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Svedberg D, Winiger RR, Berg A, Sharma H, Tellgren-Roth C, Debrunner-Vossbrinck BA, Vossbrinck CR, Barandun J. Functional annotation of a divergent genome using sequence and structure-based similarity. BMC Genomics 2024; 25:6. [PMID: 38166563 PMCID: PMC10759460 DOI: 10.1186/s12864-023-09924-y] [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: 08/27/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes. RESULTS In this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes. CONCLUSION We provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
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Affiliation(s)
- Dennis Svedberg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Rahel R Winiger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Charles R Vossbrinck
- Department of Environmental Science, Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.
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Vance DJ, Rudolph MJ, Davis SA, Mantis NJ. Structural Basis of Antibody-Mediated Inhibition of Ricin Toxin Attachment to Host Cells. Biochemistry 2023; 62:3181-3187. [PMID: 37903428 DOI: 10.1021/acs.biochem.3c00480] [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: 11/01/2023]
Abstract
Monoclonal antibodies, JB4 and SylH3, neutralize ricin toxin (RT) by inhibiting the galactose-specific lectin activity of the B subunit of the toxin (RTB), which is required for cell attachment and entry. It is not immediately apparent how the antibodies accomplish this feat, considering that RTB consists of two globular domains (D1, D2) each divided into three homologous subdomains (α, β, γ) with the two functional galactosyl-specific carbohydrate recognition domains (CRDs) situated on opposite poles (subdomains 1α and 2γ). Here, we report the X-ray crystal structures of JB4 and SylH3 Fab fragments bound to RTB in the context of RT. The structures revealed that neither Fab obstructed nor induced detectable conformational alterations in subdomains 1α or 2γ. Rather, JB4 and SylH3 Fabs recognize nearly identical epitopes within an ancillary carbohydrate recognition pocket located in subdomain 1β. Despite limited amino acid sequence similarity between SylH3 and JB4 Fabs, each paratope inserts a Phe side chain from the heavy (H) chain complementarity determining region (CDR3) into the 1β CRD pocket, resulting in local aromatic stacking interactions that potentially mimic a ligand interaction. Reconciling the fact that stoichiometric amounts of SylH3 and JB4 are sufficient to disarm RTB's lectin activity without evidence of allostery, we propose that subdomain 1β functions as a "coreceptor" required to stabilize glycan interactions principally mediated by subdomains 1α and 2γ. Further investigation into subdomain 1β will yield fundamental insights into the large family of R-type lectins and open novel avenues for countermeasures aimed at preventing toxin uptake into vulnerable tissues and cells.
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Affiliation(s)
- David J Vance
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Michael J Rudolph
- New York Structural Biology Center, New York, New York 10027, United States
| | - Simon A Davis
- New York Structural Biology Center, New York, New York 10027, United States
| | - Nicholas J Mantis
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
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Konozy EHE, Osman MEM, Dirar AI. A Comprehensive Review on Euphorbiaceae lectins: Structural and Biological Perspectives. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1956-1969. [PMID: 38105212 DOI: 10.1134/s0006297923110238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/29/2023] [Accepted: 10/18/2023] [Indexed: 12/19/2023]
Abstract
Euphorbiaceae, also known as the spurge family, is a large group of flowering plants. Despite being tropical natives, they are now widespread. Due to its medicinal and commercial importance, this family of plants attracted a lot of attention in the scientific community. The distinctive characteristic of the family is production of milky latex, which is a rich source of several lectins, the proteins that bind carbohydrates. Although their function is unclear, they are believed to defend plants against damaging phytopathogenic microorganisms, insects, and predatory animals. Additionally, they serve as crucial metabolic regulators under a variety of stressors. Detection, separation, purification, and characterization of lectins from the Euphorbiaceae family - mostly from the latex of plants - began over 40 years ago. This effort produced over 35 original research papers that were published. However, no systematic review that compiles these published data has been presented yet. This review summarizes and describes several procedures and protocols employed for extraction and purification of lectins belonging to this family. Physicochemical properties and biological activities of the lectins, along with their medicinal and pharmacological properties, have also been analyzed. Additionally, using examples of ricin and ricin agglutinin, we have structurally analyzed characteristics of the lectin known as Ribosome Inactivating Protein Type II (RIP-Type II) that belongs to this family. We anticipate that this review article will offer a useful compendium of information on this important family of lectins, show the scientists involved in lectin research the gaps in our knowledge, and offer insights for future research.
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Affiliation(s)
- Emadeldin Hassan E Konozy
- Department of Biotechnology, Africa City of Technology (ACT), Khartoum, Sudan.
