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Lai EY, Huang YT. Identifying pleiotropic genes via the composite test amidst the complexity of polygenic traits. Brief Bioinform 2024; 25:bbae327. [PMID: 39007593 PMCID: PMC11247409 DOI: 10.1093/bib/bbae327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/29/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Identifying the causal relationship between genotype and phenotype is essential to expanding our understanding of the gene regulatory network spanning the molecular level to perceptible traits. A pleiotropic gene can act as a central hub in the network, influencing multiple outcomes. Identifying such a gene involves testing under a composite null hypothesis where the gene is associated with, at most, one trait. Traditional methods such as meta-analyses of top-hit $P$-values and sequential testing of multiple traits have been proposed, but these methods fail to consider the background of genome-wide signals. Since Huang's composite test produces uniformly distributed $P$-values for genome-wide variants under the composite null, we propose a gene-level pleiotropy test that entails combining the aforementioned method with the aggregated Cauchy association test. A polygenic trait involves multiple genes with different functions to co-regulate mechanisms. We show that polygenicity should be considered when identifying pleiotropic genes; otherwise, the associations polygenic traits initiate will give rise to false positives. In this study, we constructed gene-trait functional modules using the results of the proposed pleiotropy tests. Our analysis suite was implemented as an R package PGCtest. We demonstrated the proposed method with an application study of the Taiwan Biobank database and identified functional modules comprising specific genes and their co-regulated traits.
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Affiliation(s)
- En-Yu Lai
- Institute of Statistical Science, Academia Sinica, No.128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, No.128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
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Zhang D, Xie J, Sun F, Xu R, Liu W, Xu J, Huang X, Zhang G. Pharmacological suppression of HHLA2 glycosylation restores anti-tumor immunity in colorectal cancer. Cancer Lett 2024; 589:216819. [PMID: 38522775 DOI: 10.1016/j.canlet.2024.216819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024]
Abstract
Immunotherapy aimed at inhibiting the negative co-stimulatory molecule programmed cell death-ligand 1 (PD-L1) has limited effectiveness, with clinical response rates remaining below 10%-15%. Therefore, new immune checkpoints need to be explored. Our study focused on human endogenous retrovirus H long terminal repeat-associating protein 2 (HHLA2), a highly glycosylated member of the B7 family that is widely expressed in colorectal cancer. HHLA2 expression negatively correlates with the prognosis of colorectal cancer. Glycosylation of HHLA2, which is regulated by the glycosyltransferase STT3 oligosaccharyltransferase complex catalytic subunit A (STT3A), is crucial for protein stability and expression in cell membranes. Additionally, the binding of HHLA2 to the receptors killer cell immunoglobulin-like receptor, three immunoglobulin domains and long cytoplasmic tail 3 (KIR3DL3) and transmembrane and immunoglobulin (Ig) domain containing 2 (TMIGD2) is dependent on N-glycosylation. Moreover, N-glycosylation of HHLA2 promotes immune evasion in colorectal cancer by suppressing the immune response of NK cells. Notably, the STT3A inhibitor NGI-1 enhances the anti-tumor immune response of NK cells. Our findings provide new insights and a molecular basis for targeting HHLA2 in immunotherapy for colorectal cancer.
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Affiliation(s)
- Dongze Zhang
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Jinjing Xie
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | | | - Ruyan Xu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Wenjun Liu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Jia Xu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Xue Huang
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China.
| | - Guangbo Zhang
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China; Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, 215000, China; Jiangsu Key Laboratory of Gastrointestinal Tumor Immunology, Suzhou, 215000, China.
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Boumali R, Urli L, Naim M, Soualmia F, Kinugawa K, Petropoulos I, El Amri C. Kallikrein-related peptidase's significance in Alzheimer's disease pathogenesis: A comprehensive survey. Biochimie 2024:S0300-9084(24)00076-2. [PMID: 38608749 DOI: 10.1016/j.biochi.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/19/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Alzheimer's disease (AD) and related dementias constitute an important global health challenge. Detailed understanding of the multiple molecular mechanisms underlying their pathogenesis constitutes a clue for the management of the disease. Kallikrein-related peptidases (KLKs), a lead family of serine proteases, have emerged as potential biomarkers and therapeutic targets in the context of AD and associated cognitive decline. Hence, KLKs were proposed to display multifaceted impacts influencing various aspects of neurodegeneration, including amyloid-beta aggregation, tau pathology, neuroinflammation, and synaptic dysfunction. We propose here a comprehensive survey to summarize recent findings, providing an overview of the main kallikreins implicated in AD pathophysiology namely KLK8, KLK6 and KLK7. We explore the interplay between KLKs and key AD molecular pathways, shedding light on their significance as potential biomarkers for early disease detection. We also discuss their pertinence as therapeutic targets for disease-modifying interventions to develop innovative therapeutic strategies aimed at halting or ameliorating the progression of AD and associated dementias.
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Affiliation(s)
- Rilès Boumali
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Laureline Urli
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Meriem Naim
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Feryel Soualmia
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Kiyoka Kinugawa
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France; AP-HP, Paris, France; Charles-Foix Hospital, Functional Exploration Unit for Older Patients, 94200 Ivry-sur-Seine, France
| | - Isabelle Petropoulos
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France.
| | - Chahrazade El Amri
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France.
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Drzewicka K, Zasłona Z. Metabolism-driven glycosylation represents therapeutic opportunities in interstitial lung diseases. Front Immunol 2024; 15:1328781. [PMID: 38550597 PMCID: PMC10973144 DOI: 10.3389/fimmu.2024.1328781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024] Open
Abstract
Metabolic changes are coupled with alteration in protein glycosylation. In this review, we will focus on macrophages that are pivotal in the pathogenesis of pulmonary fibrosis and sarcoidosis and thanks to their adaptable metabolism are an attractive therapeutic target. Examples presented in this review demonstrate that protein glycosylation regulates metabolism-driven immune responses in macrophages, with implications for fibrotic processes and granuloma formation. Targeting proteins that regulate glycosylation, such as fucosyltransferases, neuraminidase 1 and chitinase 1 could effectively block immunometabolic changes driving inflammation and fibrosis, providing novel avenues for therapeutic interventions.
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Hu G, Liu X, Wu D, Wang B, Wang J, Geng F. Quantitative N-glycoproteomic analysis of egg yolk powder during thermal processing. Food Res Int 2023; 174:113678. [PMID: 37981370 DOI: 10.1016/j.foodres.2023.113678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
The production of egg yolk powder often involves critical processes such as pasteurization and spray drying, however, these thermal processes will inevitably affect the functional properties of egg yolk (especially gelation and emulsification). The aim of this study was to elucidate the mechanism of the effect of pasteurized egg yolk (P-EY) and spray-dried egg yolk (SD-EY) on the functional properties through quantitative N-glycoproteomic. The results showed, compared with fresh egg yolk (F-EY), emulsifying property of mild heat-treated P-EY was slightly reduced while the gelation property did not undergo significant changes, whereas emulsifying activity (EAI) and gelation strength of vigorously heat-treated SD-EY were significantly reduced by 48.72 % and 35.73 %, respectively. During thermal processing in SD-EY, larger aggregate particles (particle size ∼10 um) were formed, and the surface hydrophobicity was reduced (93.0 %) and the zeta potential was enhanced (62.8 %). The results of quantitative N-glycoproteomic showed that 13 N-glycosylated proteins (APOB, vitellogenin, etc.) were down-regulated while only 2 N-glycosylated proteins were up-regulated; 21 N-glycosylation sites were down-regulated and 2 N-glycosylation sites were up-regulated in SD-EY, suggesting that covalent cross-linking of protein N-glycoproteins may have occurred in the process of spray-drying, which altered molecular physicochemical characteristics of the yolk solution that further affecting the processing properties of egg yolk.
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Affiliation(s)
- Gan Hu
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China; Institute for Advanced Study, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China
| | - Xialei Liu
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China
| | - Di Wu
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China
| | - Beibei Wang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China; Institute for Advanced Study, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China
| | - Jinqiu Wang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China
| | - Fang Geng
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu 610106, China.
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Lu J, Zhang W, Ma C, Pang X, Dai Y, Zhu T, Liu J, Xing L, Zhang S, Lv J. Changes in glycosylated proteins in colostrum and mature milk and their implication. Front Nutr 2023; 10:1161310. [PMID: 37396121 PMCID: PMC10311556 DOI: 10.3389/fnut.2023.1161310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction Glycosylation is one of the essential post-translational modifications that influences the function of milk proteins. Methods In the present study, 998 proteins and 764 glycosylated sites from 402 glycoproteins were identified in human milk by TMT labeling proteomics. Compared to human milk proteins, the glycoproteins were mainly enriched in cell adhesion, proteolysis, and defense/immune process. Results The abundance of 353 glycosylated sites and their 179 parent proteins was quantified. After normalization to their parent protein's abundance, 78 glycosylated sites in 56 glycoproteins and 10 glycosylated sites in 10 glycoproteins were significantly higher in colostrum and mature milk, respectively. These changed glycoproteins were mainly related to host defense. Intriguingly, one glycosylated site (Asp144) in IgA and two glycosylated sites (Asp38 and Asp1079) in tenascin are significantly upregulated even though their protein abundance was downregulated during lactation. Discussion This study helps us figure out the critical glycosylated sites in proteins that might influence their biological function in an unbiased way.
