1
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Xu T, Wang YC, Ma J, Cui Y, Wang L. In silico discovery and anti-tumor bioactivities validation of an algal lectin from Kappaphycus alvarezii genome. Int J Biol Macromol 2024:133311. [PMID: 38909728 DOI: 10.1016/j.ijbiomac.2024.133311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/25/2024]
Abstract
Lectins are proteins that bind specifically and reversibly to carbohydrates, and some of them have significant anti-tumor activities. Compared to those of lectins from land plants, there are far fewer studies on algal lectins, despite of the high biodiversity of algae. However, canonical strategies based on chromatographic feature-oriented screening cannot satisfy the requirement for algal lectin discovery. In this study, prospecting for novel OAAH family lectins throughout 358 genomes of red algae and cyanobacteria was conducted. Then 35 candidate lectins and 1843 of their simulated mutated forms were virtually screened based on predicted binding specificities to characteristic carbohydrates on cancer cells inferred by a deep learning model. A new lectin, named Siye, was discovered in Kappaphycus alvarezii genome and further verified on different cancer cells. Without causing agglutination of erythrocytes, Siye showed significant cytotoxicity to four human cancer cell lines (IC50 values ranging from 0.11 to 3.95 μg/ml), including breast adenocarcinoma HCC1937, lung carcinoma A549, liver cancer HepG2 and romyelocytic leukemia HL60. And the cytotoxicity was induced through promoting apoptosis by regulating the caspase and the p53 pathway within 24 h. This study testifies the feasibility and efficiency of the genome mining guided by evolutionary theory and artificial intelligence in the discovery of algal lectins.
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Affiliation(s)
- Tongli Xu
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266071, China
| | - Yin-Chu Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; National Basic Science Data Center, Beijing 100190, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Jiahao Ma
- Hong Kong University of Science and Technology, Clear Water Bay, 999077, Hong Kong
| | - Yulin Cui
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266071, China; Binzhou Medical University, Yantai 264003, China.
| | - Lu Wang
- School of Pharmacy, Yantai University, Yantai 264005, China.
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2
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [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: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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3
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Goumenou A, Chendo C, Combès A, Fournier T, Pichon V, Delaunay N. Characterization of Concanavalin A-based lectin sorbents for the extraction of the human chorionic gonadotropin glycoforms prior to analysis by nano liquid chromatography-high resolution mass spectrometry. J Pharm Biomed Anal 2024; 242:116022. [PMID: 38354538 DOI: 10.1016/j.jpba.2024.116022] [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: 12/08/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Human chorionic gonadotropin (hCG) is constituted of the hCGα and hCGβ subunits and is a highly glycosylated protein. Affinity supports based on immobilized Concanavalin A (Con A) lectin were used in solid phase extraction (SPE) to fractionate the hCG glycoforms according to their glycosylation state. For the first time, the lectin SPE fractions were off-line analysed by a nano liquid chromatography - high-resolution mass spectrometry (nanoLC-HRMS) method keeping the glycoforms intact. For this, home-made Con A sorbents were prepared by immobilizing lectin on Sepharose with a mean grafting yield of 98.2% (relative standard deviation (RSD) of 3.5%, n = 15). A capacity of about 100 μg of purified urinary hCG (uhCG) per ml of sorbent, grafted with a density of 10 mg of Con A per ml, was estimated. Average extraction yields of around 60% for both hCGα and hCGβ glycoforms were obtained after optimization of the extraction protocol. Intra- and inter-assay evaluation led to average RSD values of around 10%, indicating a repeatable extraction procedure. Similar results were obtained with commercial Con A-based sorbents but only after their 3rd use or after an extensive pre-conditioning step. Finally, the Con A SPE led to the fractionation of some glycoforms of uhCG, allowing the detection of an hCGα glycoform with two tetra-antennary N-glycans that couldn't be detected by direct analysis in nanoLC-HRMS without Con A SPE. Regarding a recombinant hCG, a fractionation was also observed leading to the detection of unretained hCGα glycoforms with tri-antennary N-glycans. Therefore, the combination of lectin SPE with intact protein analysis by nanoLC-HRMS can contribute to a more detailed glycosylation characterization of the hCG protein.
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Affiliation(s)
- Anastasia Goumenou
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France
| | - Christophe Chendo
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France
| | - Audrey Combès
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France
| | - Thierry Fournier
- Université Paris Cité, INSERM, "Pathophysiology & Pharmacotoxicology of the Human Placenta, pre & postnatal Microbiota", 3PHM, F-75006 Paris, France
| | - Valérie Pichon
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France; Sorbonne Université, Paris, France
| | - Nathalie Delaunay
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France.
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4
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Austin BK, Firooz A, Valafar H, Blenda AV. An Updated Overview of Existing Cancer Databases and Identified Needs. BIOLOGY 2023; 12:1152. [PMID: 37627037 PMCID: PMC10452211 DOI: 10.3390/biology12081152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Our search of existing cancer databases aimed to assess the current landscape and identify key needs. We analyzed 71 databases, focusing on genomics, proteomics, lipidomics, and glycomics. We found a lack of cancer-related lipidomic and glycomic databases, indicating a need for further development in these areas. Proteomic databases dedicated to cancer research were also limited. To assess overall progress, we included human non-cancer databases in proteomics, lipidomics, and glycomics for comparison. This provided insights into advancements in these fields over the past eight years. We also analyzed other types of cancer databases, such as clinical trial databases and web servers. Evaluating user-friendliness, we used the FAIRness principle to assess findability, accessibility, interoperability, and reusability. This ensured databases were easily accessible and usable. Our search summary highlights significant growth in cancer databases while identifying gaps and needs. These insights are valuable for researchers, clinicians, and database developers, guiding efforts to enhance accessibility, integration, and usability. Addressing these needs will support advancements in cancer research and benefit the wider cancer community.
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Affiliation(s)
- Brittany K. Austin
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
| | - Ali Firooz
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Homayoun Valafar
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Anna V. Blenda
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
- Prisma Health Cancer Institute, Prisma Health, Greenville, SC 29605, USA
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5
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Yale AR, Kim E, Gutierrez B, Hanamoto JN, Lav NS, Nourse JL, Salvatus M, Hunt RF, Monuki ES, Flanagan LA. Regulation of neural stem cell differentiation and brain development by MGAT5-mediated N-glycosylation. Stem Cell Reports 2023:S2213-6711(23)00141-8. [PMID: 37172586 DOI: 10.1016/j.stemcr.2023.04.007] [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: 12/01/2021] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
Undifferentiated neural stem and progenitor cells (NSPCs) encounter extracellular signals that bind plasma membrane proteins and influence differentiation. Membrane proteins are regulated by N-linked glycosylation, making it possible that glycosylation plays a critical role in cell differentiation. We assessed enzymes that control N-glycosylation in NSPCs and found that loss of the enzyme responsible for generating β1,6-branched N-glycans, N-acetylglucosaminyltransferase V (MGAT5), led to specific changes in NSPC differentiation in vitro and in vivo. Mgat5 homozygous null NSPCs in culture formed more neurons and fewer astrocytes compared with wild-type controls. In the brain cerebral cortex, loss of MGAT5 caused accelerated neuronal differentiation. Rapid neuronal differentiation led to depletion of cells in the NSPC niche, resulting in a shift in cortical neuron layers in Mgat5 null mice. Glycosylation enzyme MGAT5 plays a critical and previously unrecognized role in cell differentiation and early brain development.
