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Yom A, Chiang A, Lewis NE. Boltzmann Model Predicts Glycan Structures from Lectin Binding. Anal Chem 2024; 96:8332-8341. [PMID: 38720429 PMCID: PMC11162346 DOI: 10.1021/acs.analchem.3c04992] [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] [Indexed: 05/20/2024]
Abstract
Glycans are complex oligosaccharides that are involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese hamster ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego, California 92093, United States
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Immunology Center of Georgia, Augusta University, Augusta, Georgia 30912, United States
- Department of Medicine, Augusta University, Augusta, Georgia 30912, United States
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Department of Bioengineering, University of California, San Diego, California 92093, United States
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Yom A, Chiang A, Lewis NE. A Boltzmann model predicts glycan structures from lectin binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.03.543532. [PMID: 37333412 PMCID: PMC10274649 DOI: 10.1101/2023.06.03.543532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Glycans are complex oligosaccharides involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese Hamster Ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego. CA 92093, USA
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego. CA 92093, USA
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
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Mostafavi E, Esmaeilnejad B, Meysam Abtahi Foroushani S. Evaluation of cytokines and sialic acids contents in horses naturally infected with Theileria equi. Comp Immunol Microbiol Infect Dis 2020; 70:101453. [PMID: 32163745 DOI: 10.1016/j.cimid.2020.101453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 12/12/2022]
Abstract
This study was undertaken to assess the effects of T. equi infection on serum concentrations of some important cytokines including interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), and interleukin-1 beta (IL-1β), IL-1α, IL-4, IL-6, IL-8, IL-10, IL-12α, IL-12β, IL-18, as well as total, protein and lipid binding sialic acids (TSA, PBSA and LBSA). Furthermore, any probable relation among the parasitemia, cytokines and sialic acids (SAs) were calculated using Pearson correlation and simple linear regression. Almost 300 draft horses (Kurdish-breed) with age of 3-4 years old from north-west of Iran were examined and an infected group comprised of 28 mares, naturally infected with T. equi, was identified and divided into 3 subgroups according to their parasitemia rates (low <1 %, moderate 1-3 % and high 3-5 %). Twenty healthy horses were considered as a control. Characterization and differentiation of piroplasmosis were conducted using routine hematological procedures and specific PCR assay. The results revealed a significant increase (P < 0.05) in all of the cytokines and SAs in a parasitic burden-dependent fashion. Additionally, a strong and positive relation was detected among the parasitemia, cytokines and SAs. Conclusively, T. equi infection is associated with induction of severe inflammatory processes in horses and SA plays a pivotal role in pathophysiology of the disease as it is tightly correlated with the parasitemia rate.
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Affiliation(s)
- Elahe Mostafavi
- Department of Pathobiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Bijan Esmaeilnejad
- Department of Pathobiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran.
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Takabatake N, Iseki H, Ikehara Y, Kanuka H, Yokoyama N, Sekimizu K, Igarashi I. Isolation and pathogenic characterization of an OB1 variant of Babesia rodhaini which has a glycophorin A-independent pathway to murine red blood cells. Vet Parasitol 2009; 159:97-104. [DOI: 10.1016/j.vetpar.2008.10.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 09/15/2008] [Accepted: 10/07/2008] [Indexed: 11/16/2022]
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Takabatake N, Okamura M, Yokoyama N, Ikehara Y, Akimitsu N, Arimitsu N, Hamamoto H, Sekimizu K, Suzuki H, Igarashi I. Glycophorin A-knockout mice, which lost sialoglycoproteins from the red blood cell membrane, are resistant to lethal infection of Babesia rodhaini. Vet Parasitol 2007; 148:93-101. [PMID: 17651898 DOI: 10.1016/j.vetpar.2007.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 05/18/2007] [Accepted: 06/01/2007] [Indexed: 10/23/2022]
Abstract
Recent in vitro-based studies using several Babesia spp. have suggested that sialic acids and/or sialoglycoproteins on host red blood cells (RBCs) play an important role in their invasion of RBCs. In the present study, we analyzed the RBC characteristics of glycophorin A (GPA)-knockout mice and studied their in vivo susceptibility to lethal infection of Babesia rodhaini for the first time. In immunoblot and lectin blot analyses, glycoproteins containing O-linked oligosaccharides terminated with alpha2-3-linked sialic acids disappeared from the RBCs of GPA homozygous ((-/-)) mice. Flow cytometric analysis showed a remarkable reduction of Maackia amurensis lectin II binding to the surface of GPA(-/-) RBCs relative to control RBCs, indicating an appreciable loss of alpha2-3-linked sialic acids on the RBC surface of GPA(-/-) mice. Importantly, while B. rodhaini caused lethal infection in wild-type mice, the infected GPA(-/-) mice showed inhibition of parasite growth and eventually survived. These results indicate that RBC sialoglycoproteins lost in GPA(-/-) mice are involved in the in vivo growth of B. rodhaini, probably functioning as essential molecule(s) for the parasite invasion of host RBCs in the blood circulation.