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Affiliation(s)
- Jing Lu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Wenyuan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, China
| | - Changlu Ma
- Department of Food and Bio-Engineering, Beijing Vocational College of Agriculture, Beijing, China
| | - Xiaoyang Pang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, China
| | - Ying Dai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Tong Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Jinqi Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Lina Xing
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Shuwen Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, China
| | - Jiaping Lv
- Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, China
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Toul M, Slonkova V, Mican J, Urminsky A, Tomkova M, Sedlak E, Bednar D, Damborsky J, Hernychova L, Prokop Z. Identification, characterization, and engineering of glycosylation in thrombolyticsa. Biotechnol Adv 2023; 66:108174. [PMID: 37182613 DOI: 10.1016/j.biotechadv.2023.108174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/16/2023]
Abstract
Cardiovascular diseases, such as myocardial infarction, ischemic stroke, and pulmonary embolism, are the most common causes of disability and death worldwide. Blood clot hydrolysis by thrombolytic enzymes and thrombectomy are key clinical interventions. The most widely used thrombolytic enzyme is alteplase, which has been used in clinical practice since 1986. Another clinically used thrombolytic protein is tenecteplase, which has modified epitopes and engineered glycosylation sites, suggesting that carbohydrate modification in thrombolytic enzymes is a viable strategy for their improvement. This comprehensive review summarizes current knowledge on computational and experimental identification of glycosylation sites and glycan identity, together with methods used for their reengineering. Practical examples from previous studies focus on modification of glycosylations in thrombolytics, e.g., alteplase, tenecteplase, reteplase, urokinase, saruplase, and desmoteplase. Collected clinical data on these glycoproteins demonstrate the great potential of this engineering strategy. Outstanding combinatorics originating from multiple glycosylation sites and the vast variety of covalently attached glycan species can be addressed by directed evolution or rational design. Directed evolution pipelines would benefit from more efficient cell-free expression and high-throughput screening assays, while rational design must employ structure prediction by machine learning and in silico characterization by supercomputing. Perspectives on challenges and opportunities for improvement of thrombolytic enzymes by engineering and evolution of protein glycosylation are provided.
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Affiliation(s)
- Martin Toul
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Veronika Slonkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jan Mican
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Adam Urminsky
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Maria Tomkova
- Center for Interdisciplinary Biosciences, P. J. Safarik University in Kosice, Jesenna 5, 04154 Kosice, Slovakia
| | - Erik Sedlak
- Center for Interdisciplinary Biosciences, P. J. Safarik University in Kosice, Jesenna 5, 04154 Kosice, Slovakia
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Lenka Hernychova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Genetic Biodiversity and Posttranslational Modifications of Protease Serine Endopeptidase in Different Strains of Sordaria fimicola. BIOMED RESEARCH INTERNATIONAL 2023; 2023:2088988. [PMID: 36814796 PMCID: PMC9940969 DOI: 10.1155/2023/2088988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Genetic variations (mutation, crossing over, and recombination) act as a source for the gradual alternation in phenotype along a geographic transect where the environment changes. Posttranslational modifications (PTMs) predicted modifications successfully in different and the same species of living organisms. Protein diversity of living organisms is predicted by PTMs. Environmental stresses change nucleotides to produce alternations in protein structures, and these alternations have been examined through bioinformatics tools. The goal of the current study is to search the diversity of genes and posttranslational modifications of protease serine endopeptidase in various strains of Sordaria fimicola. The S. fimicola's genomic DNA was utilized to magnify the protease serine endopeptidase (SP2) gene; the size of the product was 700 and 1400 base pairs. Neurospora crassa was taken as the reference strain for studying the multiple sequence alignment of the nucleotide sequence. Six polymorphic sites of six strains of S. fimicola with respect to N. crassa were under observation. Different bioinformatics tools, i.e., NetPhos 3.1, NetNES 1.1 Server, YinOYang1.2, and Mod Pred, to search phosphorylation sites, acetylation, nuclear export signals, O-glycosylation, and methylation, respectively, were used to predict PTMs. The findings of the current study were 35 phosphorylation sites on the residues of serine for protease SP2 in SFS and NFS strains of S. fimicola and N. crassa. The current study supported us to get the reality of genes involved in protease production in experimental fungi. Our study examined the genetic biodiversity in six strains of S. fimicola which were caused by stressful environments, and these variations are a strong reason for evolution. In this manuscript, we predicted posttranslational modifications of protease serine endopeptidase in S. fimicola obtained from different sites, for the first time, to see the effect of environmental stress on nucleotides, amino acids, and proteases and to study PTMs by using various bioinformatics tools. This research confirmed the genetic biodiversity and PTMs in six strains of S. fimicola, and the designed primers also provided strong evidence for the presence of protease serine endopeptidase in each strain of S. fimicola.
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N-Linked Glycosylation in Chinese Hamster Ovary Cells Is Critical for Insulin-like Growth Factor 1 Signaling. Int J Mol Sci 2022; 23:ijms232314952. [PMID: 36499281 PMCID: PMC9735751 DOI: 10.3390/ijms232314952] [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: 09/15/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 12/03/2022] Open
Abstract
Cell surface proteins carrying N-glycans play important roles in inter- and intracellular processes including cell adhesion, development, and cellular recognition. Dysregulation of the glycosylation machinery has been implicated in various diseases, and investigation of global differential cell surface proteome effects due to the loss of N-glycosylation will provide comprehensive insights into their pathogenesis. Cell surface proteins isolated from Parent Pro-5 CHO cells (W5 cells), two CHO mutants with loss of N-glycosylation function derived from Pro-5 CHO (Lec1 and Lec4 cells), were subjected to proteome analysis via high-resolution LCMS. We identified 44 and 43 differentially expressed membrane proteins in Lec1 and Lec4 cells, respectively, as compared to W5 cells. The defective N-glycosylation mutants showed increased abundance of integrin subunits in Lec1 and Lec4 cells at the cell surface. We also found significantly reduced levels of IGF-1R (Insulin like growth factor-1 receptor); a receptor tyrosine kinase; and the GTPase activating protein IQGAP1 (IQ motif-containing GTPase activating protein), a highly conserved cytoplasmic scaffold protein) in Lec1 and Lec4 cells. In silico docking studies showed that the IQ domain of IQGAP1 interacts with the kinase domain of IGF-1R. The integrin signaling and insulin growth factor receptor signaling were also enriched according to GSEA analysis and pathway analysis of differentially expressed proteins. Significant reductions of phosphorylation of ERK1 and ERK2 in Lec1 and Lec4 cells were observed upon IGF-1R ligand (IGF-1 LR3) stimulation. IGF-1 LR3, known as Long arginine3-IGF-1, is a synthetic protein and lengthened analog of insulin-like growth factor 1. The work suggests a novel mechanism for the activation of IGF-1 dependent ERK signaling in CHO cells, wherein IQGAP1 plausibly functions as an IGF-1R-associated scaffold protein. Appropriate glycosylation by the enzymes MGAT1 and MGAT5 is thus essential for processing of cell surface receptor IGF-1R, a potential binding partner in IQGAP1 and ERK signaling, the integral components of the IGF pathway.
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Biochemical characterization of the β-glucosidase Glu1B from Coptotermes formosanus produced in Pichia pastoris. Enzyme Microb Technol 2022; 163:110155. [DOI: 10.1016/j.enzmictec.2022.110155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 10/22/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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Variation of Proteolytic Cleavage Sites towards the N-Terminal End of the S2 Subunit of the Novel SARS-CoV-2 Omicron Sublineage BA.2.12.1. Molecules 2022; 27:molecules27185817. [PMID: 36144551 PMCID: PMC9506045 DOI: 10.3390/molecules27185817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The prevalence of novel SARS-CoV-2 variants is also accompanied by an increased turnover rate and additional cleavage sites at the positions necessary for priming the Spike (S) protein. Of these priming sites, the proteolytically sensitive polybasic sequence of the activation loop at the S1/S2 interface and the S2′ location within the S2 subunit of the S protein are cleaved by furin and TMPRSS2, which are important for the infection of the target cell. Neutrophils, migrating to the site of infection, secrete serine proteases to fight against pathogens. The serine proteases encompass neutrophil elastase (NE), proteinase 3 (PR3), and cathepsin G (CatG), which can hydrolyze the peptide bond adjacent to the S1/S2 interface. SARS-CoV-2 might take the opportunity to hijack proteases from an immune response to support viral entry to the cell. The region near S704L within the S2 subunit, a novel amino acid substitution of SARS-CoV-2 Omicron sublineage BA.2.12.1, is located close to the S1/S2 interface. We found that NE, PR3, and CatG digested the peptide within this region; however, the S704L amino acid substitution altered cleavage sites for PR3. In conclusion, such an amino acid substitution modifies S2 antigen processing and might further impact the major histocompatibility complex (MHC) binding and T cell activation.