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Affiliation(s)
- Andrew R Yale
- Department of Anatomy & Neurobiology, University of California Irvine, Irvine, CA 92697, USA; Department of Neurology, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Estelle Kim
- Department of Neurology, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Brenda Gutierrez
- Department of Anatomy & Neurobiology, University of California Irvine, Irvine, CA 92697, USA; Department of Neurology, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - J Nicole Hanamoto
- Department of Neurology, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Nicole S Lav
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Jamison L Nourse
- Department of Neurology, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Marc Salvatus
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Robert F Hunt
- Department of Anatomy & Neurobiology, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Edwin S Monuki
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA; Department of Pathology & Laboratory Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Lisa A Flanagan
- Department of Anatomy & Neurobiology, University of California Irvine, Irvine, CA 92697, USA; Department of Neurology, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA; Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA.
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6
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Lisacek F, Tiemeyer M, Mazumder R, Aoki-Kinoshita KF. Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS AU 2023; 3:4-12. [PMID: 36711080 PMCID: PMC9875223 DOI: 10.1021/jacsau.2c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
The GlySpace Alliance was formed in 2018 among the principal investigators of three major glycoscience portals: Glyco@Expasy, GlyCosmos, and GlyGen, representing Europe, Asia, and the United States, respectively. While each of these portals has its unique user interface, the aim is to provide the same basic data set of glycan-related omics data. These portals will be introduced with the aim to enable users to find their target information in the most efficient manner, in particular, in terms of the chemical structures of glycans and their functions.
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Affiliation(s)
- Frederique Lisacek
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, University of Geneva, Geneva CH-1227, Switzerland
- Computer
Science Department & Section of Biology, University of Geneva, Geneva CH-1227, Switzerland
| | - Michael Tiemeyer
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Raja Mazumder
- George
Washington University, Washington, District of Columbia 20037, United States
| | - Kiyoko F. Aoki-Kinoshita
- Glycan
and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo 192-8577, Japan
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7
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Ward EM, Zamora CY, Schocker NS, Ghosh S, Kizer ME, Imperiali B. Engineered Glycan-Binding Proteins for Recognition of the Thomsen-Friedenreich Antigen and Structurally Related Disaccharides. ACS Chem Biol 2023; 18:70-80. [PMID: 36525666 PMCID: PMC9868099 DOI: 10.1021/acschembio.2c00683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycan-binding proteins (GBPs) are widely used reagents for basic research and clinical applications. These reagents allow for the identification and manipulation of glycan determinants without specialized equipment or time-consuming experimental methods. Existing GBPs, mainly antibodies and lectins, are limited, and discovery or creation of reagents with novel specificities is time consuming and difficult. Here, we detail the generation of GBPs from a small, hyper-thermostable DNA-binding protein by directed evolution. Yeast surface display of a variable library of rcSso7d proteins was screened to find variants with selectivity toward the cancer-associated glycan Galβ1-3GalNAcα or Thomsen-Friedenreich antigen and various relevant disaccharides. Characterization of these proteins shows them to have specificities and affinities on par with currently available lectins. The proteins can be readily functionalized with fluorophores or biotin using sortase-mediated ligation to create reagents that prove useful for glycoprotein blotting and cell staining applications. The presented methods for the development of GBPs toward specific saccharides of interest will have great impact on both biomedical and glycobiological research.
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Affiliation(s)
- Elizabeth M. Ward
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA,Microbiology Graduate Program, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Cristina Y. Zamora
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA,Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Nathaniel S. Schocker
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA,Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Soumi Ghosh
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA,Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Megan E. Kizer
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA,Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA,Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA,Corresponding author
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8
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Kreth J, Merritt J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular ecological studies. FEMS Microbiol Rev 2023; 47:fuac052. [PMID: 36564013 PMCID: PMC9936263 DOI: 10.1093/femsre/fuac052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
A more comprehensive understanding of oral diseases like caries and periodontitis is dependent on an intimate understanding of the microbial ecological processes that are responsible for disease development. With this review, we provide a comprehensive overview of relevant molecular ecology techniques that have played critical roles in the current understanding of human oral biofilm development, interspecies interactions, and microbiome biogeography. The primary focus is on relevant technologies and examples available in the oral microbiology literature. However, most, if not all, of the described technologies should be readily adaptable for studies of microbiomes from other mucosal sites in the body. Therefore, this review is intended to serve as a reference guide used by microbiome researchers as they inevitably transition into molecular mechanistic studies of the many significant phenotypes observed clinically.