- Pharmaceutical Research and Development Centre, Faculty of Pharmacy, Karary University, Omdurman, Khartoum State, Sudan
| | | | - Amina I Dirar
- Medicinal, Aromatic Plants, and Traditional Medicine Research Institute (MAPTRI), National Center for Research, Khartoum, Sudan
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Uzawa H, Kondo S, Nagatsuka T, Miyaguchi H, Seto Y, Oshita A, Dohi H, Nishida Y, Saito M, Tamiya E. Assembly of Glycochips with Mammalian GSLs Mimetics toward the On-site Detection of Biological Toxins. ACS OMEGA 2021; 6:32597-32606. [PMID: 34901608 PMCID: PMC8655786 DOI: 10.1021/acsomega.1c04154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/01/2021] [Indexed: 05/09/2023]
Abstract
According to our previously proposed scheme, each of three kinds of glycosphingolipid (GSL) derivatives, that is, lactosyl ceramide [Lac-Cer (1)] and gangliosides [GM1-Cer (2) and GT1b-Cer (3)], was installed onto the glass surface modified with Au nanoparticles. In the present study, we tried to apply microwave irradiation to promote their installing reactions. Otherwise, this procedure takes a lot of time as long as a conventional self-assembled monolayer (SAM) technique is applied. Using an advanced microwave reactor capable of adjusting ambient temperatures within a desired range, various GSL glycochips were prepared from the derivatives (1)-(3) under different microwave irradiation conditions. The overall assembling process was programed with an IC controller to finish in 1 h, and the derived GSL glycochips were evaluated in the analysis of three kinds of biological toxins [a Ricinus agglutinin (RCA120), botulinum toxin (BTX), and cholera toxin (CTX)] using a localized surface plasmon resonance (LSPR) biosensor. In the LSPR analysis, most of the irradiated GSL chips showed an enhanced response to the targeting toxin when they were irradiated under optimal temperature conditions. Lac-Cer chips showed the highest response to RCA120 (an agglutinin with β-D-Gal specificity) when the microwave irradiation was conducted at 30-35 °C. Compared to our former Lac-Cer glycochips with the conventional SAM condition, their response was enhanced by 3.6 times. Analogously, GT1b chips gained an approximately 4.1 times enhancement in their response to botulinum type C toxin (BTX/C) when the irradiation was conducted around at 45-60 °C. In the LSPR evaluation of the GM1-Cer glycochips using CTX, an optimal condition also appeared at around 30-35 °C. On the other hand, the microwave irradiation did not lead to a notable increase compared to the former GM1-Cer chips derived with the SAM technique. Judging from these experimental results, the microwave irradiation effectively promotes the installing process for all the three kinds of the GSL derivatives, while the optimal thermal condition becomes different from each other. Many bacterial and botanic proteinous toxins are composed of such carbohydrate binding domains or subunits that can discriminate both the key epitope structure and the dimension of glycoconjugates on the host cell surface. It is assumed that the optimal irradiation and thermal conditions are required to array these semi-synthetic GSL derivatives on the Au nanoparticles in a proper density and geometry for tight adhesion with each of the biological toxins.
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Affiliation(s)
- Hirotaka Uzawa
- Nanomaterials
Research Institute, Tsukuba Center, Tsukuba Central, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Satoshi Kondo
- Nanomaterials
Research Institute, Tsukuba Center, Tsukuba Central, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Takehiro Nagatsuka
- Nanomaterials
Research Institute, Tsukuba Center, Tsukuba Central, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Hajime Miyaguchi
- National
Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yasuo Seto
- National
Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Aguri Oshita
- Graduate
School of Environmental Horticulture, Chiba
University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
- Graduate
School of Advanced Integration Science, Chiba University, 1-33
Yayoi-cho, Inage-ku, Chiba, Chiba 263-8522, Japan
| | - Hirofumi Dohi
- Graduate
School of Environmental Horticulture, Chiba
University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
- Graduate
School of Advanced Integration Science, Chiba University, 1-33
Yayoi-cho, Inage-ku, Chiba, Chiba 263-8522, Japan
| | - Yoshihiro Nishida
- Graduate
School of Environmental Horticulture, Chiba
University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
- Graduate
School of Advanced Integration Science, Chiba University, 1-33
Yayoi-cho, Inage-ku, Chiba, Chiba 263-8522, Japan
| | - Masato Saito
- Department
of Applied Physics, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Tamiya
- Department
of Applied Physics, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka 565-0871, Japan
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Rudolph MJ, Poon AY, Kavaliauskiene S, Myrann AG, Reynolds-Peterson C, Davis SA, Sandvig K, Vance DJ, Mantis NJ. Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface. J Mol Biol 2021; 433:167086. [PMID: 34089718 DOI: 10.1016/j.jmb.2021.167086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/18/2021] [Accepted: 05/27/2021] [Indexed: 01/20/2023]
Abstract
Ricin toxin kills mammalian cells with notorious efficiency. The toxin's B subunit (RTB) is a Gal/GalNAc-specific lectin that attaches to cell surfaces and promotes retrograde transport of ricin's A subunit (RTA) to the trans Golgi network (TGN) and endoplasmic reticulum (ER). RTA is liberated from RTB in the ER and translocated into the cell cytoplasm, where it functions as a ribosome-inactivating protein. While antibodies against ricin's individual subunits have been reported, we now describe seven alpaca-derived, single-domain antibodies (VHHs) that span the RTA-RTB interface, including four Tier 1 VHHs with IC50 values <1 nM. Crystal structures of each VHH bound to native ricin holotoxin revealed three different binding modes, based on contact with RTA's F-G loop (mode 1), RTB's subdomain 2γ (mode 2) or both (mode 3). VHHs in modes 2 and 3 were highly effective at blocking ricin attachment to HeLa cells and immobilized asialofetuin, due to framework residues (FR3) that occupied the 2γ Gal/GalNAc-binding pocket and mimic ligand. The four Tier 1 VHHs also interfered with intracellular functions of RTB, as they neutralized ricin in a post-attachment cytotoxicity assay (e.g., the toxin was bound to cell surfaces before antibody addition) and reduced the efficiency of toxin transport to the TGN. We conclude that the RTA-RTB interface is a target of potent toxin-neutralizing antibodies that interfere with both extracellular and intracellular events in ricin's cytotoxic pathway.
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Affiliation(s)
| | - Amanda Y Poon
- Department of Biomedical Sciences, University at Albany, Albany, NY, USA; Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Simona Kavaliauskiene
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway
| | - Anne Grethe Myrann
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway
| | - Claire Reynolds-Peterson
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Simon A Davis
- New York Structural Biology Center, New York, NY, USA
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway; Department of Biosciences, University of Oslo, Oslo, Norway
| | - David J Vance
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Nicholas J Mantis
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
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de Lima LRA, da Silva LPBG, de Almeida SMV, Cahú TB, Beltrão EIC, de Carvalho Júnior LB. Lectin-carbohydrate complex evaluation by chemiluminescence. Anal Biochem 2018; 548:91-95. [PMID: 29458035 DOI: 10.1016/j.ab.2018.01.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/12/2018] [Accepted: 01/25/2018] [Indexed: 10/18/2022]
Abstract
In order to characterize the affinity between specific carbohydrate-binding proteins such as lectins, a model is proposed to study these interactions using a polysaccharide membrane to simulate such adsorption. Here, lectin-carbohydrate interactions were chemiluminescently investigated using lectins conjugated to acridinium ester (AE) and polysaccharides composed of their respective specific carbohydrates. The lectin-AE conjugates were incubated with discs (0.0314-0.6358 cm2) of phytagel, chitosan and carrageenan. The complex formation chemiluminescently detected followed the Langmuir isotherm from which constants were estimated. The association constant (Ka) and maximum binding sites on the membranes were 2.4 × 10-7 M-1 ± 0.8 × 10-7 M-1 and 1.3 × 10-3 mol. mg-1 ± 0.3 × 10-3 mol. mg-1 (Con A); 0.9 × 10-6 M-1 ± 0.4 × 10-6 M-1 and 0.021 × 10-3 mol. mg-1 ± 0.003 × 10-3 mol. mg-1 (WGA) and 2.0 × 10-6 M-1 ± 0.9 × 10-6 M-1 and 0.069 × 10-3 mol. mg-1 ± 0.010 × 10-3 mol. mg-1 (PNA). The proposed model might be useful to study binding affinity and estimate the amount of binding not limited by the sugar content in the membrane.