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14
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Knauer JF, Liers C, Hahn S, Wuestenhagen DA, Zemella A, Kellner H, Haueis L, Hofrichter M, Kubick S. Cell-free production of the bifunctional glycoside hydrolase GH78 from Xylaria polymorpha. Enzyme Microb Technol 2022; 161:110110. [PMID: 35939898 DOI: 10.1016/j.enzmictec.2022.110110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/28/2022] [Accepted: 07/31/2022] [Indexed: 11/24/2022]
Abstract
The ability to catalyze diverse reactions with relevance for chemical and pharmaceutical research and industry has led to an increasing interest in fungal enzymes. There is still an enormous potential considering the sheer amount of new enzymes from the huge diversity of fungi. Most of these fungal enzymes have not been characterized yet due to the lack of high throughput synthesis and analysis methods. This bottleneck could be overcome by means of cell-free protein synthesis. In this study, cell-free protein synthesis based on eukaryotic cell lysates was utilized to produce a functional glycoside hydrolase (GH78) from the soft-rot fungus Xylaria polymorpha (Ascomycota). The enzyme was successfully synthesized under different reaction conditions. We characterized its enzymatic activities and immobilized the protein via FLAG-Tag interaction. Alteration of several conditions including reaction temperature, template design and lysate supplementation had an influence on the activity of cell-free synthesized GH78. Consequently this led to a production of purified GH78 with a specific activity of 15.4 U mg- 1. The results of this study may be foundational for future high throughput fungal enzyme screenings, including substrate spectra analysis and mutant screenings.
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Affiliation(s)
- Jan Felix Knauer
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Takustr. 6, 14195 Berlin, Germany
| | - Christiane Liers
- Technische Universität Dresden, Internationales Hochschulinstitut Zittau, Markt 23, 02763 Zittau
| | - Stephanie Hahn
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; Berliner Hochschule für Technik, Luxemburger Str. 10, 13353 Berlin, Germany
| | - Doreen A Wuestenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Harald Kellner
- Technische Universität Dresden, Internationales Hochschulinstitut Zittau, Markt 23, 02763 Zittau
| | - Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Martin Hofrichter
- Technische Universität Dresden, Internationales Hochschulinstitut Zittau, Markt 23, 02763 Zittau
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Takustr. 6, 14195 Berlin, Germany; Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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15
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Masakari Y, Hara C, Nakazawa H, Ichiyanagi A, Umetsu M. Comparison of the stability of Mucor-derived flavin adenine dinucleotide-dependent glucose dehydrogenase and glucose oxidase. J Biosci Bioeng 2022; 134:307-310. [PMID: 35927131 DOI: 10.1016/j.jbiosc.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 10/16/2022]
Abstract
Long-term stability at near-body temperature is important for continuous glucose monitoring (CGM) sensors. However, the stability of enzymes used in CGM sensors has often been evaluated by measuring their melting temperature (Tm) values and by short heat treatment but not at around 37 °C. Glucose oxidase (GOD) is used in current CGM sensors. In this study, we evaluated the stability of modified Mucor-derived flavin adenine dinucleotide-dependent glucose dehydrogenase (designated Mr144-297) with improved thermal stability at medium to high temperatures and compared it with that of GOD. The Tm value of Mr144-297 was 61.6 ± 0.3 °C and was similar to that of GOD (61.4 ± 1.2 °C). However, Mr144-297 was clearly more stable than GOD at 40 °C and 55 °C. At 37 °C, the stability of a carbon electrode with immobilized Mr144-297 was higher than that of an electrode with GOD. Our data indicate that Mr144-297 is a more suitable enzyme for CGM sensors than is GOD.
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Affiliation(s)
- Yosuke Masakari
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda City, Chiba 278-0037, Japan; Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Chiaki Hara
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda City, Chiba 278-0037, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Atsushi Ichiyanagi
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda City, Chiba 278-0037, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
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16
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Mamo J, Kangwa M, Suarez Orellana JF, Yelemane V, Fernandez-Lahore HM, Assefa F. Purification and Characterization of Aspartic Protease Produced from Aspergillus oryzae DRDFS13 MN726447 under Solid-State Fermentation. Catal Letters 2022. [DOI: 10.1007/s10562-021-03777-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Melo Diaz JM, Peel SR, Spencer DI, Hendel JL. Extraction and purification of a High Mannose type oligosaccharide from Phaseolus lunatus beans by oxidative release with sodium hypochlorite. Carbohydr Res 2022; 517:108583. [DOI: 10.1016/j.carres.2022.108583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/20/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022]
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18
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Enhancing the Thermostability of Phytase to Boiling Point by Evolution-Guided Design. Appl Environ Microbiol 2022; 88:e0050622. [PMID: 35546578 DOI: 10.1128/aem.00506-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The good thermostability of enzymes is an important basis for their wide application in industry. In this study, the phytase APPA from Yersinia intermedia was designed by evolution-guided design. Through the collection of homologous sequences in the NCBI database, we obtained a sequence set composed of 5,569 sequences, counted the number and locations of motif N-X-T/S, and selected the sites with high frequency in evolution as candidate sites for experiments. Based on the principle that N-glycosylation modification sites are located on the protein surface, 13 mutants were designed to optimize the number and location of N-glycosylation sites. Through experimental verification, 7 single mutants with improved thermostability were obtained. The best mutant, M14, with equal catalytic efficiency as the wild-type was obtained through combined mutation. The half-life (t1/2) value of mutant M14 was improved from 3.32 min at 65°C to 25 min of at 100°C, allowing it to withstand boiling water treatment, retaining approximately 75% initial activity after a 10-min incubation at 100°C. Differential scanning calorimetry analysis revealed that while the mutants' thermodynamic stability was nearly unchanged, their kinetic stability was greatly improved, and the combined mutant exhibited strong refolding ability. The results of a in vitro digestibility test indicated that the application effect of mutant M14 was about 4.5 times that of wild-type APPA, laying a foundation for its industrial application. IMPORTANCE Due to the harsh reaction conditions of industrial production, the relative instability of enzymes limits their application in industrial production, such as for food, pharmaceuticals, and feed. For example, the pelleting process of feed includes a brief high temperature (80 to 85°C), which requires the enzyme to have excellent thermostability. Therefore, a simple and effective method to improve the thermostability of enzymes has important practical value. In this study, we make full use of the existing homologous sequences (5,569) in the database to statistically analyze the existence frequency of N-X-T/S motifs in this large sequence space to design the phytase APPA with improved thermostability and a high hit rate (~50%). We obtained the best combination mutant, M14, that can tolerate boiling water treatment and greatly improved its kinetic stability without damaging its specific activity. Simultaneously, we proved that its performance improvement is due to its enhanced refolding ability, which comes from N-glycan modification rather than amino acid replacement. Our results provide a feasible and effective method for the modification of enzyme thermostability.
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19
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Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. PLoS One 2022; 17:e0264723. [PMID: 35436320 PMCID: PMC9015119 DOI: 10.1371/journal.pone.0264723] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/15/2022] [Indexed: 12/27/2022] Open
Abstract
The serine proteases neutrophil elastase (NE), proteinase 3 (PR3), cathepsin G (CatG), and neutrophil serine protease 4 (NSP4) are secreted by activated neutrophils as a part of the innate immune response against invading pathogens. However, these serine proteases might be adopted by viruses to mediate viral surface protein priming resulting in host cell entrance and productive infection. Indeed, NE and PR3 hydrolyze the scissile peptide bond within the proteolytically sensitive polybasic sequence of the activation loop of SARS-CoV-2 located at the S1/S2 interface of the Spike (S) protein; an amino acid motif which differs from SARS-CoV-1. The occurrence of novel SARS-CoV-2 variants and substitution of distinct amino acids at the polybasic sequence prompts serious concerns regarding increased transmissibility. We propose that a novel cleavage site by CatG of the Omicron variant and the increased substrate turnover of the Delta variant by furin within the polybasic sequence should be considered for increased transmission of SARS-CoV-2 variants.
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20
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Singh Y, Regmi D, Ormaza D, Ayyalasomayajula R, Vela N, Mundim G, Du D, Minond D, Cudic M. Mucin-Type O-Glycosylation Proximal to β-Secretase Cleavage Site Affects APP Processing and Aggregation Fate. Front Chem 2022; 10:859822. [PMID: 35464218 PMCID: PMC9023740 DOI: 10.3389/fchem.2022.859822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
The amyloid-β precursor protein (APP) undergoes proteolysis by β- and γ-secretases to form amyloid-β peptides (Aβ), which is a hallmark of Alzheimer’s disease (AD). Recent findings suggest a possible role of O-glycosylation on APP’s proteolytic processing and subsequent fate for AD-related pathology. We have previously reported that Tyr681-O-glycosylation and the Swedish mutation accelerate cleavage of APP model glycopeptides by β-secretase (amyloidogenic pathway) more than α-secretase (non-amyloidogenic pathway). Therefore, to further our studies, we have synthesized additional native and Swedish-mutated (glyco)peptides with O-GalNAc moiety on Thr663 and/or Ser667 to explore the role of glycosylation on conformation, secretase activity, and aggregation kinetics of Aβ40. Our results show that conformation is strongly dependent on external conditions such as buffer ions and solvent polarity as well as internal modifications of (glyco)peptides such as length, O-glycosylation, and Swedish mutation. Furthermore, the level of β-secretase activity significantly increases for the glycopeptides containing the Swedish mutation compared to their nonglycosylated and native counterparts. Lastly, the glycopeptides impact the kinetics of Aβ40 aggregation by significantly increasing the lag phase and delaying aggregation onset, however, this effect is less pronounced for its Swedish-mutated counterparts. In conclusion, our results confirm that the Swedish mutation and/or O-glycosylation can render APP model glycopeptides more susceptible to cleavage by β-secretase. In addition, this study sheds new light on the possible role of glycosylation and/or glycan density on the rate of Aβ40 aggregation.
