophosphoryldiester phosphodiesterase-like proteins predominantly increased in PM- and GPI-AP-enriched fractions while the changes of GPI-APs in the DRM and apoplast fractions during cold acclimation were considerably different from those of other fractions. These proteins are thought to be associated with cell wall structure and properties. Therefore, this study demonstrated that each GPI-AP responded to cold acclimation in a different manner, suggesting that these changes during cold acclimation are involved in rearrangement of the extracellular matrix including the cell wall towards acquisition of freezing tolerance.
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Affiliation(s)
- Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Max-Planck-Institut für Molekulare Pflanzenphysiologie, D -14476 Potsdam, Germany
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan Cryobiofrontier Research Center, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
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Cornillot E, Dassouli A, Pachikara N, Lawres L, Renard I, Francois C, Randazzo S, Brès V, Garg A, Brancato J, Pazzi JE, Pablo J, Hung C, Teng A, Shandling AD, Huynh VT, Krause PJ, Lepore T, Delbecq S, Hermanson G, Liang X, Williams S, Molina DM, Ben Mamoun C. A targeted immunomic approach identifies diagnostic antigens in the human pathogen Babesia microti. Transfusion 2016; 56:2085-99. [PMID: 27184823 PMCID: PMC5644385 DOI: 10.1111/trf.13640] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 03/24/2016] [Accepted: 03/30/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND Babesia microti is a protozoan parasite responsible for the majority of reported cases of human babesiosis and a major risk to the blood supply. Laboratory screening of blood donors may help prevent transfusion-transmitted babesiosis but there is no Food and Drug Administration-approved screening method yet available. Development of a sensitive, specific, and highly automated B. microti antibody assay for diagnosis of acute babesiosis and blood screening could have an important impact on decreasing the health burden of B. microti infection. STUDY DESIGN AND METHODS Herein, we take advantage of recent advances in B. microti genomic analyses, field surveys of the reservoir host, and human studies in endemic areas to apply a targeted immunomic approach to the discovery of B. microti antigens that serve as signatures of active or past babesiosis infections. Of 19 glycosylphosphatidylinositol (GPI)-anchored protein candidates (BmGPI1-19) identified in the B. microti proteome, 17 were successfully expressed, printed on a microarray chip, and used to screen sera from uninfected and B. microti-infected mice and humans to determine immune responses that are associated with active and past infection. RESULTS Antibody responses to various B. microti BmGPI antigens were detected and BmGPI12 was identified as the best biomarker of infection that provided high sensitivity and specificity when used in a microarray antibody assay. CONCLUSION BmGPI12 alone or in combination with other BmGPI proteins is a promising candidate biomarker for detection of B. microti antibodies that might be useful in blood screening to prevent transfusion-transmitted babesiosis.
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Affiliation(s)
- Emmanuel Cornillot
- Institut de Biologie Computationnelle (IBC), Institut de Recherche en Cancérologie de Montpellier (IRCM-INSERM U1194), Institut régional du Cancer Montpellier (ICM) and Université de Montpellier, Montpellier, France
| | - Amina Dassouli
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut
- Laboratoire de Biologie Cellulaire et Moléculaire (LBCM-EA4558 Vaccination Antiparasitaire), UFR Pharmacie, Université de Montpellier, Montpellier, France
| | - Niseema Pachikara
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut
| | - Lauren Lawres
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut
| | - Isaline Renard
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut
| | - Celia Francois
- Laboratoire de Biologie Cellulaire et Moléculaire (LBCM-EA4558 Vaccination Antiparasitaire), UFR Pharmacie, Université de Montpellier, Montpellier, France
| | - Sylvie Randazzo
- Laboratoire de Biologie Cellulaire et Moléculaire (LBCM-EA4558 Vaccination Antiparasitaire), UFR Pharmacie, Université de Montpellier, Montpellier, France
| | - Virginie Brès
- Laboratoire de Biologie Cellulaire et Moléculaire (LBCM-EA4558 Vaccination Antiparasitaire), UFR Pharmacie, Université de Montpellier, Montpellier, France
| | - Aprajita Garg
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut
| | - Janna Brancato
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | | | | | - Chris Hung
- Antigen Discovery, Inc., Irvine, California
| | - Andy Teng
- Antigen Discovery, Inc., Irvine, California