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Affiliation(s)
- Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
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9
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Radhakrishnan A, Chellapandian H, Ramasamy P, Jeyachandran S. Back2Basics: animal lectins: an insight into a highly versatile recognition protein. JOURNAL OF PROTEINS AND PROTEOMICS 2023; 14:43-59. [PMID: 36597476 PMCID: PMC9799708 DOI: 10.1007/s42485-022-00102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/15/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
The rapid advancement of molecular research has contributed to the discovery of 'Lectin', a carbohydrate-binding protein which specifically interacts with receptors on surface glycan moieties that regulate various critical cellular activities. The first animal lectin reported was 'the asialoglycoprotein receptor' in mammalian cells which helped analyze how animal lectins differ in glycoconjugate binding. Animal lectins are classified into several families, depending on their diverse cellular localization, and the binding specificities of their Carbohydrate-Recognition Domain (CRD) modules. Earlier characterization of animal lectins classified them into two structural families, the C-type (Ca2+-dependent binding) and S-type galectins (sulfhydryl-dependent binding) lectins. The C-type lectin includes the most significant animal lectins, such as endocytic receptors, mannose receptors, selectins, and collectins. The recent developments in research based on the complexity of the carbohydrate ligands, the metabolic processes they perform, their expression levels, and their reliance on divalent cations have identified more than 100 animal lectins and classified them into around 13 different families, such as Calnexin, F-lectin, Intelectin, Chitinase-like lectin, F-box lectin, etc. Understanding their structure and expression patterns have aided in defining their significant functions including cell adhesion, antimicrobial activity, innate immunity, disease diagnostic biomarkers, and drug delivery through specific carbohydrate-protein interactions. Such extensive potential roles of animal lectins made it equally important to plant lectins among researchers. Hence, the review focuses on providing an overview of animal lectins, their taxonomy, structural characteristics, and functions in diverse aspects interconnected to their specific carbohydrate and glycoconjugate binding. Graphical abstract
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Affiliation(s)
- Akshaya Radhakrishnan
- PG & Research Department of Biotechnology & Microbiology, National College, Tiruchirappalli, Tamil Nadu 620001 India
| | - Hethesh Chellapandian
- PG & Research Department of Biotechnology & Microbiology, National College, Tiruchirappalli, Tamil Nadu 620001 India
| | - Pasiyappazham Ramasamy
- Department of Physiology, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 600077 India
| | - Sivakamavalli Jeyachandran
- PG & Research Department of Biotechnology & Microbiology, National College, Tiruchirappalli, Tamil Nadu 620001 India
- Centre for Biotechnology & Biosignal Transduction, Department of Orthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 600077 India
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10
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Liu Y, Huang Y, Zhu R, Farag MA, Capanoglu E, Zhao C. Structural elucidation approaches in carbohydrates: A comprehensive review on techniques and future trends. Food Chem 2023; 400:134118. [DOI: 10.1016/j.foodchem.2022.134118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
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11
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Song Q, Li Q, Chao S, Chen X, Li R, Lu Y, Aastrup T, Pei Z. A dynamic reversible phenylboronic acid sensor for real-time determination of protein-carbohydrate interactions on living cancer cells. Chem Commun (Camb) 2022; 58:13731-13734. [PMID: 36444745 DOI: 10.1039/d2cc05788c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Real-time detection of glycosylation on label-free cancer cell surfaces is of significance for the diagnosis and treatment of cancer. In this work, we have successfully developed a novel dynamic reversible sensor based on pH-sensitive phenylboronic esters to determine in real-time the binding kinetics of protein-carbohydrate interactions on suspension cancer cell surfaces using a quartz crystal microbalance (QCM) technique.
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Affiliation(s)
- Quanquan Song
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, P. R. China.
| | - Qian Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, P. R. China.
| | - Shuang Chao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, P. R. China.
| | - Xian Chen
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, P. R. China.
| | - Ronghui Li
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism and College of Science & Technology, Hebei Agricultural University, Huanghua, Hebei 061100, China.
| | - Yuchao Lu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism and College of Science & Technology, Hebei Agricultural University, Huanghua, Hebei 061100, China.
| | | | - Zhichao Pei
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, P. R. China.
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12
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [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] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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13
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Ji T, Zhang J. Representation of polysaccharide molecules by SNFG and 3D-SNFG methods--Take Potentilla anserina L polysaccharide molecule as an example. Biochem Biophys Res Commun 2022; 617:7-10. [PMID: 35689844 DOI: 10.1016/j.bbrc.2022.05.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
With the continuous deepening of international research in the field of biology, more and more studies have found that polysaccharides have multiple biological functions, so that polysaccharides have gradually become the research objects of more and more scientists in the world, and a large number of relevant researchers have carried out Glycobiology research, most of the current research is on the separation, extraction, structural characterization and activity experiments of polysaccharides. However, at this stage, research on the structure-activity relationship of various polysaccharides extracted from plants is relatively rare, and the representation method of polysaccharide structures is not perfect, not unified, complicated in drawing, and not beautiful and convenient to read. The SNFG (Symbol Nomenclature For Glycans) method, which is the symbolic nomenclature of polysaccharides and the 3D-SNFG method, can solve the above problems well, and can use unified rules to describe and describe the molecular structure of polysaccharides, and the painting process is more convenient and more convenient. It is beautiful and makes it easier for readers to read. In this paper, the fern hemp polysaccharide molecule is taken as an example. After drawing it with chemoffice, SNFG and 3D-SNFG are used to describe it, and then compared. It is clear at a glance that the use of SNFG and 3D-SNFG methods has been widely recognized and accepted internationally, which can provide great convenience for sugar-related research and information exchange.
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Affiliation(s)
- Tengqi Ji
- Biology Science College of Northwest Normal University, Lanzhou, 730070, China
| | - Ji Zhang
- Biology Science College of Northwest Normal University, Lanzhou, 730070, China; New Rural Development Research Institute of Northwest Normal University, Lanzhou, 730070, China.
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14
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Aoki-Kinoshita KF. Functions of Glycosylation and Related Web Resources for Its Prediction. Methods Mol Biol 2022; 2499:135-144. [PMID: 35696078 DOI: 10.1007/978-1-0716-2317-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Glycosylation involves the attachment of carbohydrate sugar chains, or glycans, onto an amino acid residue of a protein. These glycans are often branched structures and serve to modulate the function of proteins. Glycans are synthesized through a complex process of enzymatic reactions that occur in the Golgi apparatus in mammalian systems. Because there is currently no sequencer for glycans, technologies such as mass spectrometry is used to characterize glycans in a biological sample to ascertain its glycome. This is a tedious process that requires high levels of expertise and equipment. Thus, the enzymes that work on glycans, called glycogenes or glycoenzymes, have been studied to better understand glycan function. With the development of glycan-related databases and a glycan repository, bioinformatics approaches have attempted to predict the glycosylation pathway and the glycosylation sites on proteins. This chapter introduces these methods and related Web resources for understanding glycan function.
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15
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Klamer ZL, Harris CM, Beirne JM, Kelly JE, Zhang J, Haab BB. OUP accepted manuscript. Glycobiology 2022; 32:679-690. [PMID: 35352123 PMCID: PMC9280547 DOI: 10.1093/glycob/cwac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/12/2022] Open
Abstract
Glycan arrays continue to be the primary resource for determining the glycan-binding specificity of proteins. The volume and diversity of glycan-array data are increasing, but no common method and resource exist to analyze, integrate, and use the available data. To meet this need, we developed a resource of analyzed glycan-array data called CarboGrove. Using the ability to process and interpret data from any type of glycan array, we populated the database with the results from 35 types of glycan arrays, 13 glycan families, 5 experimental methods, and 19 laboratories or companies. In meta-analyses of glycan-binding proteins, we observed glycan-binding specificities that were not uncovered from single sources. In addition, we confirmed the ability to efficiently optimize selections of glycan-binding proteins to be used in experiments for discriminating between closely related motifs. Through descriptive reports and a programmatically accessible Application Programming Interface, CarboGrove yields unprecedented access to the wealth of glycan-array data being produced and powerful capabilities for both experimentalists and bioinformaticians.
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Affiliation(s)
- Zachary L Klamer
- Department of Cancer and Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, United States
| | | | | | | | | | - Brian B Haab
- Corresponding author: Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49504, United States.