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Affiliation(s)
- YashoNandini Singh
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Deepika Regmi
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
| | - David Ormaza
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Ramya Ayyalasomayajula
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Nancy Vela
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Gustavo Mundim
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Deguo Du
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Dmitriy Minond
- College of Pharmacy and Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Maré Cudic
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, United States
- *Correspondence: Maré Cudic,
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21
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Srinivasan S, Kryza T, Batra J, Clements J. Remodelling of the tumour microenvironment by the kallikrein-related peptidases. Nat Rev Cancer 2022; 22:223-238. [PMID: 35102281 DOI: 10.1038/s41568-021-00436-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
Abstract
Kallikrein-related peptidases (KLKs) are critical regulators of the tumour microenvironment. KLKs are proteolytic enzymes regulating multiple functions of bioactive molecules including hormones and growth factors, membrane receptors and the extracellular matrix architecture involved in cancer progression and metastasis. Perturbations of the proteolytic cascade generated by these peptidases, and their downstream signalling actions, underlie tumour emergence or blockade of tumour growth. Recent studies have also revealed their role in tumour immune suppression and resistance to cancer therapy. Here, we present an overview of the complex biology of the KLK family and its context-dependent nature in cancer, and discuss the different therapeutic strategies available to potentially target these proteases.
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Affiliation(s)
- Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
- Mater Research Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
- Centre for Genomics and Personalised Medicine, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.
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22
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Amobonye A, Singh S, Mukherjee K, Jobichen C, Qureshi IA, Pillai S. Structural and functional insights into fungal glutaminase using a computational approach. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Gaither C, Popp R, Zahedi RP, Borchers CH. Multiple reaction monitoring-mass spectrometry enables robust quantitation of plasma proteins regardless of whole blood processing delays that may occur in the clinic. Mol Cell Proteomics 2022; 21:100212. [PMID: 35182769 PMCID: PMC9062485 DOI: 10.1016/j.mcpro.2022.100212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/24/2022] [Accepted: 02/13/2022] [Indexed: 12/23/2022] Open
Abstract
Plasma is an important biofluid for clinical research and diagnostics. In the clinic, unpredictable delays—from minutes to hours—between blood collection and plasma generation are often unavoidable. These delays can potentially lead to protein degradation and modification and might considerably affect intact protein measurement methods such as sandwich enzyme-linked immunosorbent assays that bind proteins on two epitopes to increase specificity, thus requiring largely intact protein structures. Here, we investigated, using multiple reaction monitoring mass spectrometry (MRM-MS), how delays in plasma processing affect peptide-centric “bottom-up” proteomics. We used validated assays for proteotypic peptide surrogates of 270 human proteins to analyze plasma generated after whole blood had been kept at room temperature from 0 to 40 h to mimic delays that occur in the clinic. Moreover, we evaluated the impact of different plasma-thawing conditions on MRM-based plasma protein quantitation. We demonstrate that >90% of protein concentration measurements were unaffected by the thawing procedure and by up to 40-h delayed plasma generation, reflected by relative standard deviations (RSDs) of <30%. Of the 159 MRM assays that yielded quantitative results in 60% of the measured time points, 139 enabled a stable protein quantitation (RSD <20%), 14 showed a slight variation (RSD 20–30%), and 6 appeared unstable/irreproducible (RSD > 30%). These results demonstrate the high robustness and thus the potential for MRM-based plasma-protein quantitation to be used in a clinical setting. In contrast to enzyme-linked immunosorbent assay, peptide-based MRM assays do not require intact three-dimensional protein structures for an accurate and precise quantitation of protein concentrations in the original sample. Delays in whole blood processing often cannot be avoided in the clinic. These delays might affect measurements by intact protein assays such as ELISA. The impact on LC/MRM was evaluated using validated assays to quantify 270 proteins. >95% of the measured concentrations had RSDs <30% between delays of 0 to 40 h. Protein quantitation by LC/MRM-MS is robust against pitfalls in the clinical setting.
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Affiliation(s)
| | - Robert Popp
- MRM Proteomics Inc, Montreal, Quebec, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.
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24
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Lim SY, Ng BH, Vermulapalli D, Lau H, Carrasco Laserna AK, Yang X, Tan SH, Chan MY, Li SFY. Simultaneous Polar Metabolite and N-Glycan Extraction Workflow for Joint-Omics Analysis: A Synergistic Approach for Novel Insights into Diseases. J Proteome Res 2022; 21:643-653. [DOI: 10.1021/acs.jproteome.1c00676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Si Ying Lim
- NUS Graduate School for Integrative Sciences & Engineering (NGS), National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Bao Hui Ng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Dhruti Vermulapalli
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Hazel Lau
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Fusionopolis Way, Innovis, #08-03, Singapore 138634
| | - Anna Karen Carrasco Laserna
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
- Central Instrumentation Facility (Laguna Campus), Office of the Vice Chancellor for Research and Innovation, De La Salle University, 2041 Taft Avenue, Manila 1004, Philippines
| | - Xiaoxun Yang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Sock Hwee Tan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Mark Y. Chan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Sam Fong Yau Li
- NUS Graduate School for Integrative Sciences & Engineering (NGS), National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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25
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Forgrave LM, Wang M, Yang D, DeMarco ML. Proteoforms and their expanding role in laboratory medicine. Pract Lab Med 2022; 28:e00260. [PMID: 34950758 PMCID: PMC8672040 DOI: 10.1016/j.plabm.2021.e00260] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/31/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022] Open
Abstract
The term “proteoforms” describes the range of different structures of a protein product of a single gene, including variations in amino acid sequence and post-translational modifications. This diversity in protein structure contributes to the biological complexity observed in living organisms. As the concentration of a particular proteoform may increase or decrease in abnormal physiological states, proteoforms have long been used in medicine as biomarkers of health and disease. Notably, the analytical approaches used to analyze proteoforms have evolved considerably over the years. While ligand binding methods continue to play a large role in proteoform measurement in the clinical laboratory, unanticipated or unknown post-translational modifications and sequence variants can upend even extensively tested and vetted assays that have successfully made it through the medical regulatory process. As an alternate approach, mass spectrometry—with its high molecular selectivity—has become an essential tool in detection, characterization, and quantification of proteoforms in biological fluids and tissues. This review explores the analytical techniques used for proteoform detection and quantification, with an emphasis on mass spectrometry and its various applications in clinical research and patient care including, revealing new biomarker targets, helping improve the design of contemporary ligand binding in vitro diagnostics, and as mass spectrometric laboratory developed tests used in routine patient care.
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Affiliation(s)
- Lauren M. Forgrave
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Meng Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - David Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, Providence Health Care, 1081 Burrard St, Vancouver, V6Z 1Y6, Canada
- Corresponding author. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
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26
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Tisi A, Zerti D, Genitti G, Vicentini MT, Baccante M, Flati V, Maccarone R. Characterization of SARS-CoV-2 Entry Factors' Expression in Corneal and Limbal Tissues of Adult Human Donors Aged from 58 to 85. J Ocul Pharmacol Ther 2021; 38:56-65. [PMID: 34889660 DOI: 10.1089/jop.2021.0085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: Recent studies have shown the presence of SARS-CoV-2 entry factors on the ocular surface, identifying the eye as an additional entry route for the virus. Moreover, the coexpression of angiotensin-converting enzyme 2 (ACE2) with other SARS-CoV-2 entry factors [transmembrane protease serine 2 (TMPRSS2), transmembrane protease serine 4 (TMPRSS4), and dipeptidyl peptidase-4 (DPP4)] facilitates the virus infection. Methods: Here, we performed a study over 10 adult corneal and limbal tissues from human donors, both male and female between 58 and 85 years of age. Some of the main virus entry factors were analyzed and their expression was quantified and correlated with the age and sex of the donors through western blot. The receptors' localization was investigated through immunofluorescence. Results: Immunofluorescence confirmed the localization of ACE2 and TMPRSS2 on the ocular surface and showed, for the first time, the localization of TMPRSS4 and DPP4 in limbal and corneal epithelial superficial cells. The quantitative analysis showed that the expression of SARS-CoV-2 entry factors on corneal and limbal cells is likely to be modulated in an age-dependent manner, in agreement with the increased susceptibility to COVID-19 in the elderly. Moreover, we found a relationship between the expression of TMPRSS proteases with the activation state of limbal cells in 80-year-old donors. Conclusion: This study provides information on the expression of SARS-CoV-2 entry factors on the ocular surface of 10 adult human donors and is a first observation of a possible age-dependent modulation on corneal and limbal tissues. Our data pave the way to further investigate the susceptibility to the infection through the ocular surface in the elderly.