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Affiliation(s)
- Luiza Rayanna Amorim de Lima
- Departamento de Bioquímica and Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Cidade Universitária, 50030 Recife, Pernambuco, Brazil; Faculdade de Ciências, Educação e Tecnologia de Garanhuns (FACETEG), Universidade de Pernambuco (UPE), 50100 Garanhuns, Pernambuco, Brazil.
| | | | - Sinara Mônica Vitalino de Almeida
- Departamento de Bioquímica and Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Cidade Universitária, 50030 Recife, Pernambuco, Brazil; Faculdade de Ciências, Educação e Tecnologia de Garanhuns (FACETEG), Universidade de Pernambuco (UPE), 50100 Garanhuns, Pernambuco, Brazil
| | - Thiago Barbosa Cahú
- Departamento de Bioquímica and Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Cidade Universitária, 50030 Recife, Pernambuco, Brazil
| | - Eduardo Isidoro Carneiro Beltrão
- Departamento de Bioquímica and Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Cidade Universitária, 50030 Recife, Pernambuco, Brazil
| | - Luiz Bezerra de Carvalho Júnior
- Departamento de Bioquímica and Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Cidade Universitária, 50030 Recife, Pernambuco, Brazil
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Structural Characterization and Interaction with RCA 120 of a Highly Sulfated Keratan Sulfate from Blue Shark (Prionace glauca) Cartilage. Mar Drugs 2018; 16:md16040128. [PMID: 29662015 PMCID: PMC5923415 DOI: 10.3390/md16040128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 01/21/2023] Open
Abstract
As an important glycosaminoglycan, keratan sulfate (KS) mainly exists in corneal and cartilage, possessing various biological activities. In this study, we purified KS from blue shark (Prionace glauca) cartilage and prepared KS oligosaccharides (KSO) through keratanase II-catalyzed hydrolysis. The structures of KS and KSO were characterized using multi-dimensional nuclear magnetic resonance (NMR) spectra and liquid chromatography-mass spectrometry (LC-MS). Shark cartilage KS was highly sulfated and modified with ~2.69% N-acetylneuraminic acid (NeuAc) through α(2,3)-linked to galactose. Additionally, KS exhibited binding affinity to Ricinus communis agglutinin I (RCA120) in a concentration-dependent manner, a highly toxic lectin from beans of the castor plant. Furthermore, KSO from dp2 to dp8 bound to RCA120 in the increasing trend while the binding affinity of dp8 was superior to polysaccharide. These results define novel structural features for KS from Prionace glauca cartilage and demonstrate the potential application on ricin-antidote exploitation.
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Sugar-Binding Profiles of Chitin-Binding Lectins from the Hevein Family: A Comprehensive Study. Int J Mol Sci 2017; 18:ijms18061160. [PMID: 28556796 PMCID: PMC5485984 DOI: 10.3390/ijms18061160] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 04/28/2017] [Accepted: 05/21/2017] [Indexed: 01/16/2023] Open
Abstract
Chitin-binding lectins form the hevein family in plants, which are defined by the presence of single or multiple structurally conserved GlcNAc (N-acetylglucosamine)-binding domains. Although they have been used as probes for chito-oligosaccharides, their detailed specificities remain to be investigated. In this study, we analyzed six chitin-binding lectins, DSA, LEL, PWM, STL, UDA, and WGA, by quantitative frontal affinity chromatography. Some novel features were evident: WGA showed almost comparable affinity for pyridylaminated chitotriose and chitotetraose, while LEL and UDA showed much weaker affinity, and DSA, PWM, and STL had no substantial affinity for the former. WGA showed selective affinity for hybrid-type N-glycans harboring a bisecting GlcNAc residue. UDA showed extensive binding to high-mannose type N-glycans, with affinity increasing with the number of Man residues. DSA showed the highest affinity for highly branched N-glycans consisting of type II LacNAc (N-acetyllactosamine). Further, multivalent features of these lectins were investigated by using glycoconjugate and lectin microarrays. The lectins showed substantial binding to immobilized LacNAc as well as chito-oligosaccharides, although the extents to which they bound varied among them. WGA showed strong binding to heavily sialylated glycoproteins. The above observations will help interpret lectin-glycoprotein interactions in histochemical studies and glyco-biomarker investigations.