| | | | | | - Peter J. Krause
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Timothy Lepore
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Stephane Delbecq
- Laboratoire de Biologie Cellulaire et Moléculaire (LBCM-EA4558 Vaccination Antiparasitaire), UFR Pharmacie, Université de Montpellier, Montpellier, France
| | | | | | - Scott Williams
- Connecticut Agricultural Experiment Station, New Haven, Connecticut
| | | | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Field-Evolved Mode 1 Resistance of the Fall Armyworm to Transgenic Cry1Fa-Expressing Corn Associated with Reduced Cry1Fa Toxin Binding and Midgut Alkaline Phosphatase Expression. Appl Environ Microbiol 2015; 82:1023-1034. [PMID: 26637593 DOI: 10.1128/aem.02871-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/20/2015] [Indexed: 11/20/2022] Open
Abstract
Insecticidal protein genes from the bacterium Bacillus thuringiensis (Bt) are expressed by transgenic Bt crops (Bt crops) for effective and environmentally safe pest control. The development of resistance to these insecticidal proteins is considered the most serious threat to the sustainability of Bt crops. Resistance in fall armyworm (Spodoptera frugiperda) populations from Puerto Rico to transgenic corn producing the Cry1Fa insecticidal protein resulted, for the first time in the United States, in practical resistance, and Bt corn was withdrawn from the local market. In this study, we used a field-collected Cry1Fa corn-resistant strain (456) of S. frugiperda to identify the mechanism responsible for field-evolved resistance. Binding assays detected reduced Cry1Fa, Cry1Ab, and Cry1Ac but not Cry1Ca toxin binding to midgut brush border membrane vesicles (BBMV) from the larvae of strain 456 compared to that from the larvae of a susceptible (Ben) strain. This binding phenotype is descriptive of the mode 1 type of resistance to Bt toxins. A comparison of the transcript levels for putative Cry1 toxin receptor genes identified a significant downregulation (>90%) of a membrane-bound alkaline phosphatase (ALP), which translated to reduced ALP protein levels and a 75% reduction in ALP activity in BBMV from 456 compared to that of Ben larvae. We cloned and heterologously expressed this ALP from susceptible S. frugiperda larvae and demonstrated that it specifically binds with Cry1Fa toxin. This study provides a thorough mechanistic description of field-evolved resistance to a transgenic Bt crop and supports an association between resistance and reduced Cry1Fa toxin binding and levels of a putative Cry1Fa toxin receptor, ALP, in the midguts of S. frugiperda larvae.
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Cortes LK, Vainauskas S, Dai N, McClung CM, Shah M, Benner JS, Corrêa IR, VerBerkmoes NC, Taron CH. Proteomic identification of mammalian cell surface derived glycosylphosphatidylinositol-anchored proteins through selective glycan enrichment. Proteomics 2015; 14:2471-84. [PMID: 25262930 PMCID: PMC4260145 DOI: 10.1002/pmic.201400148] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/16/2014] [Accepted: 09/23/2014] [Indexed: 11/09/2022]
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are an important class of glycoproteins that are tethered to the surface of mammalian cells via the lipid GPI. GPI-APs have been implicated in many important cellular functions including cell adhesion, cell signaling, and immune regulation. Proteomic identification of mammalian GPI-APs en masse has been limited technically by poor sensitivity for these low abundance proteins and the use of methods that destroy cell integrity. Here, we present methodology that permits identification of GPI-APs liberated directly from the surface of intact mammalian cells through exploitation of their appended glycans to enrich for these proteins ahead of LC-MS/MS analyses. We validate our approach in HeLa cells, identifying a greater number of GPI-APs from intact cells than has been previously identified from isolated HeLa membranes and a lipid raft preparation. We further apply our approach to define the cohort of endogenous GPI-APs that populate the distinct apical and basolateral membrane surfaces of polarized epithelial cell monolayers. Our approach provides a new method to achieve greater sensitivity in the identification of low abundance GPI-APs from the surface of live cells and the nondestructive nature of the method provides new opportunities for the temporal or spatial analysis of cellular GPI-AP expression and dynamics.
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40
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Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:776. [PMID: 26442085 DOI: 10.3389/fpls.2015.00776issn=1664-462x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/10/2015] [Indexed: 05/25/2023]
Abstract
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.