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Affiliation(s)
- Annamaria Tisi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Darin Zerti
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Germano Genitti
- UOSD Eye Bank of L'Aquila - C.R.R. for corneas donation and transplantation for Abruzzo and Molise regions, S. Salvatore Hospital, L'Aquila, Italy
| | - Maria Teresa Vicentini
- UOSD Eye Bank of L'Aquila - C.R.R. for corneas donation and transplantation for Abruzzo and Molise regions, S. Salvatore Hospital, L'Aquila, Italy
| | - Mariangela Baccante
- UOSD Eye Bank of L'Aquila - C.R.R. for corneas donation and transplantation for Abruzzo and Molise regions, S. Salvatore Hospital, L'Aquila, Italy
| | - Vincenzo Flati
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Rita Maccarone
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
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Polypeptide-GalNAc-Transferase-13 Shows Prognostic Impact in Breast Cancer. Cancers (Basel) 2021; 13:cancers13225616. [PMID: 34830771 PMCID: PMC8616257 DOI: 10.3390/cancers13225616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Breast cancer is a public health concern and is currently the fifth cause of mortality worldwide. Identification of different biological subtypes is essential for clinical management; therefore, the role of pathologists is essential and useful tools for immunohistochemistry diagnosis are needed. Polypeptide-GalNAc-transferases are emerging novel biomarkers related to cancer behavior and GalNAc-T13, correlated with aggressiveness in some tumors, is an interesting candidate. Few monoclonal antibodies reacting with native proteins, and not affected by fixation and paraffin embedding, have been reported. The aim of this work was to develop a useful monoclonal antibody anti-GalNAc-T13 and to assess its potential significance in breast cancer diagnosis. We evaluated 6 human breast cancer cell lines, 338 primary breast tumors and 48 metastatic lymph nodes and looked for clinical significance correlating GalNAc-T13 expression with patients' clinical features and survival. We found high GalNAc-T13 expression in 43.8% of the cases and observed a significant higher expression in metastatic lymph nodes, correlating with worse overall survival. We hypothesized several possible molecular mechanisms and their implications. We conclude that GalNAc-T13 may be a novel biomarker in breast cancer, useful for routine pathological diagnosis. Elucidation of molecular mechanisms related to aggressiveness should contribute to understand the role of GalNAc-T13 in breast cancer biology.
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28
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Li HW, Liu MB, Jiang X, Song T, Feng SX, Wu JY, Deng PF, Wang XY. GALNT14 regulates ferroptosis and apoptosis of ovarian cancer through the EGFR/mTOR pathway. Future Oncol 2021; 18:149-161. [PMID: 34643088 DOI: 10.2217/fon-2021-0883] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Chemoresistance usually occurs in ovarian cancer. We aimed to explore the mechanisms of chemoresistance. Methods: Western blotting assay was used to detect the expression of GALNT14. Further cell function experiments were performed to investigate the effect of GALNT14 in ovarian cancer. Results: GALNT14 is significantly upregulated in ovarian cancer. Downregulation of GALNT14 significantly inhibits both apoptosis and ferroptosis of ovarian cancer cells. A further mechanism assay illustrated that downregulation of GALNT14 suppresses the activity of the mTOR pathway through modifying O-glycosylation of EGFR. Finally, an additive effect promoting cell death occurs with a combination of an mTOR inhibitor and cisplatin. Conclusion: Our study might provide a promising method to overcome cisplatin resistance for patients with ovarian cancer.
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Affiliation(s)
- Hua-Wen Li
- Department of Gynecology, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, The First Affiliated Hospital of Faculty of Medicine Macau University of Science & Technology, Zhuhai, Guangdong 519000, China.,Department of Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510080, China
| | - Mu-Biao Liu
- Department of Gynecology, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, The First Affiliated Hospital of Faculty of Medicine Macau University of Science & Technology, Zhuhai, Guangdong 519000, China
| | - Xue Jiang
- Department of Gynecology, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, The First Affiliated Hospital of Faculty of Medicine Macau University of Science & Technology, Zhuhai, Guangdong 519000, China
| | - Ting Song
- Department of Gynecology, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, The First Affiliated Hospital of Faculty of Medicine Macau University of Science & Technology, Zhuhai, Guangdong 519000, China
| | - Shu-Xian Feng
- Department of Gynecology, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, The First Affiliated Hospital of Faculty of Medicine Macau University of Science & Technology, Zhuhai, Guangdong 519000, China
| | - Jing-Ya Wu
- Department of Gynecology, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, The First Affiliated Hospital of Faculty of Medicine Macau University of Science & Technology, Zhuhai, Guangdong 519000, China
| | - Peng-Fei Deng
- Department of Gynecology, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, The First Affiliated Hospital of Faculty of Medicine Macau University of Science & Technology, Zhuhai, Guangdong 519000, China
| | - Xiao-Yu Wang
- Department of Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510080, China
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29
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Regulation of meprin metalloproteases in mucosal homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119158. [PMID: 34626680 DOI: 10.1016/j.bbamcr.2021.119158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
Mucus is covering the entire epithelium of the gastrointestinal tract (GIT), building the interface for the symbiosis between microorganisms and their host. Hence, a disrupted mucosal barrier or alterations of proper mucus composition, including the gut microbiota, can cause severe infection and inflammation. Meprin metalloproteases are well-known to cleave various pro-inflammatory molecules, contributing to the onset and progression of pathological conditions including sepsis, pulmonary hypertension or inflammatory bowel disease (IBD). Moreover, meprins have an impact on migration and infiltration of immune cells like monocytes or leukocytes during intestinal inflammation by cleaving tight junction proteins or cell adhesion molecules, thereby disrupting epithelial cell barrier and promoting transendothelial cell migration. Interestingly, both meprin α and meprin β are susceptibility genes for IBD. However, both genes are significantly downregulated in inflamed intestinal tissue in contrast to healthy donors. Therefore, a detailed understanding of the underlying molecular mechanisms is the basis for developing new and effective therapies against manifold pathologies like IBD. This review focuses on the regulation of meprin metalloproteases and its impact on physiological and pathological conditions related to mucosal homeostasis.
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30
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Martin CE, Murray AS, Sala-Hamrick KE, Mackinder JR, Harrison EC, Lundgren JG, Varela FA, List K. Posttranslational modifications of serine protease TMPRSS13 regulate zymogen activation, proteolytic activity, and cell surface localization. J Biol Chem 2021; 297:101227. [PMID: 34562451 PMCID: PMC8503615 DOI: 10.1016/j.jbc.2021.101227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 12/01/2022] Open
Abstract
TMPRSS13, a member of the type II transmembrane serine protease (TTSP) family, harbors four N-linked glycosylation sites in its extracellular domain. Two of the glycosylated residues are located in the scavenger receptor cysteine-rich (SRCR) protein domain, while the remaining two sites are in the catalytic serine protease (SP) domain. In this study, we examined the role of N-linked glycosylation in the proteolytic activity, autoactivation, and cellular localization of TMPRSS13. Individual and combinatory site-directed mutagenesis of the glycosylated asparagine residues indicated that glycosylation of the SP domain is critical for TMPRSS13 autoactivation and catalytic activity toward one of its protein substrates, the prostasin zymogen. Additionally, SP domain glycosylation-deficient TMPRSS13 displayed impaired trafficking of TMPRSS13 to the cell surface, which correlated with increased retention in the endoplasmic reticulum. Importantly, we showed that N-linked glycosylation was a critical determinant for subsequent phosphorylation of endogenous TMPRSS13. Taken together, we conclude that glycosylation plays an important role in regulating TMPRSS13 activation and activity, phosphorylation, and cell surface localization.
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Affiliation(s)
- Carly E Martin
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Andrew S Murray
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA; Division of Hematological Malignancies and Cellular Therapy, Duke University, Durham, North Carolina, USA
| | | | - Jacob R Mackinder
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA
| | - Evan C Harrison
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA
| | - Joseph G Lundgren
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Fausto A Varela
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Karin List
- Department of Pharmacology, Wayne State University, Detroit, Michigan, USA; Department of Oncology, Wayne State University, Detroit, Michigan, USA.
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31
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Singh Y, Ormaza D, Massetti A, Minond D, Cudic M. Tyrosine O-GalNAc Alters the Conformation and Proteolytic Susceptibility of APP Model Glycopeptides. ACS Chem Neurosci 2021; 12:2974-2980. [PMID: 34324289 PMCID: PMC8378340 DOI: 10.1021/acschemneuro.1c00387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
The amyloid-β precursor protein (APP) undergoes proteolytic cleavage by α-,
β-, and γ-secretases, to determine its fate in Alzheimer’s disease
(AD) pathogenesis. Recent findings suggest a possible role of
O-glycosylation in APP’s proteolytic processing. Therefore, we
synthesized native and Swedish-double-mutated APP (glyco)peptides with
Tyr681-O-GalNAc. We studied conformational changes and
proteolytic processing using circular dichroism (CD) spectroscopy and enzyme cleavage
assay, respectively. CD analysis was carried out in four solvent systems to evaluate
peptide environment and O-glycosylation induced conformational changes.
The Swedish mutation and Tyr681-O-GalNAc were the key
factors driving conformational changes. Furthermore, the level of α- and
β-secretase activity was increased by the presence of mutation and this effect was
more pronounced for its glycosylated analogues. Our results suggest that
O-glycosylation of Tyr681 can induce a conformational
change in APP and affect its proteolytic processing fate toward the amyloidogenic
pathway.