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16
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Imberty A, Bonnardel F, Lisacek F. UniLectin, A One-Stop-Shop to Explore and Study Carbohydrate-Binding Proteins. Curr Protoc 2021; 1:e305. [PMID: 34826352 DOI: 10.1002/cpz1.305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
All eukaryotic cells are covered with a dense layer of glycoconjugates, and the cell walls of bacteria are made of various polysaccharides, putting glycans in key locations for mediating protein-protein interactions at cell interfaces. Glycan function is therefore mainly defined as binding to other molecules, and lectins are proteins that specifically recognize and interact non-covalently with glycans. UniLectin was designed based on insight into the knowledge of lectins, their classification, and their biological role. This modular platform provides a curated and periodically updated classification of lectins along with a set of comparative and visualization tools, as well as structured results of screening comprehensive sequence datasets. UniLectin can be used to explore lectins, find precise information on glycan-protein interactions, and mine the results of predictive tools based on HMM profiles. This usage is illustrated here with two protocols. The first one highlights the fine-tuned role of the O blood group antigen in distinctive pathogen recognition, while the second compares the various bacterial lectin arsenals that clearly depend on living conditions of species even in the same genus. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Searching for the structural details of lectins binding the O blood group antigen Basic Protocol 2: Comparing the lectomes of related organisms in different environments.
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Affiliation(s)
- Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - François Bonnardel
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France.,SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department, UniGe, Geneva, Switzerland
| | - Frédérique Lisacek
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department, UniGe, Geneva, Switzerland.,Section of Biology, UniGe, Geneva, Switzerland
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17
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Goumenou A, Delaunay N, Pichon V. Recent Advances in Lectin-Based Affinity Sorbents for Protein Glycosylation Studies. Front Mol Biosci 2021; 8:746822. [PMID: 34778373 PMCID: PMC8585745 DOI: 10.3389/fmolb.2021.746822] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/23/2021] [Indexed: 01/29/2023] Open
Abstract
Glycosylation is one of the most significant post-translational modifications occurring to proteins, since it affects some of their basic properties, such as their half-life or biological activity. The developments in analytical methodologies has greatly contributed to a more comprehensive understanding of the quantitative and qualitative characteristics of the glycosylation state of proteins. Despite those advances, the difficulty of a full characterization of glycosylation still remains, mainly due to the complexity of the glycoprotein and/or glycopeptide mixture especially when they are present in complex biological samples. For this reason, various techniques that allow a prior selective enrichment of exclusively glycosylated proteins or glycopeptides have been developed in the past and are coupled either on- or off- line with separation and detection methods. One of the most commonly implemented enrichment methods includes the use of lectin proteins immobilized on various solid supports. Lectins are a group of different, naturally occurring proteins that share a common characteristic, which concerns their affinity for specific sugar moieties of glycoproteins. This review presents the different formats and conditions for the use of lectins in affinity chromatography and in solid phase extraction, including their use in dispersive mode, along with the recent progress made on either commercial or home-made lectin-based affinity sorbents, which can lead to a fast and automated glycosylation analysis.
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Affiliation(s)
- Anastasia Goumenou
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Nathalie Delaunay
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Valérie Pichon
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France.,Sorbonne University, Paris, France
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18
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Genetically encoded multivalent liquid glycan array displayed on M13 bacteriophage. Nat Chem Biol 2021; 17:806-816. [PMID: 33958792 PMCID: PMC8380037 DOI: 10.1038/s41589-021-00788-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA 'barcoded' M13 virions that display 30-1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins, such as CD22, on cells in vitro and immune cells in a live mouse. From a mixture of multivalent glycan probes, LiGAs identify the glycoconjugates with optimal avidity necessary for binding to lectins on living cells in vitro and in vivo.
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19
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Paton B, Suarez M, Herrero P, Canela N. Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis. Int J Mol Sci 2021; 22:ijms22115788. [PMID: 34071388 PMCID: PMC8198018 DOI: 10.3390/ijms22115788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Ageing is a complex process which implies the accumulation of molecular, cellular and organ damage, leading to an increased vulnerability to disease. In Western societies, the increase in the elderly population, which is accompanied by ageing-associated pathologies such as cardiovascular and mental diseases, is becoming an increasing economic and social burden for governments. In order to prevent, treat and determine which subjects are more likely to develop these age-related diseases, predictive biomarkers are required. In this sense, some studies suggest that glycans have a potential role as disease biomarkers, as they modify the functions of proteins and take part in intra- and intercellular biological processes. As the glycome reflects the real-time status of these interactions, its characterisation can provide potential diagnostic and prognostic biomarkers for multifactorial diseases. This review gathers the alterations in protein glycosylation profiles that are associated with ageing and age-related diseases, such as cancer, type 2 diabetes mellitus, metabolic syndrome and several chronic inflammatory diseases. Furthermore, the review includes the available techniques for the determination and characterisation of glycans, such as liquid chromatography, electrophoresis, nuclear magnetic resonance and mass spectrometry.
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Affiliation(s)
- Beatrix Paton
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Manuel Suarez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Correspondence: (M.S.); (P.H.)
| | - Pol Herrero
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
- Correspondence: (M.S.); (P.H.)