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Affiliation(s)
- Thomas Badet
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
| | - Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
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41
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Meinken J, Walker G, Cooper CR, Min XJ. MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav077. [PMID: 26255309 PMCID: PMC4529745 DOI: 10.1093/database/bav077] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/14/2015] [Indexed: 12/15/2022]
Abstract
The subcellular location of a protein is a key factor in determining the molecular function of the protein in an organism. MetazSecKB is a secretome and subcellular proteome knowledgebase specifically designed for metazoan, i.e. human and animals. The protein sequence data, consisting of over 4 million entries with 121 species having a complete proteome, were retrieved from UniProtKB. Protein subcellular locations including secreted and 15 other subcellular locations were assigned based on either curated experimental evidence or prediction using seven computational tools. The protein or subcellular proteome data can be searched and downloaded using several different types of identifiers, gene name or keyword(s), and species. BLAST search and community annotation of subcellular locations are also supported. Our primary analysis revealed that the proteome sizes, secretome sizes and other subcellular proteome sizes vary tremendously in different animal species. The proportions of secretomes vary from 3 to 22% (average 8%) in metazoa species. The proportions of other major subcellular proteomes ranged approximately 21–43% (average 31%) in cytoplasm, 20–37% (average 30%) in nucleus, 3–19% (average 12%) as plasma membrane proteins and 3–9% (average 6%) in mitochondria. We also compared the protein families in secretomes of different primates. The Gene Ontology and protein family domain analysis of human secreted proteins revealed that these proteins play important roles in regulation of human structure development, signal transduction, immune systems and many other biological processes. Database URL:http://proteomics.ysu.edu/secretomes/animal/index.php
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Affiliation(s)
- John Meinken
- Department of Computer Science and Information Systems, Center for Applied Chemical Biology and
| | - Gary Walker
- Center for Applied Chemical Biology and Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Chester R Cooper
- Center for Applied Chemical Biology and Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Xiang Jia Min
- Center for Applied Chemical Biology and Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
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Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ü, Kõks S, Salumets A. Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment. Proteomics 2015; 15:1906-20. [PMID: 25603787 DOI: 10.1002/pmic.201400297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/01/2014] [Accepted: 01/15/2015] [Indexed: 12/27/2022]
Abstract
A significant proportion of mammalian fertilization is mediated through the proteomic composition of the sperm surface. These protein constituents can present as biomarkers to control and regulate breeding of agricultural animals. Previous studies have addressed the bovine sperm cell apical plasma membrane (PM) proteome with nitrogen cavitation enrichment. Alternative workflows would enable to expand the compositional data more globally around the entire sperm's surface. We used a cell surface biotin-labeling in combination with differential centrifugation to enrich sperm surface proteins. Using nano-LC MS/MS, 338 proteins were confidently identified in the PM-enriched proteome. Functional categories of sperm-egg interaction, protein turnover, metabolism as well as molecular transport, spermatogenesis, and signal transduction were represented by proteins with high quantitative signal in our study. A highly significant degree of enrichment was found for transmembrane and PM-targeted proteins. Among them, we also report proteins previously not described on bovine sperm (CPQ, CD58, CKLF, CPVL, GLB1L3, and LPCAT2B) of which CPQ and CPVL cell surface localization was further validated. A descriptive overview of the bovine sperm PM integral and peripheral proteins is provided to complement future studies on animal reproduction and its relation to sperm cell surface. All MS data have been deposited in the ProteomeXchange with identifier PXD001096 (http://proteomecentral.proteomexchange.org/dataset/PXD001096).