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Affiliation(s)
- YashoNandini Singh
- Department of Chemistry and Biochemistry, Charles E, Schmidt College of Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | - David Ormaza
- Department of Chemistry and Biochemistry, Charles E, Schmidt College of Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | - Alessandra Massetti
- Department of Chemistry and Biochemistry, Charles E, Schmidt College of Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | - Dmitriy Minond
- College of Pharmacy and Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3301 College Ave, Fort Lauderdale, Florida 33314, United States
| | - Maré Cudic
- Department of Chemistry and Biochemistry, Charles E, Schmidt College of Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
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32
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Amorim ST, Stafuzza NB, Kluska S, Peripolli E, Pereira ASC, Muller da Silveira LF, de Albuquerque LG, Baldi F. Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle. Anim Genet 2021; 53:35-48. [PMID: 34407235 DOI: 10.1111/age.13124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 11/27/2022]
Abstract
Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P < 10 - 8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.
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Affiliation(s)
- S T Amorim
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - N B Stafuzza
- Instituto de Zootecnia - Centro de Pesquisa em Bovinos de Corte, Rodovia Carlos Tonanni, Km94, Sertãozinho, 14174-000, Brazil
| | - S Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - E Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - A S C Pereira
- Faculdade de Zootecnia e Engenharia de Alimentos, Núcleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, CEP 13635-900, Brazil
| | - L F Muller da Silveira
- Faculdade de Zootecnia e Engenharia de Alimentos, Núcleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, CEP 13635-900, Brazil
| | - L G de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
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Rivera-Pérez C, Hernández-Saavedra NY. Review: Post-translational modifications of marine shell matrix proteins. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110641. [PMID: 34182126 DOI: 10.1016/j.cbpb.2021.110641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/13/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022]
Abstract
Shell matrix proteins (SMPs) are key components for the Mollusk shell biomineralization. SMPs function has been hypothesized in several proteins by bioinformatics analysis, and through in vitro crystallization assays. However, studies of the post-translational modifications (PTMs) of SMPs, which contribute to their structure and the function, are limited. This review provides the current status of the SMPs with the most common PTMs described (glycosylation, phosphorylation, and disulfide bond formation) and their role in shell biomineralization. Also, recent studies based on recombinant production of SMPs are discussed. Finally, recommendations for the study of SMPs and their PTMs are provided. The review showed that PTMs are widely distributed in SMPs, and their presence on SMPs may contribute to the modulation of their activity in some SMPs, contributing to the crystal growth formation and differentiation through different mechanisms, however, in a few cases the lack of the PTMs do not alter their inherent function.
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Affiliation(s)
- Crisalejandra Rivera-Pérez
- CONACYT, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico.
| | - Norma Y Hernández-Saavedra
- Molecular Genetics Laboratory, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23096, Baja California Sur, Mexico
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34
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Rosini E, Volpi NA, Ziffels B, Grimaldi A, Sacchi S, Neri D, Pollegioni L. An antibody-based enzymatic therapy for cancer treatment: The selective localization of D-amino acid oxidase to EDA fibronectin. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 36:102424. [PMID: 34174417 DOI: 10.1016/j.nano.2021.102424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
In order to generate an antibody directed enzyme prodrug therapy, here we designed a chimeric protein by fusing the F8 antibody that recognizes the EDA of fibronectin (expressed on the tumor neovasculature) and an evolved variant of the ROS-generating enzyme D-amino acid oxidase (DAAO). The F8(scFv)-DAAO-Q144R recombinant protein is expressed by both CHO-S and E. coli cells. The F8(scFv)-DAAO-Q144R from E. coli cells is fully soluble, shows a high specific activity, is more thermostable in blood than the native DAAO, possesses a binding affinity for EDA well suited for efficient tumor accumulation, and localizes in tumor tissues. Notably, the F8(scFv)-DAAO-Q144R conjugate generates a stronger cytotoxicity to tumor cells than the native enzyme, especially when an inhibitor of heme oxygenase-1 (HO-1) is used, making it a promising candidate for a selective antitumor oxidative therapy controlled by the substrate addition, in the so called "activity on demand", thus sparing normal tissue from damage.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.
| | - Noemi Antonella Volpi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Barbara Ziffels
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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35
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Ward S, O'Sullivan JM, O'Donnell JS. The Biological Significance of von Willebrand Factor O-Linked Glycosylation. Semin Thromb Hemost 2021; 47:855-861. [PMID: 34130346 DOI: 10.1055/s-0041-1726373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Glycosylation is a key posttranslational modification, known to occur on more than half of all secreted proteins in man. As such, the role of N- and O-linked glycan structures in modulating various aspects of protein biology is an area of much research. Given their prevalence, it is perhaps unsurprising that variations in glycan structures have been demonstrated to play critical roles in modulating protein function and have been implicated in the pathophysiology of human diseases. von Willebrand factor (VWF), a plasma glycoprotein that is essential for normal hemostasis, is heavily glycosylated, containing 13 N-linked and 10 O-linked glycans. Together, these carbohydrate chains account for 20% of VWF monomeric mass, and have been shown to modulate VWF structure, function, and half-life. In this review, we focus on the specific role played by O-linked glycans in modulating VWF biology. Specifically, VWF O-linked glycans have been shown to modulate tertiary protein structure, susceptibility to ADAMTS13 proteolysis, platelet tethering, and VWF circulatory half-life.
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Affiliation(s)
- Soracha Ward
- Haemostasis Research Group, Irish Centre for Vascular Biology, School of Pharmacy and Bimolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jamie M O'Sullivan
- Haemostasis Research Group, Irish Centre for Vascular Biology, School of Pharmacy and Bimolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James S O'Donnell
- Haemostasis Research Group, Irish Centre for Vascular Biology, School of Pharmacy and Bimolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland.,National Coagulation Centre, St James's Hospital, Dublin, Ireland
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36
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Király M, Kiss BD, Horváth P, Drahos L, Mirzahosseini A, Pálfy G, Antal I, Ludányi K. Investigating thermal stability based on the structural changes of lactase enzyme by several orthogonal methods. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00637. [PMID: 34136367 PMCID: PMC8182373 DOI: 10.1016/j.btre.2021.e00637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 11/21/2022]
Abstract
Thermal stability of lactase (β-galactosidase) enzyme has been studied by a variety of physico-chemical methods. β-galactosidase is the main active ingredient of medications for lactose intolerance. It is typically produced industrially by the Aspergillus oryzae filamentous fungus. Lactase was used as a model to help understand thermal stability of enzyme-type biopharmaceuticals. Enzyme activity (hydrolyzation of lactose) of β-galactosidase was determined after storing the solid enzyme substance at various temperatures. For a better understanding of the relationship between structure and activity changes we determined the mass and size of the molecules with gel electrophoresis and dynamic light scattering and detected aggregation processes. A bottom-up proteomic procedure was used to determine the primary amino acid sequence and to investigate changes in the N-glycosylation pattern of the protein. NMR and CD spectroscopic methods were used to observe changes in higher order structures and to reveal relationships between structural and functional changes.
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Affiliation(s)
- Márton Király
- Department of Pharmaceutics, Faculty of Pharmacy, Semmelweis University, Hőgyes Endre u. 7., 1092, Budapest, Hungary
| | - Borbála Dalmadi Kiss
- Department of Pharmaceutics, Faculty of Pharmacy, Semmelweis University, Hőgyes Endre u. 7., 1092, Budapest, Hungary
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Semmelweis University, Hőgyes Endre u. 7., 1092, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., H-1117, Budapest, Hungary
| | - Arash Mirzahosseini
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Semmelweis University, Hőgyes Endre u. 7., 1092, Budapest, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. sétány 1/A, 1117, Budapest, Hungary
- Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, 1538, Budapest, P.O.B. 32, Hungary
| | - István Antal
- Department of Pharmaceutics, Faculty of Pharmacy, Semmelweis University, Hőgyes Endre u. 7., 1092, Budapest, Hungary
| | - Krisztina Ludányi
- Department of Pharmaceutics, Faculty of Pharmacy, Semmelweis University, Hőgyes Endre u. 7., 1092, Budapest, Hungary
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37
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Mikolajczyk K, Bereznicka A, Szymczak-Kulus K, Haczkiewicz-Lesniak K, Szulc B, Olczak M, Rossowska J, Majorczyk E, Kapczynska K, Bovin N, Lisowska M, Kaczmarek R, Miazek A, Czerwinski M. Missing the sweet spot: one of the two N-glycans on human Gb3/CD77 synthase is expendable. Glycobiology 2021; 31:1145-1162. [PMID: 33978735 DOI: 10.1093/glycob/cwab041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/23/2021] [Accepted: 04/29/2021] [Indexed: 02/07/2023] Open
Abstract
N-glycosylation is a ubiquitous posttranslational modification that may influence folding, subcellular localization, secretion, solubility and oligomerization of proteins. In this study, we examined the effects of N-glycans on the activity of human Gb3/CD77 synthase, which catalyzes the synthesis of glycosphingolipids with terminal Galα1 → 4Gal (Gb3 and the P1 antigen) and Galα1 → 4GalNAc disaccharides (the NOR antigen). The human Gb3/CD77 synthase contains two occupied N-glycosylation sites at positions N121 and N203. Intriguingly, we found that while the N-glycan at N203 is essential for activity and correct subcellular localization, the N-glycan at N121 is dispensable and its absence did not reduce, but, surprisingly, even increased the activity of the enzyme. The fully N-glycosylated human Gb3/CD77 synthase and its glycoform missing the N121 glycan correctly localized in the Golgi, whereas a glycoform without the N203 site partially mislocalized in the endoplasmic reticulum. A double mutein missing both N-glycans was inactive and accumulated in the endoplasmic reticulum. Our results suggest that the decreased specific activity of human Gb3/CD77 synthase glycovariants results from their improper subcellular localization and, to a smaller degree, a decrease in enzyme solubility. Taken together, our findings show that the two N-glycans of human Gb3/CD77 synthase have opposing effects on its properties, revealing a dual nature of N-glycosylation and potentially a novel regulatory mechanism controlling the biological activity of proteins.