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
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20
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Nagai-Okatani C, Zou X, Fujita N, Sogabe I, Arakawa K, Nagai M, Angata K, Zhang Y, Aoki-Kinoshita KF, Kuno A. LM-GlycomeAtlas Ver. 2.0: An Integrated Visualization for Lectin Microarray-based Mouse Tissue Glycome Mapping Data with Lectin Histochemistry. J Proteome Res 2021; 20:2069-2075. [PMID: 33657805 DOI: 10.1021/acs.jproteome.0c00907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Laser microdissection-assisted lectin microarray has been used to obtain quantitative and qualitative information on glycans on proteins expressed in microscopic regions of formalin-fixed paraffin-embedded tissue sections. For the effective visualization of this "tissue glycome mapping" data, a novel online tool, LM-GlycomeAtlas (https://glycosmos.org/lm_glycomeatlas/index), was launched in the freely available glycoscience portal, the GlyCosmos Portal (https://glycosmos.org). In LM-GlycomeAtlas Version 1.0, nine tissues from normal mice were used to provide one data set of glycomic profiles. Here we introduce an updated version of LM-GlycomeAtlas, which includes more spatial information. We designed it to deposit multiple data sets of glycomic profiles with high-resolution histological images, which included staining images with multiple lectins on the array. The additionally implemented interfaces allow users to display multiple histological images of interest (e.g., diseased and normal mice), thereby facilitating the evaluation of tissue glycomic profiling and glyco-pathological analysis. Using these updated interfaces, 451 glycomic profiling data and 42 histological images obtained from 14 tissues of normal and diseased mice were successfully visualized. By easy integration with other tools for glycoproteomic data and protein glycosylation machinery, LM-GlycomeAtlas will be one of the most valuable open resources that contribute to both glycoscience and proteomics communities.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Noriaki Fujita
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Isami Sogabe
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Kouiti Arakawa
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Misugi Nagai
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kiyoko F Aoki-Kinoshita
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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21
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Bonnardel F, Mariethoz J, Pérez S, Imberty A, Lisacek F. LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. Nucleic Acids Res 2021; 49:D1548-D1554. [PMID: 33174598 PMCID: PMC7778903 DOI: 10.1093/nar/gkaa1019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
Lectins are non-covalent glycan-binding proteins mediating cellular interactions but their annotation in newly sequenced organisms is lacking. The limited size of functional domains and the low level of sequence similarity challenge usual bioinformatics tools. The identification of lectin domains in proteomes requires the manual curation of sequence alignments based on structural folds. A new lectin classification is proposed. It is built on three levels: (i) 35 lectin domain folds, (ii) 109 classes of lectins sharing at least 20% sequence similarity and (iii) 350 families of lectins sharing at least 70% sequence similarity. This information is compiled in the UniLectin platform that includes the previously described UniLectin3D database of curated lectin 3D structures. Since its first release, UniLectin3D has been updated with 485 additional 3D structures. The database is now complemented by two additional modules: PropLec containing predicted β-propeller lectins and LectomeXplore including predicted lectins from sequences of the NBCI-nr and UniProt for every curated lectin class. UniLectin is accessible at https://www.unilectin.eu/.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
- Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
| | - Serge Pérez
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
- Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
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22
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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23
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Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. Int J Mol Sci 2020; 21:ijms21249336. [PMID: 33302373 PMCID: PMC7762546 DOI: 10.3390/ijms21249336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 01/10/2023] Open
Abstract
Glycosylation plays a crucial role in various diseases and their etiology. This has led to a clear understanding on the functions of carbohydrates in cell communication, which eventually will result in novel therapeutic approaches for treatment of various disease. Glycomics has now become one among the top ten technologies that will change the future. The direct implication of glycosylation as a hallmark of cancer and for cancer therapy is well established. As in proteomics, where bioinformatics tools have led to revolutionary achievements, bioinformatics resources for glycosylation have improved its practical implication. Bioinformatics tools, algorithms and databases are a mandatory requirement to manage and successfully analyze large amount of glycobiological data generated from glycosylation studies. This review consolidates all the available tools and their applications in glycosylation research. The achievements made through the use of bioinformatics into glycosylation studies are also presented. The importance of glycosylation in cancer diagnosis and therapy is discussed and the gap in the application of widely available glyco-informatic tools for cancer research is highlighted. This review is expected to bring an awakening amongst glyco-informaticians as well as cancer biologists to bridge this gap, to exploit the available glyco-informatic tools for cancer.
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24
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Rodriguez EL, Poddar S, Iftekhar S, Suh K, Woolfork AG, Ovbude S, Pekarek A, Walters M, Lott S, Hage DS. Affinity chromatography: A review of trends and developments over the past 50 years. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1157:122332. [PMID: 32871378 PMCID: PMC7584770 DOI: 10.1016/j.jchromb.2020.122332] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022]
Abstract
The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.
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Affiliation(s)
| | - Saumen Poddar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Sazia Iftekhar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Ashley G Woolfork
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Susan Ovbude
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Allegra Pekarek
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Morgan Walters
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Shae Lott
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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25
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Kasai K. Frontal affinity chromatography: An excellent method of analyzing weak biomolecular interactions based on a unique principle. Biochim Biophys Acta Gen Subj 2020; 1865:129761. [PMID: 33086119 DOI: 10.1016/j.bbagen.2020.129761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Not only strong biomolecular interactions but also weak interactions play important roles in ensuring appropriate operations of many biological systems. Although a thorough investigation of the latter is essential in understanding life science, few suitable research tools are available because of inherent difficulties. SCOPE OF REVIEW Frontal affinity chromatography (FAC) is a versatile method that overcomes the inherent difficulties to provide accurate information on weak interactions. Since its concept and merit are not widely recognized, a comprehensive interpretation of FAC is provided in this review to encourage its application among researchers. MAJOR CONCLUSION FAC is based on a unique principle of measuring the binding strength by the delayed migration of an analyte through an affinity column. Its utility was elucidated via the lectin-glycan interactions. GENERAL SIGNIFICANCE FAC has a great potential as a research tool to solve many difficult problems in general bioscience that are relevant to almost all researchers.
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Affiliation(s)
- Kenichi Kasai
- Teikyo University, 2-11-1 Kaga, Itabashiku, Tokyo 1738605, Japan.
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26
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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27
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Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics. Int J Mol Sci 2020; 21:ijms21186727. [PMID: 32937895 PMCID: PMC7556027 DOI: 10.3390/ijms21186727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of glycobiology, glycomics, and glycoproteomics technologies, a large amount of glycoscience data has been generated. Subsequently, a number of glycobiology databases covering glycan structure, the glycosylation sites, the protein scaffolds, and related glycogenes have been developed to store, analyze, and integrate these data. However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins. In this study, the representative databases of glycan structure, glycoprotein, glycan-protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics are reviewed. We hope this overview could assist readers in searching for information on glycoproteins of interest, and promote further clinical application of glycobiology.
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28
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Xie Y, Sheng Y, Li Q, Ju S, Reyes J, Lebrilla CB. Determination of the glycoprotein specificity of lectins on cell membranes through oxidative proteomics. Chem Sci 2020; 11:9501-9512. [PMID: 34094216 PMCID: PMC8162070 DOI: 10.1039/d0sc04199h] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
The cell membrane is composed of a network of glycoconjugates including glycoproteins and glycolipids that presents a dense matrix of carbohydrates playing critical roles in many biological processes. Lectin-based technology has been widely used to characterize glycoconjugates in tissues and cell lines. However, their specificity toward their putative glycan ligand and sensitivity in situ have been technologically difficult to study. Additionally, because they recognize primarily glycans, the underlying glycoprotein targets are generally not known. In this study, we employed lectin proximity oxidative labeling (Lectin PROXL) to identify cell surface glycoproteins that contain glycans that are recognized by lectins. Commonly used lectins were modified with a probe to produce hydroxide radicals in the proximity of the labeled lectins. The underlying polypeptides of the glycoproteins recognized by the lectins are oxidized and identified by the standard proteomic workflow. As a result, approximately 70% of identified glycoproteins were oxidized in situ by all the lectin probes, while only 5% of the total proteins were oxidized. The correlation between the glycosites and oxidation sites demonstrated the effectiveness of the lectin probes. The specificity and sensitivity of each lectin were determined using site-specific glycan information obtained through glycomic and glycoproteomic analyses. Notably, the sialic acid-binding lectins and the fucose-binding lectins had higher specificity and sensitivity compared to other lectins, while those that were specific to high mannose glycans have poor sensitivity and specificity. This method offers an unprecedented view of the interactions of lectins with specific glycoproteins as well as protein networks that are mediated by specific glycan types on cell membranes.
