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Akune-Taylor Y, Kon A, Aoki-Kinoshita KF. In silico simulation of glycosylation and related pathways. Anal Bioanal Chem 2024; 416:3687-3696. [PMID: 38748247 PMCID: PMC11180631 DOI: 10.1007/s00216-024-05331-8] [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: 10/10/2023] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/18/2024]
Abstract
Glycans participate in a vast number of recognition systems in diverse organisms in health and in disease. However, glycans cannot be sequenced because there is no sequencer technology that can fully characterize them. There is no "template" for replicating glycans as there are for amino acids and nucleic acids. Instead, glycans are synthesized by a complicated orchestration of multitudes of glycosyltransferases and glycosidases. Thus glycans can vary greatly in structure, but they are not genetically reproducible and are usually isolated in minute amounts. To characterize (sequence) the glycome (defined as the glycans in a particular organism, tissue, cell, or protein), glycosylation pathway prediction using in silico methods based on glycogene expression data, and glycosylation simulations have been attempted. Since many of the mammalian glycogenes have been identified and cloned, it has become possible to predict the glycan biosynthesis pathway in these systems. By then incorporating systems biology and bioprocessing technologies to these pathway models, given the right enzymatic parameters including enzyme and substrate concentrations and kinetic reaction parameters, it is possible to predict the potentially synthesized glycans in the pathway. This review presents information on the data resources that are currently available to enable in silico simulations of glycosylation and related pathways. Then some of the software tools that have been developed in the past to simulate and analyze glycosylation pathways will be described, followed by a summary and vision for the future developments and research directions in this area.
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Affiliation(s)
- Yukie Akune-Taylor
- Glycan and Life Systems Integration Center, Soka University, Tokyo, Japan
| | - Akane Kon
- Graduate School of Science and Engineering, Soka University, Tokyo, Japan
| | - Kiyoko F Aoki-Kinoshita
- Glycan and Life Systems Integration Center, Soka University, Tokyo, Japan.
- Graduate School of Science and Engineering, Soka University, Tokyo, Japan.
- iGCORE, Nagoya University, Nagoya, Japan.
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2
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Kumar P, Tomita T, Gerken TA, Ballard CJ, Lee YS, Weiss LM, Samara NL. A Toxoplasma gondii O-glycosyltransferase that modulates bradyzoite cyst wall rigidity is distinct from host homologues. Nat Commun 2024; 15:3792. [PMID: 38710711 DOI: 10.1038/s41467-024-48253-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
Infection with the apicomplexan protozoan Toxoplasma gondii can be life-threatening in immunocompromised hosts. Transmission frequently occurs through the oral ingestion of T. gondii bradyzoite cysts, which transition to tachyzoites, disseminate, and then form cysts containing bradyzoites in the central nervous system, resulting in latent infection. Encapsulation of bradyzoites by a cyst wall is critical for immune evasion, survival, and transmission. O-glycosylation of the protein CST1 by the mucin-type O-glycosyltransferase T. gondii (Txg) GalNAc-T3 influences cyst wall rigidity and stability. Here, we report X-ray crystal structures of TxgGalNAc-T3, revealing multiple features that are strictly conserved among its apicomplexan homologues. This includes a unique 2nd metal that is coupled to substrate binding and enzymatic activity in vitro and cyst wall O-glycosylation in T. gondii. The study illustrates the divergence of pathogenic protozoan GalNAc-Ts from their host homologues and lays the groundwork for studying apicomplexan GalNAc-Ts as therapeutic targets in disease.
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Affiliation(s)
- Pranav Kumar
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA
| | - Tadakimi Tomita
- Department of Pathology, Albert Einstein College of Medicine, Bronx, 1300 Morris Park Avenue, New York, 10461, USA
| | - Thomas A Gerken
- Departments of Biochemistry and Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Collin J Ballard
- Departments of Biochemistry and Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yong Sok Lee
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, 1300 Morris Park Avenue, New York, 10461, USA
- Department of Medicine (Infectious Disease), Albert Einstein College of Medicine, Bronx 1300 Morris Park Avenue, New York, 10461, USA
| | - Nadine L Samara
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA.
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Teng D, Wang W, Jia W, Song J, Gong L, Zhong L, Yang J. The effects of glycosylation modifications on monocyte recruitment and foam cell formation in atherosclerosis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167027. [PMID: 38237743 DOI: 10.1016/j.bbadis.2024.167027] [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: 09/16/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
The monocyte recruitment and foam cell formation have been intensively investigated in atherosclerosis. Nevertheless, as the study progressed, it was obvious that crucial molecules participated in the monocyte recruitment and the membrane proteins in macrophages exhibited substantial glycosylation modifications. These modifications can exert a significant influence on protein functions and may even impact the overall progression of diseases. This article provides a review of the effects of glycosylation modifications on monocyte recruitment and foam cell formation. By elaborating on these effects, we aim to understand the underlying mechanisms of atherogenesis further and to provide new insights into the future treatment of atherosclerosis.