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Affiliation(s)
- Krzysztof Mikolajczyk
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Anna Bereznicka
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Katarzyna Szymczak-Kulus
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Katarzyna Haczkiewicz-Lesniak
- Department of Ultrastructural Research, Faculty of Medicine, Wroclaw Medical University, Chalubinskiego St. 6a, 50-368, Wroclaw, Poland
| | - Bozena Szulc
- Faculty of Biotechnology, University of Wroclaw, Joliot-Curie St. 14A, 50-383 Wroclaw, Poland
| | - Mariusz Olczak
- Faculty of Biotechnology, University of Wroclaw, Joliot-Curie St. 14A, 50-383 Wroclaw, Poland
| | - Joanna Rossowska
- Flow Cytometry Core Facility, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Edyta Majorczyk
- Faculty of Physiotherapy and Physical Education, Opole University of Technology, Proszkowska St. 76, 45-758 Opole, Poland
| | - Katarzyna Kapczynska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya St 16/10, Moscow 117997 Russia
| | - Marta Lisowska
- Department of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Radoslaw Kaczmarek
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Arkadiusz Miazek
- Department of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
| | - Marcin Czerwinski
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla St. 12, 53-114 Wroclaw, Poland
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Study on the activity of recombinant mutant tissue-type plasminogen activator fused with the C-terminal fragment of hirudin. J Thromb Thrombolysis 2021; 52:880-888. [PMID: 33826053 DOI: 10.1007/s11239-021-02440-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/26/2021] [Indexed: 12/12/2022]
Abstract
In the present study, bifunctional fusion proteins were designed by fusing the kringle 2 and protease domains of tissue-type plasminogen activator (tPA) to the C-terminal fragment of hirudin. The thrombolytic and anticoagulant activities of these recombinant proteins from mammalian cells were investigated using in vitro coagulation models and chromogenic assays. The results showed that all assayed tPA mutants retained catalytic activity. The C-terminal fragment of hirudin may have weak affinity to thrombin and thus was insufficient to suppress thrombin-mediated fibrin agglutination. The strength of the thrombolytic activity only relied on the selected tPA sequences, and the fibrinolytic efficiency of single-chain protein significantly decreased. Our data indicate that truncated tPA combined with a hirudin peptide may provide a framework for the further development of a new antithrombotic agent.
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Metabolic Labeling of Live Stem Cell for In Vitro Imaging and In Vivo Tracking. Methods Mol Biol 2021. [PMID: 30997638 DOI: 10.1007/7651_2019_224] [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: 08/22/2023]
Abstract
Stem cell therapy offers promising solutions to diseases and injuries that traditional medicines and therapies can't effectively cure. To get and explain their full therapeutic potentials, the survival, viability, integration, homing, and differentiation of stem cells after transplant must be clearly understood. To meet these urgent needs, noninvasive stem cell imaging and tracking technologies have been developed. Metabolic labeling technique is one of the most powerful tools for live cell imaging and tracking. In addition, it has many advantages for in vivo live cell imaging and tracking such as low background, correlation of survival, and very toxic and nontoxic by-products. Herein, we described the fundamental information and process of metabolic labeling techniques and suggested optimal condition for in vitro and in vivo imaging and tracking of human umbilical cord blood-derived endothelial progenitor cells (hUCB-EPCs). Based on this study, metabolic labeling techniques can be helpful for understanding the safety and effectiveness of stem cell-based therapy and determining the utility of stem cells in downstream experiments.
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40
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Zhou Y, Qiu N, Mine Y, Keast R, Meng Y. Comparative N-Glycoproteomic Analysis Provides Novel Insights into the Deterioration Mechanisms in Chicken Egg Vitelline Membrane during High-Temperature Storage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2354-2363. [PMID: 33566602 DOI: 10.1021/acs.jafc.0c07557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The weakening of chicken egg vitelline membrane (CEVM) is one of the most important factors influencing egg quality during high-temperature storage. Therefore, a comparative N-glycoproteomic analysis of CEVM after 10 days of storage at 30 °C was performed to explore the roles of protein N-glycosylation in membrane deterioration. In total, 399 N-glycosites corresponding to 198 proteins were identified, of which 46 N-glycosites from 30 proteins were significantly altered. Gene ontology analysis revealed that these differentially N-glycosylated proteins (DGPs) were involved in antibacterial activity, glycosaminoglycan binding, lipid binding, and aminopeptidase activity. Removal of the N-glycans in Mucin-5B may result in a loss of CEVM's mechanical properties. The N-glycosites enriched in the apolipoprotein B β2 domain in CEVM were significantly changed, which may contribute to lipid composition modifications during storage. Moreover, N-glycosites in several metalloproteases were located within the functional domain or active site region, indicating that the decreased N-glycosylation levels may affect their structural stability, specific substrate binding, or enzyme activity. These findings provide novel insights into the roles of protein N-glycosylation during membrane weakening.
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Affiliation(s)
- Yu Zhou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Ning Qiu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Yoshinori Mine
- Department of Food Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Russell Keast
- CASS Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125, Australia
| | - Yaqi Meng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
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41
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Dong L, McKinstry WJ, Pan L, Newman J, Ren B. Crystal structure of fungal tannase from Aspergillus niger. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:267-277. [DOI: 10.1107/s2059798320016484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/20/2020] [Indexed: 11/11/2022]
Abstract
Tannases are serine esterases that were first discovered in fungi more than one and half centuries ago. They catalyze the hydrolysis of the gallolyl ester bonds in gallotannins to release gallic acid, which is an important intermediate in the chemical and pharmaceutical industries. Since their discovery, fungal tannases have found wide industrial applications, although there is scarce knowledge about these enzymes at the molecular level, including their catalytic and substrate-binding sites. While this lack of knowledge hinders engineering efforts to modify the enzymes, many tannases have been isolated from various fungal strains in a search for the desired enzymatic properties. Here, the first crystal structure of a fungal tannase, that from Aspergillus niger, is reported. The enzyme possesses a typical α/β-hydrolase-fold domain with a large inserted cap domain, which together form a bowl-shaped hemispherical shape with a surface concavity surrounded by N-linked glycans. Gallic acid is bound at the junction of the two domains within the concavity by forming two hydrogen-bonding networks with neighbouring residues. One is formed around the carboxyl group of the gallic acid and involves residues from the hydrolase-fold domain, including those from the catalytic triad, which consists of Ser206, His485 and Asp439. The other is formed around the three hydroxyl groups of the compound, with the involvement of residues mainly from the cap domain, including Gln238, Gln239, His242 and Ser441. Gallic acid is bound in a sandwich-like mode by forming a hydrophobic contact with Ile442. All of these residues are found to be highly conserved among fungal and yeast tannases.
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Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
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Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
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43
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Bascuñán P, Gabrieli P, Mameli E, Catteruccia F. Mating-regulated atrial proteases control reinsemination rates in Anopheles gambiae females. Sci Rep 2020; 10:21974. [PMID: 33319823 PMCID: PMC7738481 DOI: 10.1038/s41598-020-78967-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/25/2020] [Indexed: 11/20/2022] Open
Abstract
Anopheles gambiae mosquitoes are the most important vectors of human malaria. The reproductive success of these mosquitoes relies on a single copulation event after which the majority of females become permanently refractory to further mating. This refractory behavior is at least partially mediated by the male-synthetized steroid hormone 20-hydroxyecdysone (20E), which is packaged together with other seminal secretions into a gelatinous mating plug and transferred to the female atrium during mating. In this study, we show that two 20E-regulated chymotrypsin-like serine proteases specifically expressed in the reproductive tract of An. gambiae females play an important role in modulating the female susceptibility to mating. Silencing these proteases by RNA interference impairs correct plug processing and slows down the release of the steroid hormone 20E from the mating plug. In turn, depleting one of these proteases, the Mating Regulated Atrial Protease 1 (MatRAP1), reduces female refractoriness to further copulation, so that a significant proportion of females mate again. Microscopy analysis reveals that MatRAP1 is localized on a previously undetected peritrophic matrix-like structure surrounding the mating plug. These data provide novel insight into the molecular mechanisms shaping the post-mating biology of these important malaria vectors.
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Affiliation(s)
- Priscila Bascuñán
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy
- Centers for Disease Control and Prevention, Entomology Branch, Atlanta, GA, USA
| | - Paolo Gabrieli
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy
- Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Enzo Mameli
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Dipartimento di Medicina Sperimentale, Università degli studi di Perugia, Perugia, Italy.