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Affiliation(s)
- Sergo Kasvandik
- Proteomics Core Facility, Institute of Technology, University of Tartu, Tartu, Estonia.,Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia
| | - Gerly Sillaste
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | - Agne Velthut-Meikas
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,Center for Biology of Integrated Systems, Tallinn University of Technology, Tallinn, Estonia
| | - Aavo-Valdur Mikelsaar
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Triin Hallap
- Department of Reproductive Biology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Peeter Padrik
- Animal Breeders Association of Estonia, Keava, Kehtna vald, Raplamaa, Estonia
| | - Tanel Tenson
- Proteomics Core Facility, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ülle Jaakma
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Reproductive Biology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Sulev Kõks
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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Cens T, Rousset M, Collet C, Charreton M, Garnery L, Le Conte Y, Chahine M, Sandoz JC, Charnet P. Molecular characterization and functional expression of the Apis mellifera voltage-dependent Ca2+ channels. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 58:12-27. [PMID: 25602183 DOI: 10.1016/j.ibmb.2015.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 06/04/2023]
Abstract
Voltage-gated Ca(2+) channels allow the influx of Ca(2+) ions from the extracellular space upon membrane depolarization and thus serve as a transducer between membrane potential and cellular events initiated by Ca(2+) transients. Most insects are predicted to possess three genes encoding Cavα, the main subunit of Ca(2+) channels, and several genes encoding the two auxiliary subunits, Cavβ and Cavα2δ; however very few of these genes have been cloned so far. Here, we cloned three full-length cDNAs encoding the three Cavα subunits (AmelCav1a, AmelCav2a and AmelCav3a), a cDNA encoding a novel variant of the Cavβ subunit (AmelCavβc), and three full-length cDNAs encoding three Cavα2δ subunits (AmelCavα2δ1 to 3) of the honeybee Apis mellifera. We identified several alternative or mutually exclusive exons in the sequence of the AmelCav2 and AmelCav3 genes. Moreover, we detected a stretch of glutamine residues in the C-terminus of the AmelCav1 subunit that is reminiscent of the motif found in the human Cav2.1 subunit of patients with Spinocerebellar Ataxia type 6. All these subunits contain structural domains that have been identified as functionally important in their mammalian homologues. For the first time, we could express three insect Cavα subunits in Xenopus oocytes and we show that AmelCav1a, 2a and 3a form Ca(2+) channels with distinctive properties. Notably, the co-expression of AmelCav1a or AmelCav2a with AmelCavβc and AmCavα2δ1 produces High Voltage-Activated Ca(2+) channels. On the other hand, expression of AmelCav3a alone leads to Low Voltage-Activated Ca(2+) channels.
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Affiliation(s)
- Thierry Cens
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR 5247, Place Eugène Bataillon, 34095 Montpellier cedex 5, France; Centre de Recherche de Biochimie Macromoléculaire (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France; Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
| | - Matthieu Rousset
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR 5247, Place Eugène Bataillon, 34095 Montpellier cedex 5, France; Centre de Recherche de Biochimie Macromoléculaire (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France; Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
| | - Claude Collet
- INRA UR 406 Abeilles et Environnement, 228 Route de l'aérodrome, Domaine Saint Paul, Site Agroparc, CS40509, 84914 Avignon cedex 9, France.
| | - Mercedes Charreton
- INRA UR 406 Abeilles et Environnement, 228 Route de l'aérodrome, Domaine Saint Paul, Site Agroparc, CS40509, 84914 Avignon cedex 9, France.
| | - Lionel Garnery
- Laboratoire Evolution Génome et Spéciation (LEGS), CNRS UPR 9034, Avenue de la Terrasse, Bâtiment 13, 91198 Gif sur Yvette, France.
| | - Yves Le Conte
- INRA UR 406 Abeilles et Environnement, 228 Route de l'aérodrome, Domaine Saint Paul, Site Agroparc, CS40509, 84914 Avignon cedex 9, France.
| | - Mohamed Chahine
- Centre de recherche, Institut universitaire en santé mentale de Québec, 2601 Chemin de la Canardière, Québec Québec G1J 2G3, Canada.
| | - Jean-Christophe Sandoz
- Laboratoire Evolution Génome et Spéciation (LEGS), CNRS UPR 9034, Avenue de la Terrasse, Bâtiment 13, 91198 Gif sur Yvette, France.
| | - Pierre Charnet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR 5247, Place Eugène Bataillon, 34095 Montpellier cedex 5, France; Centre de Recherche de Biochimie Macromoléculaire (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293 Montpellier cedex 5, France; Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
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Tapken W, Murphy AS. Membrane nanodomains in plants: capturing form, function, and movement. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1573-86. [PMID: 25725094 DOI: 10.1093/jxb/erv054] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The plasma membrane is the interface between the cell and the external environment. Plasma membrane lipids provide scaffolds for proteins and protein complexes that are involved in cell to cell communication, signal transduction, immune responses, and transport of small molecules. In animals, fungi, and plants, a substantial subset of these plasma membrane proteins function within ordered sterol- and sphingolipid-rich nanodomains. High-resolution microscopy, lipid dyes, pharmacological inhibitors of lipid biosynthesis, and lipid biosynthetic mutants have been employed to examine the relationship between the lipid environment and protein activity in plants. They have also been used to identify proteins associated with nanodomains and the pathways by which nanodomain-associated proteins are trafficked to their plasma membrane destinations. These studies suggest that plant membrane nanodomains function in a context-specific manner, analogous to similar structures in animals and fungi. In addition to the highly conserved flotillin and remorin markers, some members of the B and G subclasses of ATP binding cassette transporters have emerged as functional markers for plant nanodomains. Further, the glycophosphatidylinositol-anchored fasciclin-like arabinogalactan proteins, that are often associated with detergent-resistant membranes, appear also to have a functional role in membrane nanodomains.