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Affiliation(s)
- Da Teng
- Yantai Yuhuangding Hospital affiliated to Qingdao University, Yantai, Shandong, People's Republic of China; Qingdao University, Qingdao, Shandong, People's Republic of China
| | - Wenlong Wang
- Yantai Yuhuangding Hospital affiliated to Qingdao University, Yantai, Shandong, People's Republic of China; Qingdao University, Qingdao, Shandong, People's Republic of China
| | - Wenjuan Jia
- Yantai Yuhuangding Hospital affiliated to Qingdao University, Yantai, Shandong, People's Republic of China; Qingdao University, Qingdao, Shandong, People's Republic of China
| | - Jikai Song
- Yantai Yuhuangding Hospital affiliated to Qingdao University, Yantai, Shandong, People's Republic of China; Qingdao University, Qingdao, Shandong, People's Republic of China
| | - Lei Gong
- Yantai Yuhuangding Hospital affiliated to Qingdao University, Yantai, Shandong, People's Republic of China
| | - Lin Zhong
- Yantai Yuhuangding Hospital affiliated to Qingdao University, Yantai, Shandong, People's Republic of China.
| | - Jun Yang
- Yantai Yuhuangding Hospital affiliated to Qingdao University, Yantai, Shandong, People's Republic of China; Qingdao University, Qingdao, Shandong, People's Republic of China.
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Li Y, Wang H, Chen Y, Ding L, Ju H. In Situ Glycan Analysis and Editing in Living Systems. JACS AU 2024; 4:384-401. [PMID: 38425935 PMCID: PMC10900212 DOI: 10.1021/jacsau.3c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 03/02/2024]
Abstract
Besides proteins and nucleic acids, carbohydrates are also ubiquitous building blocks of living systems. Approximately 70% of mammalian proteins are glycosylated. Glycans not only provide structural support for living systems but also act as crucial regulators of cellular functions. As a result, they are considered essential pieces of the life science puzzle. However, research on glycans has lagged far behind that on proteins and nucleic acids. The main reason is that glycans are not direct products of gene coding, and their synthesis is nontemplated. In addition, the diversity of monosaccharide species and their linkage patterns contribute to the complexity of the glycan structures, which is the molecular basis for their diverse functions. Research in glycobiology is extremely challenging, especially for the in situ elucidation of glycan structures and functions. There is an urgent need to develop highly specific glycan labeling tools and imaging methods and devise glycan editing strategies. This Perspective focuses on the challenges of in situ analysis of glycans in living systems at three spatial levels (i.e., cell, tissue, and in vivo) and highlights recent advances and directions in glycan labeling, imaging, and editing tools. We believe that examining the current development landscape and the existing bottlenecks can drive the evolution of in situ glycan analysis and intervention strategies and provide glycan-based insights for clinical diagnosis and therapeutics.
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Affiliation(s)
- Yiran Li
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Haiqi Wang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Yunlong Chen
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Lin Ding
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
- Chemistry
and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
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Martins M, Vieira J, Pereira-Leite C, Saraiva N, Fernandes AS. The Golgi Apparatus as an Anticancer Therapeutic Target. BIOLOGY 2023; 13:1. [PMID: 38275722 PMCID: PMC10813373 DOI: 10.3390/biology13010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
Although the discovery of the Golgi apparatus (GA) was made over 125 years ago, only a very limited number of therapeutic approaches have been developed to target this complex organelle. The GA serves as a modification and transport center for proteins and lipids and also has more recently emerged as an important store for some ions. The dysregulation of GA functions is implicated in many cellular processes associated with cancer and some GA proteins are indeed described as cancer biomarkers. This dysregulation can affect protein modification, localization, and secretion, but also cellular metabolism, redox status, extracellular pH, and the extracellular matrix structure. Consequently, it can directly or indirectly affect cancer progression. For these reasons, the GA is an appealing anticancer pharmacological target. Despite this, no anticancer drug specifically targeting the GA has reached the clinic and few have entered the clinical trial stage. Advances in nanodelivery approaches may help change this scenario by specifically targeting tumor cells and/or the GA through passive, active, or physical strategies. This article aims to examine the currently available anticancer GA-targeted drugs and the nanodelivery strategies explored for their administration. The potential benefits and challenges of modulating and specifically targeting the GA function in the context of cancer therapy are discussed.
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Affiliation(s)
- Marta Martins
- CBIOS—Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024 Lisboa, Portugal; (M.M.); (J.V.); (C.P.-L.)