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Huang Q, Chen YP, Wang RW, Cheng S, Evans JD. Host-Parasite Interactions and Purifying Selection in a Microsporidian Parasite of Honey Bees. PLoS One 2016; 11:e0147549. [PMID: 26840596 PMCID: PMC4739525 DOI: 10.1371/journal.pone.0147549] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/05/2016] [Indexed: 01/01/2023] Open
Abstract
To clarify the mechanisms of Nosema ceranae parasitism, we deep-sequenced both honey bee host and parasite mRNAs throughout a complete 6-day infection cycle. By time-series analysis, 1122 parasite genes were significantly differently expressed during the reproduction cycle, clustering into 4 expression patterns. We found reactive mitochondrial oxygen species modulator 1 of the host to be significantly down regulated during the entire infection period. Our data support the hypothesis that apoptosis of honey bee cells was suppressed during infection. We further analyzed genome-wide genetic diversity of this parasite by comparing samples collected from the same site in 2007 and 2013. The number of SNP positions per gene and the proportion of non-synonymous substitutions per gene were significantly reduced over this time period, suggesting purifying selection on the parasite genome and supporting the hypothesis that a subset of N. ceranae strains might be dominating infection.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, Maryland, 20705, United States of America
- * E-mail: (QH); (JDE)
| | - Yan Ping Chen
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, Maryland, 20705, United States of America
| | - Rui Wu Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China
- Center for Ecological and Environmental Science, Northwestern Polytechnical University, Xi’an, 710072, China
- * E-mail: (QH); (JDE)
| | - Shang Cheng
- Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, Maryland, 20705, United States of America
- * E-mail: (QH); (JDE)
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Brandon DL, Adams LM. Milk matrix effects on antibody binding analyzed by enzyme-linked immunosorbent assay and biolayer interferometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3593-3598. [PMID: 25822824 DOI: 10.1021/acs.jafc.5b01136] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biolayer interferometry (BLI) was employed to study the impact of the milk matrix on the binding of ricin to asialofetuin (ASF) and to antibodies. This optical sensing platform used ligands immobilized covalently or via biotin-streptavidin linkage, and the results were compared to those obtained by enzyme-linked immunosorbent assay (ELISA). In sandwich ELISA, the binding of ricin to ASF was dramatically decreased when galactose was present during the analyte or detection antibody binding step. Low concentrations of milk (1%, v/v) produced a similar reduction in ricin binding to ASF but not to a high-affinity monoclonal antibody (mAb), increasing the dissociation rate of ASF-ricin complexes up to 100-fold. The effect of milk on the binding of ricin to ASF was ascribable to dialyzable factors, and milk sugar can account for these effects. The use of high-affinity mAbs in ELISA effectively limits the milk matrix effect on ricin analysis.
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Affiliation(s)
- David L Brandon
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, United States Department of Agriculture (USDA) Agricultural Research Service, 800 Buchanan Street, Albany, California 94710, United States
| | - Lisa M Adams
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, United States Department of Agriculture (USDA) Agricultural Research Service, 800 Buchanan Street, Albany, California 94710, United States
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Purification, Characterization, and cDNA Cloning of a Lectin from the MushroomPleurocybella porrigens. Biosci Biotechnol Biochem 2014; 73:702-9. [DOI: 10.1271/bbb.80774] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Nagatsuka T, Uzawa H, Sato K, Kondo S, Izumi M, Yokoyama K, Ohsawa I, Seto Y, Neri P, Mori H, Nishida Y, Saito M, Tamiya E. Localized surface plasmon resonance detection of biological toxins using cell surface oligosaccharides on glyco chips. ACS APPLIED MATERIALS & INTERFACES 2013; 5:4173-80. [PMID: 23668627 DOI: 10.1021/am4002937] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We have detected biological toxins using localized surface plasmon resonance (LSPR) and synthetic glycosyl ceramides (β-lactoside, globosyl trisaccharide (Gb3), or GM1 pentasaccharide) attached to gold (Au) nanoparticles. The particle diameters ranged from 5-100 nm. The detection sensitivity for three toxins (ricin, Shiga toxin, and cholera toxin) was found to depend not only on the attached glycoside but also on the diameter of the Au nanoparticles. For the detection of ricin, the 20-nm β-lactoside-coated Au nanoparticle exhibited the highest LSPR response, whereas 40-nm Gb3- and GM1-coated Au nanoparticles gave the best results for Shiga toxin and cholera toxin, respectively. In addition, a blocking process on the nanoparticle surface greatly improved the detection sensitivity for cholera toxin. The LSPR system enabled us to detect ricin at 30 ng/mL, Shiga toxin at 10 ng/mL, and the cholera toxin at 20 ng/mL.
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Affiliation(s)
- Takehiro Nagatsuka
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Japan
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13
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Bayer H, Essig K, Stanzel S, Frank M, Gildersleeve JC, Berger MR, Voss C. Evaluation of riproximin binding properties reveals a novel mechanism for cellular targeting. J Biol Chem 2012; 287:35873-86. [PMID: 22872642 PMCID: PMC3476256 DOI: 10.1074/jbc.m112.368548] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 08/05/2012] [Indexed: 11/06/2022] Open
Abstract
Riproximin is a cytotoxic type II ribosome-inactivating protein showing high selectivity for tumor cell lines. Its binding to cell surface glycans is crucial for subsequent internalization and cytotoxicity. In this paper, we describe a unique mechanism of interaction and discuss its implications for the cellular targeting and cytotoxicity of riproximin. On a carbohydrate microarray, riproximin specifically bound to two types of asialo-glycans, namely to bi- and triantennary complex N-glycan structures (NA2/NA3) and to repetitive N-acetyl-D-galactosamine (GalNAc), the so-called clustered Tn antigen, a cancer-specific O-glycan on mucins. Two glycoproteins showing high riproximin binding, the NA3-presenting asialofetuin and the clustered Tn-rich asialo-bovine submaxillary mucin, were subsequently chosen as model glycoproteins to mimic the binding interactions of riproximin with the two types of glycans. ELISA analyses were used to relate the two binding specificities of riproximin to its two sugar binding sites. The ability of riproximin to cross-link the two model proteins revealed that binding of the two types of glycoconjugates occurs within different binding sites. The biological implications of these binding properties were analyzed in cellular assays. The cytotoxicity of riproximin was found to depend on its specific and concomitant interaction with the two glycoconjugates as well as on dynamic avidity effects typical for lectins binding to multivalent glycoproteins. The presence of definite, cancer-related structures on the cells to be targeted determines the therapeutic potency of riproximin. Due to its cross-linking ability, riproximin is expected to show a high degree of specificity for cells exposing both NA2/NA3 and clustered Tn structures.