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Affiliation(s)
- Wiebke Tapken
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Angus S Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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Mo J, Li J. In silico analysis for structure, function and T-cell epitopes of a hypothetical conserved (HP-C) protein coded by PVX_092425 in Plasmodium vivax. Pathog Glob Health 2015; 109:61-7. [PMID: 25706099 DOI: 10.1179/2047773215y.0000000005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
OBJECTIVE Plasmodium spp. merozoite glycosylphosphatidylinositol-anchored proteins (GPI-APs) considered as protective immunogen in novel vaccines against malaria. To analyze the structure and function of a hypothetical conserved (HP-C) GPI-AP coded by gene PVX_092425 from Plasmodium vivax, and find its potential T-cell epitopes for further vivax malaria vaccine study. METHODS The structure, function and T-cell epitopes of the HP-C protein named Pvx_092425 were analyzed and predicted by online and offline bioinformatics software. RESULTS The bioinformatics data showed that the Pvx_092425 is an 830 amino acid (AA) long polypeptide encoded by five exons gene PVX_092425.It contains a pectin lyase-like superfamily, an AA repeats region, a cys-rich region and a transmembrane domain (TM) in C-terminal region. The alignment analysis drew it has a unique AA repeats region among Plasmodium spp. It was located in the cytoplasm, secretory system or cellular nucleus of P. vivax merozoite. For the sequence, the fragment of I823-V829 inserts in the interior side of the membrane, and M1--A812 belongs to the cytoplasmic tail. It has seven protein-protein binding sites. The peptides with the best predicted binding affinities were human leucocyte antigen (HLA) HLA-A*0203, HLA-DRB1*0101 and HLA- DRB1*0701.Among these predicted peptides, 582FLWDKALFD590 epitope interacted with HLA-DRB1*0101 allele showed best binding affinity compared to others. Structural analysis explained that the epitope fits well into the epitope-binding groove of HLA-DRB1*0101. CONCLUSIONS It proposes that the Pvx_092425 plays a key role during erythrocyte stage and generates information that is useful for development of blood-stage vaccine to block the merozoites invasion.
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Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:776. [PMID: 26442085 PMCID: PMC4585107 DOI: 10.3389/fpls.2015.00776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/10/2015] [Indexed: 05/04/2023]
Abstract
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.
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Affiliation(s)
- Thomas Badet
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
| | - Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
- *Correspondence: Sylvain Raffaele, Laboratoire des Interactions Plante Micro-organismes, 24 Chemin de Borde Rouge – Auzeville, 31326 Castanet Tolosan, France
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Moreno-Pérez DA, Dégano R, Ibarrola N, Muro A, Patarroyo MA. Determining the Plasmodium vivax VCG-1 strain blood stage proteome. J Proteomics 2014; 113:268-280. [PMID: 25316051 DOI: 10.1016/j.jprot.2014.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/17/2014] [Accepted: 10/02/2014] [Indexed: 01/31/2023]
Abstract
Plasmodium vivax is the second most prevalent parasite species causing malaria in humans living in tropical and subtropical areas throughout the world. There have been few P. vivax proteomic studies to date and they have focused on using clinical isolates, given the technical difficulties concerning how to maintain an in vitro culture of this species. This study was thus focused on identifying the P. vivax VCG-1 strain proteome during its blood lifecycle through LC-MS/MS; this led to identifying 734 proteins, thus increasing the overall number reported for P. vivax to date. Some of them have previously been related to reticulocyte invasion, parasite virulence and growth and others are new molecules possibly playing a functional role during metabolic processes, as predicted by Database for Annotation, Visualization and Integrated Discovery (DAVID) functional analysis. This is the first large-scale proteomic analysis of a P. vivax strain adapted to a non-human primate model showing the parasite protein repertoire during the blood lifecycle. Database searches facilitated the in silico prediction of proteins proposed for evaluation in further experimental assays regarding their potential as pharmacologic targets or as component of a totally efficient vaccine against malaria caused by P. vivax. BIOLOGICAL SIGNIFICANCE P. vivax malaria continues being a public health problem around world. Although considerable progress has been made in understanding genome- and transcriptome-related P. vivax biology, there are few proteome studies, currently representing only 8.5% of the predicted in silico proteome reported in public databases. A high-throughput proteomic assay was used for discovering new P. vivax intra-reticulocyte asexual stage molecules taken from parasites maintained in vivo in a primate model. The methodology avoided the main problem related to standardising an in vitro culture system to obtain enough samples for protein identification and annotation. This study provides a source of potential information contributing towards a basic understanding of P. vivax biology related to parasite proteins which are of significant importance for the malaria research community.