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Affiliation(s)
- Yixuan Xie
- Department of Chemistry, University of California Davis Davis California USA
| | - Ying Sheng
- Department of Chemistry, Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis Davis California USA
| | - Qiongyu Li
- Department of Chemistry, University of California Davis Davis California USA
| | - Seunghye Ju
- Department of Chemistry, University of California Davis Davis California USA
| | - Joe Reyes
- Marine Science Institute, University of the Philippines Diliman Quezon City Philippines
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis Davis California USA
- Department of Biochemistry, University of California Davis Davis California USA
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29
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Angata K, Sawaki H, Tsujikawa S, Ocho M, Togayachi A, Narimatsu H. Glycogene Expression Profiling of Hepatic Cells by RNA-Seq Analysis for Glyco-Biomarker Identification. Front Oncol 2020; 10:1224. [PMID: 32850363 PMCID: PMC7402167 DOI: 10.3389/fonc.2020.01224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/15/2020] [Indexed: 01/01/2023] Open
Abstract
Glycans are primarily generated by “glycogenes,” which consist of more than 200 genes for glycosynthesis, including sugar-nucleotide synthases, sugar-nucleotide transporters, and glycosyltransferases. Measuring the expression level of glycogenes is one of the approaches to analyze the glycomes of particular biological and clinical samples. To develop an effective strategy for identifying the glycosylated biomarkers, we performed transcriptome analyses using quantitative real-time polymerase chain reaction (qRT-PCR) arrays and RNA sequencing (RNA-Seq). First, we measured and analyzed the transcriptome from the primary culture of human liver cells and hepatocarcinoma cells using RNA-Seq. This analysis revealed similar but distinctive expression profiles of glycogenes among hepatic cells as indicated by the qRT-PCR arrays, which determined a copy number of 186 glycogenes. Both data sets indicated that altered expression of glycosyltransferases affect the glycosylation of particular glycoproteins, which is consistent with the mass analysis data. Moreover, RNA-Seq analysis can uncover mutations in glycogenes and search differently expressed genes out of more than 50,000 distinct human gene transcripts including candidate biomarkers that were previously reported for hepatocarcinoma cells. Identification of candidate glyco-biomarkers from the expression profile of the glycogenes and proteins from liver cancer tissues available from public database emphasized the possibility that even though the expression level of biomarkers might not be altered, the expression of the glycogenes modifying biomarkers, generating glyco-biomarkers, might be different. Pathway analysis revealed that ~20% of the glycogenes exhibited different expression levels in normal and cancer cells. Thus, transcriptome analyses using both qRT-PCR array and RNA-Seq in combination with glycome and glycoproteome analyses can be advantageous to identify “glyco-biomarkers” by reinforcing information at the expression levels of both glycogenes and proteins.
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Affiliation(s)
- Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiromichi Sawaki
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Shigeko Tsujikawa
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Makoto Ocho
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Akira Togayachi
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hisashi Narimatsu
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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30
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Kightlinger W, Warfel KF, DeLisa MP, Jewett MC. Synthetic Glycobiology: Parts, Systems, and Applications. ACS Synth Biol 2020; 9:1534-1562. [PMID: 32526139 PMCID: PMC7372563 DOI: 10.1021/acssynbio.0c00210] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Protein glycosylation, the attachment of sugars to amino acid side chains, can endow proteins with a wide variety of properties of great interest to the engineering biology community. However, natural glycosylation systems are limited in the diversity of glycoproteins they can synthesize, the scale at which they can be harnessed for biotechnology, and the homogeneity of glycoprotein structures they can produce. Here we provide an overview of the emerging field of synthetic glycobiology, the application of synthetic biology tools and design principles to better understand and engineer glycosylation. Specifically, we focus on how the biosynthetic and analytical tools of synthetic biology have been used to redesign glycosylation systems to obtain defined glycosylation structures on proteins for diverse applications in medicine, materials, and diagnostics. We review the key biological parts available to synthetic biologists interested in engineering glycoproteins to solve compelling problems in glycoscience, describe recent efforts to construct synthetic glycoprotein synthesis systems, and outline exemplary applications as well as new opportunities in this emerging space.
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Affiliation(s)
- Weston Kightlinger
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, 123 Wing Drive, Ithaca, New York 14853, United States
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Weill Hall, Ithaca, New York 14853, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
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31
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Bonnardel F, Mariethoz J, Salentin S, Robin X, Schroeder M, Perez S, Lisacek F, Imberty A. UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. Nucleic Acids Res 2020; 47:D1236-D1244. [PMID: 30239928 PMCID: PMC6323968 DOI: 10.1093/nar/gky832] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 01/02/2023] Open
Abstract
Lectins, and related receptors such as adhesins and toxins, are glycan-binding proteins from all origins that decipher the glycocode, i.e. the structural information encoded in the conformation of complex carbohydrates present on the surface of all cells. Lectins are still poorly classified and annotated, but since their functions are based on ligand recognition, their 3D-structures provide a solid foundation for characterization. UniLectin3D is a curated database that classifies lectins on origin and fold, with cross-links to literature, other databases in glycosciences and functional data such as known specificity. The database provides detailed information on lectins, their bound glycan ligands, and features their interactions using the Protein–Ligand Interaction Profiler (PLIP) server. Special care was devoted to the description of the bound glycan ligands with the use of simple graphical representation and numerical format for cross-linking to other databases in glycoscience. We conceived the design of the database architecture and the navigation tools to account for all organisms, as well as to search for oligosaccharide epitopes complexed within specified binding sites. UniLectin3D is accessible at https://www.unilectin.eu/unilectin3D.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.,Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Xavier Robin
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,Computational Structural Biology Group, SIB Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland.,Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
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32
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Frontal Affinity Chromatography: A Highly Suitable Retardation Phenomenon-Based Research Tool for Analyzing Weak Interactions Between Biomolecules. Methods Mol Biol 2020. [PMID: 32306312 DOI: 10.1007/978-1-0716-0430-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The greatest advantage of frontal affinity chromatography (FAC) is that the analyte concentration does not need to be taken into consideration, and this renders FAC an extremely favorable analytical tool for weak interactions. In this short review, we propose a straightforward explanation of the underlying mechanism. When FAC is performed using analyte solutions at relatively high concentrations, concentration-dependent retardation is observed due to competition among analyte molecules, and the elution volume changes depending on the degree of saturation of the immobilized ligand.However, when the analyte concentration is very low, no competition occurs among the analytes, and the elution volume reaches a constant value, which reflects the proportion of bound state to free state of a single analyte molecule. Therefore, the binding strength can be determined using a minimum analyte concentration.