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Affiliation(s)
- Helene Bayer
- Toxicology and Chemotherapy Unit, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
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Nagatsuka T, Uzawa H, Sato K, Ohsawa I, Seto Y, Nishida Y. Glycotechnology for decontamination of biological agents: a model study using ricin and biotin-tagged synthetic glycopolymers. ACS APPLIED MATERIALS & INTERFACES 2012; 4:832-837. [PMID: 22214533 DOI: 10.1021/am201493q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two types of biotin-tagged glycopolymers carrying lactose or glucose in clusters along the polyacrylamide backbone were prepared and subjected to decontamination analyses with the plant toxin ricin. A buffer solution containing the toxin was treated with one glycopolymer followed by streptavidin-magnetic particles. Supernatant solutions were analyzed with surface plasmon resonance and capillary electrophoresis, and revealed that the lactose glycopolymer "captured" this toxin more effectively than the glucose polymer. Free toxin was not detectable in the supernatant after treatment with the glycopolymer and magnetic particles; >99% decontamination was achieved for this potentially fatal biological toxin.
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Affiliation(s)
- Takehiro Nagatsuka
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba 305-8565, Japan
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15
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Wu AM, Singh T, Liu JH, André S, Lensch M, Siebert HC, Krzeminski M, Bonvin AMJJ, Kaltner H, Wu JH, Gabius HJ. Adhesion/growth-regulatory galectins: insights into their ligand selectivity using natural glycoproteins and glycotopes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 705:117-41. [PMID: 21618107 DOI: 10.1007/978-1-4419-7877-6_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Albert M Wu
- Glyco-Immunochemistry Research Laboratory, Institute of Molecular and Cellular Biology, College of Medicine, Chang-Gung University, Kwei-Shan, Tao-Yuan, 333, Taiwan.
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16
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Wang W, Hale C, Goulding D, Haslam SM, Tissot B, Lindsay C, Michell S, Titball R, Yu J, Toribio AL, Rossi R, Dell A, Bradley A, Dougan G. Mannosidase 2, alpha 1 deficiency is associated with ricin resistance in embryonic stem (ES) cells. PLoS One 2011; 6:e22993. [PMID: 21886775 PMCID: PMC3160287 DOI: 10.1371/journal.pone.0022993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 07/11/2011] [Indexed: 12/19/2022] Open
Abstract
Host gene products required for mediating the action of toxins are potential targets for reversing or controlling their pathogenic impact following exposure. To identify such targets libraries of insertional gene-trap mutations generated with a PiggyBac transposon in Blm-deficient embryonic stem cells were exposed to the plant toxin, ricin. Resistant clones were isolated and genetically characterised and one was found to be a homozygous mutant of the mannosidase 2, alpha 1 (Man2α1) locus with a matching defect in the homologous allele. The causality of the molecular lesion was confirmed by removal of the transposon following expression of PB-transposase. Comparative glycomic and lectin binding analysis of the Man2α1 (-/-) ricin resistant cells revealed an increase in the levels of hybrid glycan structures and a reduction in terminal β-galactose moieties, potential target receptors for ricin. Furthermore, naïve ES cells treated with inhibitors of the N-linked glycosylation pathway at the mannosidase 2, alpha 1 step exhibited either full or partial resistance to ricin. Therefore, we conclusively identified mannosidase 2, alpha 1 deficiency to be associated with ricin resistance.
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Affiliation(s)
- Wei Wang
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Christine Hale
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail:
| | - Dave Goulding
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Stuart M. Haslam
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, South Kensington, London, United Kingdom
| | - Bérangère Tissot
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, South Kensington, London, United Kingdom
| | - Christopher Lindsay
- Cellular Toxicity Team, Biomedical Sciences Department, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Stephen Michell
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Rick Titball
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Jun Yu
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Royal College, Glasgow, Scotland, United Kingdom
| | - Ana Luisa Toribio
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Raffaella Rossi
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Anne Dell
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, South Kensington, London, United Kingdom
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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Thompson R, Creavin A, O’Connell M, O’Connor B, Clarke P. Optimization of the enzyme-linked lectin assay for enhanced glycoprotein and glycoconjugate analysis. Anal Biochem 2011; 413:114-22. [DOI: 10.1016/j.ab.2011.02.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 02/07/2011] [Accepted: 02/08/2011] [Indexed: 11/28/2022]
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18
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He XP, Wang XW, Jin XP, Zhou H, Shi XX, Chen GR, Long YT. Epimeric Monosaccharide−Quinone Hybrids on Gold Electrodes toward the Electrochemical Probing of Specific Carbohydrate−Protein Recognitions. J Am Chem Soc 2011; 133:3649-57. [DOI: 10.1021/ja110478j] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Xiao-Peng He
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, and ‡School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, People’s Republic of China
| | - Xiu-Wen Wang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, and ‡School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, People’s Republic of China
| | - Xiao-Ping Jin
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, and ‡School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, People’s Republic of China
| | - Hao Zhou
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, and ‡School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, People’s Republic of China
| | - Xiao-Xin Shi
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, and ‡School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, People’s Republic of China
| | - Guo-Rong Chen
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, and ‡School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, People’s Republic of China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, and ‡School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, People’s Republic of China
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Krzeminski M, Singh T, André S, Lensch M, Wu AM, Bonvin AMJJ, Gabius HJ. Human galectin-3 (Mac-2 antigen): defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region. Biochim Biophys Acta Gen Subj 2010; 1810:150-61. [PMID: 21070836 DOI: 10.1016/j.bbagen.2010.11.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/29/2010] [Accepted: 11/02/2010] [Indexed: 11/29/2022]
Abstract
BACKGROUND Human galectin-3 (Mac-2 antigen) is a cell-type-specific multifunctional effector owing to selective binding of distinct cell-surface glycoconjugates harboring β-galactosides. The structural basis underlying the apparent preferences for distinct glycoproteins and for expression is so far unknown. METHODS We strategically combined solid-phase assays on 43 natural glycoproteins with a new statistical approach to fully flexible computational docking and also processed the proximal promoter region in silico. RESULTS The degree of branching in N-glycans and clustering of core 1 O-glycans are positive modulators for avidity. Sialylation of N-glycans in α2-6 linkage and of core 1 O-glycans in α2-3 linkage along with core 2 branching was an unfavorable factor, despite the presence of suited glycans in the vicinity. The lectin-ligand contact profile was scrutinized for six natural di- and tetrasaccharides enabling a statistical grading by analyzing flexible docking trajectories. The computational analysis of the proximal promoter region delineated putative sites for Lmo2/c-Ets-1 binding and new sites with potential for RUNX binding. GENERAL SIGNIFICANCE These results identify new features of glycan selectivity and ligand contact by combining solid-phase assays with in silico work as well as of reactivity potential of the promoter.