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Affiliation(s)
- D A Moreno-Pérez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, Colombia; Universidad del Rosario, Calle 63D No. 24-31, Bogotá, Colombia; IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.
| | - R Dégano
- Unidad de Proteómica, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.
| | - N Ibarrola
- Unidad de Proteómica, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.
| | - A Muro
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.
| | - M A Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, Colombia; Universidad del Rosario, Calle 63D No. 24-31, Bogotá, Colombia.
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Ponsuwanna P, Kümpornsin K, Chookajorn T. Genome-wide prediction of the polymorphic Ser gene family in Tetrahymena thermophila based on motif analysis. PLoS One 2014; 9:e105201. [PMID: 25133747 PMCID: PMC4136848 DOI: 10.1371/journal.pone.0105201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 07/21/2014] [Indexed: 11/18/2022] Open
Abstract
Even though antigenic variation is employed among parasitic protozoa for host immune evasion, Tetrahymena thermophila, a free-living ciliate, can also change its surface protein antigens. These cysteine-rich glycosylphosphatidylinositol (GPI)-linked surface proteins are encoded by a family of polymorphic Ser genes. Despite the availability of T. thermophila genome, a comprehensive analysis of the Ser family is limited by its high degree of polymorphism. In order to overcome this problem, a new approach was adopted by searching for Ser candidates with common motif sequences, namely length-specific repetitive cysteine pattern and GPI anchor site. The candidate genes were phylogenetically compared with the previously identified Ser genes and classified into subtypes. Ser candidates were often found to be located as tandem arrays of the same subtypes on several chromosomal scaffolds. Certain Ser candidates located in the same chromosomal arrays were transcriptionally expressed at specific T. thermophila developmental stages. These Ser candidates selected by the motif analysis approach can form the foundation for a systematic identification of the entire Ser gene family, which will contribute to the understanding of their function and the basis of T. thermophila antigenic variation.
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Affiliation(s)
- Patrath Ponsuwanna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Krittikorn Kümpornsin
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanat Chookajorn
- Center of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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Queiroz RML, Charneau S, Bastos IMD, Santana JM, Sousa MV, Roepstorff P, Ricart CAO. Cell surface proteome analysis of human-hosted Trypanosoma cruzi life stages. J Proteome Res 2014; 13:3530-41. [PMID: 24978697 DOI: 10.1021/pr401120y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chagas' disease is a neglected infectious illness, caused by the protozoan Trypanosoma cruzi. It remains a challenging health issue in Latin America, where it is endemic, and so far there is no immunoprophylatic vaccine or satisfactory chemotherapic treatment for its chronic stage. The present work addressed the analysis of the plasma membrane (PM) subproteome from T. cruzi human-hosted life stages, trypomastigote and axenic amastigote, by two complementary PM protein enrichment techniques followed by identification using an LC-MS/MS approach. The results revealed an extensive repertoire of proteins in the PM subproteomes, including enzymes that might be suitable candidates for drug intervention. The comparison of the cell surface proteome among the life forms revealed some potentially stage-specific enzymes, although the majority was shared by both stages. Bioinformatic analysis showed that the vast majority of the identified proteins are membrane-derived and/or possess predicted transmembrane domains. They are mainly involved in host cell infection, protein adhesion, cell signaling, and the modulation of mammalian host immune response. Several virulence factors and proteins potentially capable of acting at a number of metabolic pathways of the host and also to regulate cell differentiation of the parasite itself were also found.
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Affiliation(s)
- Rayner M L Queiroz
- Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília, Brazil
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Cheon SA, Jung J, Choo JH, Oh DB, Kang HA. Characterization of putative glycosylphosphatidylinositol-anchoring motifs for surface display in the methylotrophic yeast Hansenula polymorpha. Biotechnol Lett 2014; 36:2085-94. [DOI: 10.1007/s10529-014-1582-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/05/2014] [Indexed: 11/24/2022]
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