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33
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Bonnardel F, Perez S, Lisacek F, Imberty A. Structural Database for Lectins and the UniLectin Web Platform. Methods Mol Biol 2020; 2132:1-14. [PMID: 32306309 DOI: 10.1007/978-1-0716-0430-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The search for new biomolecules requires a clear understanding of biosynthesis and degradation pathways. This view applies to most metabolites as well as other molecule types such as glycans whose repertoire is still poorly characterized. Lectins are proteins that recognize specifically and interact noncovalently with glycans. This particular class of proteins is considered as playing a major role in biology. Glycan-binding is based on multivalence, which gives lectins a unique capacity to interact with surface glycans and significantly contribute to cell-cell recognition and interactions. Lectins have been studied for many years using multiple technologies and part of the resulting information is available online in databases. Unfortunately, the connectivity of these databases with the most popular omics databases (genomics, proteomics, and glycomics) remains limited. Moreover, lectin diversity is extended and requires setting out a flexible classification that remains compatible with new sequences and 3D structures that are continuously released. We have designed UniLectin as a new insight into the knowledge of lectins, their classification, and their biological role. This platform encompasses UniLectin3D, a curated database of lectin 3D structures that follows a periodically updated classification, a set of comparative and visualizing tools and gradually released modules dedicated to specific lectins predicted in sequence databases. The second module is PropLec, focused on β-propeller lectin prediction in all species based on five distinct family profiles. This chapter describes how UniLectin can be used to explore the diversity of lectins, their 3D structures, and associated functional information as well as to perform reliable predictions of β-propeller lectins.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department, UniGe, Geneva, Switzerland
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, Geneva, Switzerland. .,Computer Science Department, UniGe, Geneva, Switzerland. .,Section of Biology, UniGe, Geneva, Switzerland.
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France.
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34
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Lim B, Kydd L, Jaworski J. A Peptide-Lectin Fusion Strategy for Developing a Glycan Probe for Use in Various Assay Formats. CHEMOSENSORS 2019; 7. [PMID: 32793433 PMCID: PMC7423246 DOI: 10.3390/chemosensors7040055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
While nucleic acid and protein analysis approaches continue to see significant breakthroughs, analytical strategies for glycan determination have by comparison seen slower technological advances. Here we provide a strategy for glycan probe development using an engineered lectin fusion that can be incorporated into various common pathology lab assay formats including Western blot and agglutination assays. In this proof of concept, we use the natural lectin, Pseudomonas fluorescens agglutinin (PFA), capable of binding core Man alpha(1-3)-Man alpha(1-6)-Man units, where this lectin has previously been shown to bind to the glycans presented by the gp120 coat protein of (HIV) Human Immunodeficiency Virus. In our strategy, we engineered the lectin to possess a fusion of the biotin mimetic tag equence of amino acids V-S-H-P-Q-A-P-F. With the glycan receptive PFA directly linked to the biotin mimic, we could facilitate a probe for various standard clinical assay formats by virtue of coupling to streptavidin-HRP (horseradish peroxidase) or streptavidin beads for Western blot and agglutination assays respectively. We found the PFA fusion retained low nanomolar affinity for gp120 by ELISA (Enzyme Linked Immunosorbent Assay) and microscale thermophoresis. This probe engineering strategy proved effective in the relevant assay formats that may now allow detection for the presence of glycans containing the core Man alpha(1-3)-Man alpha(1-6)-Man units recognized by PFA.
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35
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Sakai K, Hiemori K, Tateno H, Hirabayashi J, Gonoi T. Fucose-specific lectin of Aspergillus fumigatus: binding properties and effects on immune response stimulation. Med Mycol 2019; 57:71-83. [PMID: 29370403 DOI: 10.1093/mmy/myx163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022] Open
Abstract
Aspergillus fumigatus is the major causative fungus of aspergillosis, and many studies have explored the relationship between A. fumigatus and pathogenicity. In the current study, we focused on a fucose-specific lectin, FleA, as a novel molecule which related to the pathogenicity of A. fumigatus. The disruption of the fleA gene did not lead to clear morphological changes compared to parental strain under several stress conditions in culture, but germination become earlier. In comparison with parental strain, the pathogenicity of disruptant was enhanced in a mouse infection model. The pattern of conidial phagocytosis and adhesion to cultured cells did not explain this enhanced pathogenicity. FleA was reported to contain six conserved fucose-binding sites; the analysis of constructed FleA point mutants revealed nonequivalent contribution of the fucose-binding sites to fucose binding. Based on the immune response induced in the cultured cells upon exposure to wild-type and mutant FleA, we propose a model of the FleA molecule in A. fumigatus infection.
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Affiliation(s)
- Kanae Sakai
- Medical Mycology Research Center, Chiba University, Japan
| | - Keiko Hiemori
- Department of Life Science and Biotechnology, Biotechnology Research Institute for Drug Discovery, AIST, Japan
| | - Hiroaki Tateno
- Department of Life Science and Biotechnology, Biotechnology Research Institute for Drug Discovery, AIST, Japan
| | - Jun Hirabayashi
- Department of Life Science and Biotechnology, Biotechnology Research Institute for Drug Discovery, AIST, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, Japan
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36
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Abstract
This chapter describes the Multiple Carbohydrate Alignment with Weights (MCAW) tool, which is available as a part of the RINGS (Resource for INformatics of Glycomes at Soka) website. It implements a combination of KCaM (Aoki, Yamaguchi, Ueda, et al., Nucl Acids Res 32:W267-W272, 2004), a pairwise glycan alignment algorithm, and ClustalW (Thompson, Higgins, Gibson, Nucleic Acids Res 22:4673-80, 1994), a weighted multiple protein sequence alignment algorithm. This tool computes the multiple glycan alignment by first computing a guide tree to determine the order by which to progressively add glycans to the multiple alignment. The dynamic programming algorithm results in a glycan profile of the alignment glycans, containing "monosaccharide positions" indicating the ratio of monosaccharides and their glycosidic bonds that are aligned at the corresponding position. This tool has been used to analyze databases of glycan array experimental data, incorporating weights to reflect the biological significance of certain glycans over others. As a result, it has been shown that the alignments obtained are biologically relevant, matching the results as found in the literature.