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Affiliation(s)
- Mickaël Krzeminski
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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20
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Yen MH, Wu AM, Yang Z, Gong YP, Chang ET. Recognition roles of the carbohydrate glycotopes of human and bovine lactoferrins in lectin-N-glycan interactions. Biochim Biophys Acta Gen Subj 2010; 1810:139-49. [PMID: 21055448 DOI: 10.1016/j.bbagen.2010.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 10/10/2010] [Accepted: 10/15/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND Lactoferrin is an iron-binding protein belonging to the transferrin family. In addition to iron homeostasis, lactoferrin is also thought to have anti-microbial, anti-inflammatory, and anticancer activities. Previous studies showed that all lactoferrins are glycosylated in the human body, but the recognition roles of their carbohydrate glycotopes have not been well addressed. METHODS The roles of human and bovine lactoferrins involved in lectin-N-glycan recognition processes were analyzed by enzyme-linked lectinosorbent assay with a panel of applied and microbial lectins. RESULTS AND CONCLUSIONS Both native and asialo human/bovine lactoferrins reacted strongly with four Man-specific lectins - Concanavalia ensiformis agglutinin, Morniga M, Pisum sativum agglutinin, and Lens culinaris lectin. They also reacted well with PA-IIL, a LFuc>Man-specific lectin isolated from Pseudomonas aeruginosa. Both human and bovine lactoferrins also recognized a sialic acid specific lectin-Sambucus nigra agglutinin, but not their asialo products. Both native and asialo bovine lactoferrins, but not the human ones, exhibited strong binding with a GalNAc>Gal-specific lectin-Wisteria floribunda agglutinin. Human native lactoferrins and its asialo products bound well with four Gal>GalNAc-specific type-2 ribosome inactivating protein family lectins-ricin, abrin-a, Ricinus communis agglutinin 1, and Abrus precatorius agglutinin (APA), while the bovine ones reacted only with APA. GENERAL SIGNIFICANCE This study provides essential knowledge regarding the different roles of bioactive sites of lactoferrins in lectin-N-glycan recognition processes.
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Affiliation(s)
- Meng-Hsiu Yen
- Glyco-Immunochemistry Research Labortory, Institute of Molecular and Cellular Biology, College of Medicine, Chang Gung University, Tao-yuan, Taiwan
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21
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Detection of residual toxin in tissues of ricin-poisoned mice by sandwich enzyme-linked immunosorbent assay and immunoprecipitation. Anal Biochem 2010; 401:211-6. [DOI: 10.1016/j.ab.2010.02.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2009] [Revised: 02/08/2010] [Accepted: 02/25/2010] [Indexed: 11/17/2022]
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22
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Nagatsuka T, Uzawa H, Ohsawa I, Seto Y, Nishida Y. Use of lactose against the deadly biological toxin ricin. ACS APPLIED MATERIALS & INTERFACES 2010; 2:1081-5. [PMID: 20369893 DOI: 10.1021/am900846r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Developing a technology for detecting and decontaminating biological toxins is needed. Ricin from Ricinus communis is a highly poisonous toxin; it was formerly used for an assassination in London and in postal attacks in the United States. Ricin is readily available from castor beans and could be used as a biological agent. We propose using glycotechnology against the illegal use of ricin. Lactose (a natural ligand of this toxin) was incorporated into polyacrylamide-based glycopolymers at variable sugar densities (18-100%) and evaluated with surface plasmon resonance (SPR) spectroscopy and the real agent, ricin. Glycopolymers (18-65% lactose densities) effectively interfered with the toxin-lactoside adhesion event (>99% efficiency within 20 min). This supported the notion of using the mammary sugar lactose against a deadly biological toxin.
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Affiliation(s)
- Takehiro Nagatsuka
- National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, 305-8565, Japan
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23
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Wu AM, Lisowska E, Duk M, Yang Z. Lectins as tools in glycoconjugate research. Glycoconj J 2010; 26:899-913. [PMID: 18368479 DOI: 10.1007/s10719-008-9119-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 02/17/2008] [Accepted: 02/20/2008] [Indexed: 11/26/2022]
Abstract
Lectins are ubiquitous proteins of nonimmune origin, present in plants, microorganisms, animals and humans which specifically bind defined monosugars or oligosaccharide structures. Great progress has been made in recent years in understanding crucial roles played by lectins in many biological processes. Elucidation of carbohydrate specificity of human and animal lectins is of great importance for better understanding of these processes. Long before the role of carbohydrate-protein interactions had been explored, many lectins, mostly of plant origin, were identified, characterized and applied as useful tools in studying glycoconjugates. This review focuses on the specificity-based lectin classification and the methods of measuring lectin-carbohydrate interactions, which are used for determination of lectin specificity or for identification and characterization of glycoconjugates with lectins of known specificity. The most frequently used quantitative methods are shortly reviewed and the methods elaborated and used in our laboratories, based on biotinylated lectins, are described. These include the microtiter plate enzyme-linked lectinosorbent assay, lectinoblotting and lectin-glycosphingolipid interaction on thin-layer plates. Some chemical modifications of lectin ligands on the microtiter plates and blots (desialylation, Smith degradation, beta-elimination), which extend the applicability of these methods, are also described.