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Affiliation(s)
- Noriyuki Takabatake
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan
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Okamura M, Yokoyama N, Takabatake N, Okubo K, Ikehara Y, Igarashi I. Babesia bovis: Subcellular localization of host erythrocyte membrane components during their asexual growth. Exp Parasitol 2007; 116:91-4. [PMID: 17207481 DOI: 10.1016/j.exppara.2006.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2006] [Revised: 11/08/2006] [Accepted: 11/09/2006] [Indexed: 11/23/2022]
Abstract
In the present study, the subcellular localization of the host red blood cell (RBC) membrane components, the alpha2-3-linked sialic acid (SA) residues and the lipid bilayer, was observed during the asexual growth of Babesia bovis using two erythrocyte probes, the SA-specific lectin (MALII) and the lipophilic fluorescent (PKH2) probes, respectively. In confocal laser scanning microscopy with MALII, the SA residues on the surface of parasitized RBCs appeared to accumulate into the intracellular parasites as the parasites matured as well as to remain on the surface of extracellular parasites. Furthermore, when PKH2-labeled RBCs were infected with B. bovis, PKH2 signals were also observed around both the intracellular and the extracellular parasites, similarly to the results of MALII. These results indicated that the components derived from the host erythrocyte membrane are incorporated into the intracellular parasites during their asexual growth within the parasitized RBC, suggesting the possible formation of a parasitophorous vacuole-based network or a parasite surface coat.
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Affiliation(s)
- Masashi Okamura
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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Okamura M, Yokoyama N, Takabatake N, Okubo K, Ikehara Y, Igarashi I. Modification of Host Erythrocyte Membranes by Trypsin and Chymotrypsin Treatments and Effects on the In Vitro Growth of Bovine and Equine Babesia Parasites. J Parasitol 2007; 93:208-11. [PMID: 17436968 DOI: 10.1645/ge-914r.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the present study, we investigated the effects of protease pretreatments of host erythrocytes (RBC) on the in vitro growth of bovine Babesia parasites (Babesia bovis and B. bigemina) and equine Babesia parasites (B. equi and B. caballi). The selected proteases, trypsin and chymotrypsin, clearly modified several membrane proteins of both bovine and equine RBC, as demonstrated by SDS-PAGE analysis; however, the protease treatments also modified the sialic acid content exclusively in bovine RBC, as demonstrated by lectin blot analysis. An in vitro growth assay using the protease-treated RBC showed that the trypsin-treated bovine RBC, but not the chymotrypsin-treated ones, significantly reduced the growth of B. bovis and B. bigemina as compared to the control. In contrast, the growth of B. equi and B. caballi was not affected by any of these proteases. Thus, the bovine, but not the equine, Babesia parasites require the trypsin-sensitive membrane (sialoglyco) proteins to infect the RBC.
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Affiliation(s)
- Masashi Okamura
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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TAKABATAKE N, OKAMURA M, YOKOYAMA N, OKUBO K, IKEHARA Y, IGARASHI I. Involvement of a Host Erythrocyte Sialic Acid Content in Babesia bovis Infection. J Vet Med Sci 2007; 69:999-1004. [DOI: 10.1292/jvms.69.999] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Noriyuki TAKABATAKE
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine
| | - Masashi OKAMURA
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine
| | - Naoaki YOKOYAMA
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine
| | - Kazuhiro OKUBO
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine
| | - Yuzuru IKEHARA
- Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology
| | - Ikuo IGARASHI
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine
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Okubo K, Yokoyama N, Takabatake N, Okamura M, Igarashi I. Amount of cholesterol in host membrane affects erythrocyte invasion and replication byBabesia bovis. Parasitology 2006; 134:625-30. [PMID: 17147838 DOI: 10.1017/s0031182006001910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
SUMMARYCholesterol is a major component of the erythrocyte membrane. In the present study, we investigated the effects of cholesterol reduction in host bovine erythrocytes (RBC) on the growth ofBabesia bovis, a major bovine haemoprotozoon. Anin vitrogrowth assay with bovine RBC that had been prepared by pre-treatment with a cholesterol depletion agent (methyl-β-cyclodextrin, MCD) showed that the culture with 5 mmMCD-treated RBC inhibited the growth ofB. bovissignificantly as compared with that with the control RBC. In further experiments, the treatment with 5 mmMCD was proved to suppress both activities of the parasite, erythrocyte invasion and replication within the infected RBC. In contrast, a slight reduction in the membrane cholesterol by 1 mmMCD treatment promoted both their growth and erythrocyte invasion activity. These results indicate that erythrocyte invasion and replication byB. bovisare affected by the amount of cholesterol in the host erythrocyte membrane.
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Affiliation(s)
- K Okubo
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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