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Maurya A, Bhattacharya A, Khare SK. Enzymatic Remediation of Polyethylene Terephthalate (PET)-Based Polymers for Effective Management of Plastic Wastes: An Overview. Front Bioeng Biotechnol 2020; 8:602325. [PMID: 33330434 PMCID: PMC7710609 DOI: 10.3389/fbioe.2020.602325] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
Globally, plastic-based pollution is now recognized as one of the serious threats to the environment. Among different plastics, polyethylene terephthalate (PET) occupies a pivotal place, its excess presence as a waste is a major environmental concern. Mechanical, thermal, and chemical-based treatments are generally used to manage PET pollution. However, these methods are usually expensive or generate secondary pollutants. Hence, there is a need for a cost-effective and environment-friendly method for efficient management of PET-based plastic wastes. Considering this, enzymatic treatment or recycling is one of the important methods to curb PET pollution. In this regard, PET hydrolases have been explored for the treatment of PET wastes. These enzymes act on PET and end its breakdown into monomeric units and subsequently results in loss of weight. However, various factors, specifically PET crystallinity, temperature, and pH, are known to affect this enzymatic process. For effective hydrolysis of PET, high temperature is required, which facilitates easy accessibility of substrate (PET) to enzymes. However, to function at this high temperature, there is a requirement of thermostable enzymes. The thermostability could be enhanced using glycosylation, immobilization, and enzyme engineering. Furthermore, the use of surfactants, additives such as Ca2+, Mg2+, and hydrophobins (cysteine-rich proteins), has also been reported to enhance the enzymatic PET hydrolysis through facilitating easy accessibility of PET polymers. The present review encompasses a brief overview of the use of enzymes toward the management of PET wastes. Various methods affecting the treatment process and different constraints arising thereof are also systematically highlighted in the review.
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Affiliation(s)
- Ankita Maurya
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Amrik Bhattacharya
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
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45
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He M, Zhang Y, Li H, Liu M, Dong N, Wu Q. A common CORIN variant in hypertension reduces corin intracellular trafficking by exposing an inhibitory N-terminus. Biochem Biophys Res Commun 2020; 530:35-41. [DOI: 10.1016/j.bbrc.2020.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022]
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46
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Ugonotti J, Chatterjee S, Thaysen-Andersen M. Structural and functional diversity of neutrophil glycosylation in innate immunity and related disorders. Mol Aspects Med 2020; 79:100882. [PMID: 32847678 DOI: 10.1016/j.mam.2020.100882] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
The granulated neutrophils are abundant innate immune cells that utilize bioactive glycoproteins packed in cytosolic granules to fight pathogenic infections, but the neutrophil glycobiology remains poorly understood. Facilitated by technological advances in glycoimmunology, systems glycobiology and glycoanalytics, a considerable body of literature reporting on novel aspects of neutrophil glycosylation has accumulated. Herein, we summarize the building knowledge of the structural and functional diversity displayed by N- and O-linked glycoproteins spatiotemporally expressed and sequentially brought-into-action across the diverse neutrophil life stages during bone marrow maturation, movements to, from and within the blood circulation and microbicidal processes at the inflammatory sites in peripheral tissues. It transpires that neutrophils abundantly decorate their granule glycoproteins including neutrophil elastase, myeloperoxidase and cathepsin G with peculiar glyco-signatures not commonly reported in other areas of human glycobiology such as hyper-truncated chitobiose core- and paucimannosidic-type N-glycans and monoantennary complex-type N-glycans. Sialyl Lewisx, Lewisx, poly-N-acetyllactosamine extensions and core 1-/2-type O-glycans are also common neutrophil glyco-signatures. Granule-specific glycosylation is another fascinating yet not fully understood feature of neutrophils. Recent literature suggests that unconventional biosynthetic pathways and functions underpin these prominent neutrophil-associated glyco-phenotypes. The impact of glycosylation on key neutrophil effector functions including extravasation, degranulation, phagocytosis and formation of neutrophil extracellular traps during normal physiological conditions and in innate immune-related diseases is discussed. We also highlight new technologies that are expected to further advance neutrophil glycobiology and briefly discuss the untapped diagnostic and therapeutic potential of neutrophil glycosylation that could open avenues to combat the increasingly prevalent innate immune disorders.
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Affiliation(s)
- Julian Ugonotti
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, 2109, Australia.
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47
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Siddiqui R, Rajendran K, Abdella B, Ayub Q, Lim SY, Khan NA. Naegleria fowleri: differential genetic expression following treatment with Hesperidin conjugated with silver nanoparticles using RNA-Seq. Parasitol Res 2020; 119:2351-2358. [PMID: 32451717 DOI: 10.1007/s00436-020-06711-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/05/2020] [Indexed: 10/24/2022]
Abstract
Naegleria fowleri causes a deadly infection known as primary amoebic meningoencephalitis (PAM). To our knowledge, there are very few transcriptome studies conducted on these brain-eating amoebae, despite rise in the number of cases. Although the Naegleria genome has been sequenced, currently, it is not well annotated. Transcriptome level studies are needed to help understand the pathology and biology of this fatal parasitic infection. Recently, we showed that nanoparticles loaded with the flavonoid Hesperidin (HDN) are potential novel antimicrobial agents. N. fowleri trophozoites were treated with and without HDN-conjugated with silver nanoparticles (AgNPs) and silver only, and then, 50% minimum inhibitory concentration (MIC) was determined. The results revealed that the MIC of HDN-conjugated AgNPs was 12.5 microg/mL when treated for 3 h. As no reference genome exists for N. fowleri, de novo RNA transcriptome analysis using RNA-Seq and differential gene expression analysis was performed using the Trinity software. Analysis revealed that more than 2000 genes were differentially expressed in response to N. fowleri treatment with HDN-conjugated AgNPs. Some of the genes were linked to oxidative stress response, DNA repair, cell division, cell signalling and protein synthesis. The downregulated genes were linked with processes such as protein modification, synthesis of aromatic amino acids, when compared with untreated N. fowleri. Further transcriptome studies will lead to understanding of genetic mechanisms of the biology and pathogenesis and/or the identification of much needed drug candidates.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, University City, Sharjah, United Arab Emirates
| | - Kavitha Rajendran
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway, Malaysia
| | - Bahaa Abdella
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway, Malaysia.,Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Qasim Ayub
- Monash University Malaysia Genomics Facility, School of Science, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Shu Yong Lim
- Monash University Malaysia Genomics Facility, School of Science, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Naveed Ahmed Khan
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, University City, Sharjah, United Arab Emirates.
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48
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Stabilization of Glycosylated β-Glucosidase by Intramolecular Crosslinking Between Oxidized Glycosidic Chains and Lysine Residues. Appl Biochem Biotechnol 2020; 192:325-337. [DOI: 10.1007/s12010-020-03321-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
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49
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Mikolajczyk K, Kaczmarek R, Czerwinski M. How glycosylation affects glycosylation: the role of N-glycans in glycosyltransferase activity. Glycobiology 2020; 30:941-969. [PMID: 32363402 DOI: 10.1093/glycob/cwaa041] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/15/2022] Open
Abstract
N-glycosylation is one of the most important posttranslational modifications of proteins. It plays important roles in the biogenesis and functions of proteins by influencing their folding, intracellular localization, stability and solubility. N-glycans are synthesized by glycosyltransferases, a complex group of ubiquitous enzymes that occur in most kingdoms of life. A growing body of evidence shows that N-glycans may influence processing and functions of glycosyltransferases, including their secretion, stability and substrate/acceptor affinity. Changes in these properties may have a profound impact on glycosyltransferase activity. Indeed, some glycosyltransferases have to be glycosylated themselves for full activity. N-glycans and glycosyltransferases play roles in the pathogenesis of many diseases (including cancers), so studies on glycosyltransferases may contribute to the development of new therapy methods and novel glycoengineered enzymes with improved properties. In this review, we focus on the role of N-glycosylation in the activity of glycosyltransferases and attempt to summarize all available data about this phenomenon.
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Affiliation(s)
- Krzysztof Mikolajczyk
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
| | - Radoslaw Kaczmarek
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
| | - Marcin Czerwinski
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
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50
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Glyoxyl-Activated Agarose as Support for Covalently Link Novo-Pro D: Biocatalysts Performance in the Hydrolysis of Casein. Catalysts 2020. [DOI: 10.3390/catal10050466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This study aimed to evaluate the performance of a commercial protease (Novo-Pro D (NPD)), both in soluble and immobilized forms, in the hydrolysis of proteins (using casein as model protein). Immobilization of the protease NPD on 6% agarose activated with glyoxyl groups for 24 h at 20 °C and pH 10.0 allowed preparing immobilized biocatalyst with around 90% immobilization yield, 92% recovered activity versus small substrate, and a thermal stability 5.3-fold higher than the dialyzed soluble enzyme at 50 °C and pH 8.0. Immobilization times longer than 24 h lead to a decrease in the recovered activity and did not improve the biocatalyst stability. At 50 °C and pH 6.5, the immobilized NPD was around 20-fold more stable than the dialyzed soluble protease. Versus casein, the immobilized NDP presented a 10% level of activity, but it allowed hydrolyzing casein (26 g/L) at 50 °C and pH 6.5 up to a 40% degree of hydrolysis (DH) after 2 h reaction, while under the same conditions, only a 34% DH was achieved with soluble NPD. In addition, the immobilized NPD showed good reusability, maintaining the DH of casein for at least ten 2h-reaction batches.
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