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Affiliation(s)
- Albert M Wu
- Glyco-Immunochemistry Research Laboratory, Institute of Molecular and Cellular Biology, Chang-Gung University, Kwei-san, Taoyuan 333, Taiwan.
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24
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Blome MC, Petro KA, Schengrund CL. Surface plasmon resonance analysis of ricin binding to plasma membranes isolated from NIH 3T3 cells. Anal Biochem 2009; 396:212-6. [PMID: 19800858 DOI: 10.1016/j.ab.2009.09.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/24/2009] [Accepted: 09/30/2009] [Indexed: 11/28/2022]
Abstract
As the potential for bioterrorism has appeared to increase, the need for simple systems for identifying potential inhibitors of the binding of such biological agents to cell membranes has increased. In this work, surface plasmon resonance (SPR) was used to monitor binding of ricin, a ribosome-inactivating protein, to the plasma membranes of NIH 3T3 cells. Once conditions were established, efficacy of the system for monitoring effectiveness of compounds at inhibiting ricin binding was ascertained by determining the IC(50) values for asialofetuin (ASF) and for bovine serum albumin derivatized with an average of 34 lactosyl moieties (BSA-Lac(34)). Results indicated that SPR is an efficient method for measuring adherence of a toxin to isolated cell plasma membranes. SPR can also indicate whether a compound that is an effective inhibitor of binding when a single ligand such as ASF is used will be as effective when used in studies with cells that may express multiple cell surface ligands for ricin and/or the inhibitor.
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Affiliation(s)
- Matthew C Blome
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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25
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Wu AM, Wu JH, Liu JH, Chen YY, Singha B, Chow LP, Lin JY. Roles of mammalian structural units, ligand cluster and polyvalency in the Abrus precatorius agglutinin and glycoprotein recognition process. Mol Immunol 2009; 46:3427-37. [DOI: 10.1016/j.molimm.2009.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/29/2009] [Accepted: 07/13/2009] [Indexed: 11/24/2022]
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26
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Pohleven J, Obermajer N, Sabotic J, Anzlovar S, Sepcić K, Kos J, Kralj B, Strukelj B, Brzin J. Purification, characterization and cloning of a ricin B-like lectin from mushroom Clitocybe nebularis with antiproliferative activity against human leukemic T cells. Biochim Biophys Acta Gen Subj 2008; 1790:173-81. [PMID: 19100814 DOI: 10.1016/j.bbagen.2008.11.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 11/19/2008] [Accepted: 11/22/2008] [Indexed: 11/30/2022]
Abstract
BACKGROUND Lectins are a diverse group of carbohydrate-binding proteins exhibiting numerous biological activities and functions. METHODS Two-step serial carbohydrate affinity chromatography was used to isolate a lectin from the edible mushroom clouded agaric (Clitocybe nebularis). It was characterized biochemically, its gene and cDNA cloned and the deduced amino acid sequence analyzed. Its activity was tested by hemagglutination assay and carbohydrate-binding specificity determined by glycan microarray analysis. Its effect on proliferation of several human cell lines was determined by MTS assay. RESULTS A homodimeric lectin with 15.9-kDa subunits agglutinates human group A, followed by B, O, and bovine erythrocytes. Hemagglutination was inhibited by glycoprotein asialofetuin and lactose. Glycan microarray analysis revealed that the lectin recognizes human blood group A determinant GalNAcalpha1-3(Fucalpha1-2)Galbeta-containing carbohydrates, and GalNAcbeta1-4GlcNAc (N,N'-diacetyllactosediamine). The lectin exerts antiproliferative activity specific to human leukemic T cells. CONCLUSIONS The protein belongs to the ricin B-like lectin superfamily, and has been designated as C. nebularis lectin (CNL). Its antiproliferative effect appears to be elicited by binding to carbohydrate receptors on human leukemic T cells. GENERAL SIGNIFICANCE CNL is one of the few mushroom ricin B-like lectins that have been identified and the only one so far shown to possess immunomodulatory properties.
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Affiliation(s)
- Jure Pohleven
- Department of Biotechnology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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Neo-glycopeptides: the importance of sugar core conformation in oxime-linked glycoprobes for interaction studies. Glycoconj J 2008; 25:879-87. [DOI: 10.1007/s10719-008-9150-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 05/16/2008] [Accepted: 05/20/2008] [Indexed: 10/21/2022]
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28
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Liu W, Chen Y, Yan M. Surface plasmon resonance imaging of limited glycoprotein samples. Analyst 2008; 133:1268-73. [PMID: 18709206 DOI: 10.1039/b804235g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A surface plasmon resonance imaging method has been developed for high throughput recognition and determination of low level glycoproteins with limited sample volume at least down to 50 nL. Chicken ovalbumin and immunoglobulin G were chosen as model compounds while bovine serum albumin and lysozyme were used as control. Each protein, at a concentration of 0.0080-1.0 mg mL(-1), was printed on one gold sensing film, and the films were simultaneously reacted with a probe solution and viewed using a laboratory-built surface plasmon resonance imaging system. The imaging signals were dependent on the concentration and the type of analyte, with a limit of detection down to at least 0.5 ng. The glycoproteins dotted at either 1.0 mg mL(-1) or 0.010 mg mL(-1) were easily differentiated from the non-glycoproteins by reaction with 200 nM concanavalin A (con A), giving a limit of recognition down also to 0.5 ng glycoprotein. This imaging method was hence considered a new tool for analyzing glycoproteins.