- Department of Biomedical Sciences, University of Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain
| | - João Vieira
- CBIOS—Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024 Lisboa, Portugal; (M.M.); (J.V.); (C.P.-L.)
- Department of Biomedical Sciences, University of Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain
| | - Catarina Pereira-Leite
- CBIOS—Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024 Lisboa, Portugal; (M.M.); (J.V.); (C.P.-L.)
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Nuno Saraiva
- CBIOS—Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024 Lisboa, Portugal; (M.M.); (J.V.); (C.P.-L.)
| | - Ana Sofia Fernandes
- CBIOS—Universidade Lusófona’s Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024 Lisboa, Portugal; (M.M.); (J.V.); (C.P.-L.)
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Luo W, Sun L. O-Linked N-Acetylglucosamine Transferase Regulates Bone Homeostasis Through Alkaline Phosphatase Pathway in Diabetic Periodontitis. Mol Biotechnol 2023:10.1007/s12033-023-00947-0. [PMID: 37951846 DOI: 10.1007/s12033-023-00947-0] [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: 07/26/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023]
Abstract
Periodontitis is one of the most common complications of diabetes, which seriously affects patients' life quality. It is important to find the key factors and mechanisms to improve the treatment of periodontitis. In our study, high glucose (HG) and lipopolysaccharide (LPS) treated human periodontal ligament cells (hPDLCs) and LPS treated diabetic mice was used to establish the diabetic periodontitis model in vitro and in vivo. O-linked beta-N-acetylglucosamine glycosylation (O-GlcNAcylation) and O-linked N-acetylglucosamine transferase (OGT) protein levels were detected by western blot assay. Cell counting kit-8, alkaline phosphatase (ALP), and alizarin red staining (ARS) assays were used to observe the O-GlcNAcylation and OGT effects on cell viability and osteoblast differentiation. Co-immunoprecipitation (Co-IP) assay was used to detect the relationship between OGT and ALP. The results showed that the levels of OGT and O-GlcNAcylation were significantly increased in both cell and mouse models. ALP and ARS staining results showed that silencing of OGT or inhibition of O-glycosylation notably improved osteogenic differentiation, increased the osteoprotegerin (OPG) protein levels and decreased the receptor activator for nuclear factor-κB Ligand (RANKL) protein levels of the HG and LPS treated hPDLCs. In diabetic periodontitis mice, knockdown of OGT relieved the injury of gingival tissue, increased the ALP and OPG levels and decreased the RANKL levels. Besides, ALP interacted with OGT protein, and OGT protein was found to act on ALP serine 513 glycosylation. In conclusion, our study demonstrated that excessive O-GlcNAcylation could restrain osteoblast differentiation by O-glycosylation in ALP.
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Affiliation(s)
- Wei Luo
- Beijing Hanhe Daguanying Dental Clinic, No. 182 Guang'an Menwai Street, Xicheng District, 100055, Beijing, China.
| | - Lu Sun
- Department of Stomatology, The First Medical Center of Chinese PLA General Hospital, 100853, Beijing, China
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Sanchez PR, Head SA, Qian S, Qiu H, Roy A, Jin Z, Zheng W, Liu JO. Modulation of the Endomembrane System by the Anticancer Natural Product Superstolide/ZJ-101. Int J Mol Sci 2023; 24:9575. [PMID: 37298526 PMCID: PMC10253484 DOI: 10.3390/ijms24119575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Marine natural products represent a unique source for clinically relevant drugs due to their vast molecular and mechanistic diversity. ZJ-101 is a structurally simplified analog of the marine natural product superstolide A, isolated from the New Caledonian sea sponge Neosiphonia Superstes. The mechanistic activity of the superstolides has until recently remained a mystery. Here, we have identified potent antiproliferative and antiadhesive effects of ZJ-101 on cancer cell lines. Furthermore, through dose-response transcriptomics, we found unique dysregulation of the endomembrane system by ZJ-101 including a selective inhibition of O-glycosylation via lectin and glycomics analysis. We applied this mechanism to a triple-negative breast cancer spheroid model and identified a potential for the reversal of 3D-induced chemoresistance, suggesting a potential for ZJ-101 as a synergistic therapeutic agent.
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Affiliation(s)
- Phillip R. Sanchez
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD 20892, USA;
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sarah A. Head
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Shan Qian
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, The University of Iowa, Iowa City, IA 52242, USA (Z.J.)
| | - Haibo Qiu
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, The University of Iowa, Iowa City, IA 52242, USA (Z.J.)
| | - Avishek Roy
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, The University of Iowa, Iowa City, IA 52242, USA (Z.J.)
| | - Zhendong Jin
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, The University of Iowa, Iowa City, IA 52242, USA (Z.J.)
| | - Wei Zheng
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD 20892, USA;
| | - Jun O. Liu
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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