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Affiliation(s)
- Wei Liu
- Beijing National Laboratory of Molecular Science, Laboratory of Analytical Chemistry for Life Science, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100080, PR China
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29
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Blome MC, Schengrund CL. Multivalent binding of ricin to bovine serum albumin-based neoglycoconjugates. Toxicon 2008; 51:1214-24. [DOI: 10.1016/j.toxicon.2008.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 02/08/2008] [Accepted: 02/11/2008] [Indexed: 10/22/2022]
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30
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Linman MJ, Taylor JD, Yu H, Chen X, Cheng Q. Surface plasmon resonance study of protein-carbohydrate interactions using biotinylated sialosides. Anal Chem 2008; 80:4007-13. [PMID: 18461973 DOI: 10.1021/ac702566e] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Lectins are carbohydrate binding proteins found in plants, animals, and microorganisms. They serve as important models for understanding protein-carbohydrate interactions at the molecular level. We report here the fabrication of a novel sensing interface of biotinylated sialosides to probe lectin-carbohydrate interactions using surface plasmon resonance spectroscopy (SPR). The attachment of carbohydrates to the surface using biotin-NeutrAvidin interactions and the implementation of an inert hydrophilic hexaethylene glycol spacer (HEG) between the biotin and the carbohydrate result in a well-defined interface, enabling desired orientational flexibility and enhanced access of binding partners. The specificity and sensitivity of lectin binding were characterized using Sambucus nigra agglutinin (SNA) and other lectins including Maackia amurensis lectin (MAL), concanavalin A (Con A), and wheat germ agglutinin (WGA). The results indicate that alpha2,6-linked sialosides exhibit high binding affinity to SNA, while alteration in sialyl linkage and terminal sialic acid structure compromises the affinity by a varied degree. Quantitative analysis yields an equilibrium dissociation constant (KD) of 777 +/- 93 nM for SNA binding to Neu5Ac alpha2,6-LHEB. Transient SPR kinetics confirms the K D value from the equilibrium binding studies. A linear relationship was obtained in the 10-100 microg/mL range with limit of detection of approximately 50 nM. Weak interactions with MAL, Con A, and WGA were also quantified. The control experiment with bovine serum albumin indicates that nonspecific interaction on this surface is insignificant over the concentration range studied. Multiple experiments can be performed on the same substrate using a glycine stripping buffer, which selectively regenerates the surface without damaging the sialoside or the biotin-NeutrAvidin interface. This surface design retains a high degree of native affinity for the carbohydrate motifs, allowing distinction of sialyl linkages and investigation pertaining to the effect of functional group on binding efficiency. It could be easily modified to identify and quantify binding patterns of any low-affinity biologically relevant systems, opening new avenues for probing carbohydrate-protein interactions in real time.
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Affiliation(s)
- Matthew J Linman
- Department of Chemistry, University of California, Riverside, California 92521, USA
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Pauk VV, Tuktarova IA, Nasibullin TR, Zueva LP, Adel'guzhina AK, Khusnutdinova EK, Mustafina OE. [Paraoxonase 1 gene polymorphism 192Q/R in old men and long-livers from Tatars ethnic group]. Mol Biol 2007; 41:601-7. [PMID: 17936978 DOI: 10.1134/s0026893307040127] [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] [Indexed: 11/23/2022]
Abstract
Comparison in genotype and allele frequencies of people groups of younger (from 1 till 20 years), middle (21-55 years), elderly (56-74 years), senile (75-89 years) age and long-livers (90-109 years) have been performed (only 1116 person) with the purpose of analysis of molecular-genetic bases of ageing and longevity of the person. Allele variants of PON1 gene have been identified by polymerase chain reaction in a combination with restriction analysis. In the general sample of Tatars genotypes PON1*Q/*Q, PON1*Q/*R and PON1*R/*R are revealed with frequencies of 46.15, 44.35 and 9.5%, alleles PON1*Q and PON1*R are found with frequencies of 68.32 and 31.68% accordingly. Statistically significant distinctions on frequencies of genotypes and alleles between separate age groups are found. It has appeared, that frequency of PON1*R allele (28.46%) is lowered among old men in comparison with those among persons of younger age (37.42%, P = 0.009). However essentially above in group of long-livers, than in group of old men, frequencies allele PON1*R (P = 0.005) and genotype PON1*R/*R (P = 0.01).
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Wu AM, Wu JH, Tsai MS, Yang Z, Sharon N, Herp A. Differential affinities of Erythrina cristagalli lectin (ECL) toward monosaccharides and polyvalent mammalian structural units. Glycoconj J 2007; 24:591-604. [PMID: 17805962 DOI: 10.1007/s10719-007-9063-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 05/06/2007] [Accepted: 07/02/2007] [Indexed: 12/01/2022]
Abstract
Previous studies on the carbohydrate specificities of Erythrina cristagalli lectin (ECL) were mainly limited to analyzing the binding of oligo-antennary Galbeta1-->4GlcNAc (II). In this report, a wider range of recognition factors of ECL toward known mammalian ligands and glycans were examined by enzyme-linked lectinosorbent and inhibition assays, using natural polyvalent glycotopes, and a glycan array assay. From the results, it is shown that GalNAc was an active ligand, but its polyvalent structural units, in contrast to those of Gal, were poor inhibitors. Among soluble natural glycans tested for 50% molecular mass inhibition, Streptococcus pneumoniae type 14 capsular polysaccharide of polyvalent II was the most potent inhibitor; it was 2.1 x 10(4), 3.9 x 10(3) and 2.4 x 10(3) more active than Gal, tri-antennary II and monomeric II, respectively. Most type II-containing glycoproteins were also potent inhibitors, indicating that special polyvalent II and Galbeta1-related structures play critically important roles in lectin binding. Mapping all information available, it can be concluded that: [a] Galbeta1-->4GlcNAc (II) and some Galbeta1-related oligosaccharides, rather than GalNAc-related oligosaccharides, are the core structures for lectin binding; [b] their polyvalent II forms within macromolecules are a potent recognition force for ECL, while II monomer and oligo-antennary II forms play only a limited role in binding; [c] the shape of the lectin binding domains may correspond to a cavity type with Galbeta1-->4GlcNAc as the core binding site with additional one to four sugars subsites, and is most complementary to a linear trisaccharide, Galbeta1-->4GlcNAcbeta1-->6Gal. These analyses should facilitate the understanding of the binding function of ECL.
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Affiliation(s)
- Albert M Wu
- Glyco-Immunochemistry Research Laboratory, Institute of Molecular and Cellular Biology, Chang-Gung University, Kwei-san, Tao-yuan 333, Taiwan.
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