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37
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Bernardi B, Kayacan Y, Wendland J. Expansion of a Telomeric FLO/ALS-Like Sequence Gene Family in Saccharomycopsis fermentans. Front Genet 2018; 9:536. [PMID: 30542368 PMCID: PMC6277891 DOI: 10.3389/fgene.2018.00536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023] Open
Abstract
Non-Saccharomyces species have been recognized for their beneficial contribution to fermented food and beverages based on their volatile compound formation and their ability to ferment glucose into ethanol. At the end of fermentation brewer's yeast flocculate which provides an easy means of separation of yeasts from green beer. Flocculation in Saccharomyces cerevisiae requires a set of flocculation genes. These FLO-genes, FLO1, FLO5, FLO9, FLO10, and FLO11, are located at telomeres and transcription of these adhesins is regulated by Flo8 and Mss11. Here, we show that Saccharomycopsis fermentans, an ascomycete yeast distantly related to S. cerevisiae, possesses a very large FLO/ALS-like Sequence (FAS) family encompassing 34 genes. Fas proteins are variable in size and divergent in sequence and show similarity to the Flo1/5/9 family. Fas proteins show the general build with a signal peptide, an N-terminal carbohydrate binding PA14 domain, a central region differing by the number of repeats and a C-terminus with a consensus sequence for GPI-anchor attachment. Like FLO genes in S. cerevisiae, FAS genes are mostly telomeric with several paralogs at each telomere. We term such genes that share evolutionary conserved telomere localization "telologs" and provide several other examples. Adhesin expression in S. cerevisiae and filamentation in Candida albicans is regulated by Flo8 and Mss11. In Saccharomycopsis we identified only a single protein with similarity to Flo8 based on sequence similarity and the presence of a LisH domain.
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Affiliation(s)
- Beatrice Bernardi
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yeseren Kayacan
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jürgen Wendland
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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38
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Hirano M. An Endocytic Receptor, Megalin-Ligand Interactions: Effects of Glycosylation. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1752.1j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Hirano M. An Endocytic Receptor, Megalin-Ligand Interactions: Effects of Glycosylation. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1752.1e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Gadde R, Cd D, Sheela SR. Placental protein 13: An important biological protein in preeclampsia. J Circ Biomark 2018; 7:1849454418786159. [PMID: 30023011 PMCID: PMC6047241 DOI: 10.1177/1849454418786159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/28/2018] [Indexed: 12/26/2022] Open
Abstract
Placental protein 13 (PP13), a glycan binding protein predominantly expressed in syncytiotrophoblast, dimeric in nature, lacks N-terminal signal peptide, bypasses the endoplasmic reticulum, and secretes into maternal circulation as exosomes or microvesicles. PP13 has jelly roll fold conformation with conserved carbohydrate recognition domain which specifically binds to β-galactosides of the glycan receptors during placentation. PP13 binds to glycosylated receptors on human erythrocytes and brings about hemagglutination by the property of lectin activity; other functions are immunoregulation and vasodilation during placentation and vascularization. The gene LGALS13 located on 19q13.2 comprising four exons expresses a 32-kDa protein with 139 amino acid residues, PP13. Impaired expression due to mutation in the gene leads to a nonfunctional truncated PP13. The low serum levels predict high risk for the onset of preeclampsia or obstetric complications. Hence, PP13 turned to be an early marker for risk assessment of preeclampsia. The recombinant PP13 and monoclonal antibodies availability help for replenishing PP13 in conditions with low serum levels and for detection and prevention of preeclampsia, respectively.
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Affiliation(s)
- Ranjeeta Gadde
- Department of Biochemistry, Sri Devaraj Urs Medical College, Kolar, India
| | - Dayanand Cd
- Department of Biochemistry, Sri Devaraj Urs Medical College, Kolar, India
| | - S R Sheela
- Department of Obstetrics and Gynecology, Sri Devaraj Urs Medical College, Kolar, India
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41
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Iwaki J, Hirabayashi J. Carbohydrate-Binding Specificity of Human Galectins: An Overview by Frontal Affinity Chromatography. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1728.1sj] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jun Iwaki
- National Institute of Advanced Industrial Science and Technology
| | - Jun Hirabayashi
- National Institute of Advanced Industrial Science and Technology
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42
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Iwaki J, Hirabayashi J. Carbohydrate-Binding Specificity of Human Galectins: An Overview by Frontal Affinity Chromatography. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1728.1se] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jun Iwaki
- National Institute of Advanced Industrial Science and Technology
| | - Jun Hirabayashi
- National Institute of Advanced Industrial Science and Technology
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43
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Dosekova E, Filip J, Bertok T, Both P, Kasak P, Tkac J. Nanotechnology in Glycomics: Applications in Diagnostics, Therapy, Imaging, and Separation Processes. Med Res Rev 2017; 37:514-626. [PMID: 27859448 PMCID: PMC5659385 DOI: 10.1002/med.21420] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/08/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022]
Abstract
This review comprehensively covers the most recent achievements (from 2013) in the successful integration of nanomaterials in the field of glycomics. The first part of the paper addresses the beneficial properties of nanomaterials for the construction of biosensors, bioanalytical devices, and protocols for the detection of various analytes, including viruses and whole cells, together with their key characteristics. The second part of the review focuses on the application of nanomaterials integrated with glycans for various biomedical applications, that is, vaccines against viral and bacterial infections and cancer cells, as therapeutic agents, for in vivo imaging and nuclear magnetic resonance imaging, and for selective drug delivery. The final part of the review describes various ways in which glycan enrichment can be effectively done using nanomaterials, molecularly imprinted polymers with polymer thickness controlled at the nanoscale, with a subsequent analysis of glycans by mass spectrometry. A short section describing an active glycoprofiling by microengines (microrockets) is covered as well.
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Affiliation(s)
- Erika Dosekova
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Jaroslav Filip
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Tomas Bertok
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Peter Both
- School of Chemistry, Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Peter Kasak
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Jan Tkac
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
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Hirano M, Totani K, Fukuda T, Gu J, Suzuki A. N-Glycoform-dependent interactions of megalin with its ligands. Biochim Biophys Acta Gen Subj 2017; 1861:3106-3118. [DOI: 10.1016/j.bbagen.2016.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/30/2016] [Accepted: 10/19/2016] [Indexed: 12/18/2022]
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Preparation of a polyclonal antibody that recognizes a unique galactoseβ1-4fucose disaccharide epitope. Carbohydr Res 2015; 412:50-5. [DOI: 10.1016/j.carres.2015.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/13/2015] [Accepted: 04/22/2015] [Indexed: 11/19/2022]
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Takeuchi T, Tamura M, Ishii N, Ishikida H, Sugimoto S, Suzuki D, Nishiyama K, Takahashi H, Natsugari H, Arata Y. Purification of galectin-1 mutants using an immobilized Galactoseβ1-4Fucose affinity adsorbent. Protein Expr Purif 2015; 111:82-6. [PMID: 25858314 DOI: 10.1016/j.pep.2015.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/19/2022]
Abstract
Galectins are a family of lectins characterized by their carbohydrate recognition domains containing eight conserved amino acid residues, which allows the binding of galectin to β-galactoside sugars such as Galβ1-4GlcNAc. Since galectin-glycan interactions occur extracellularly, recombinant galectins are often used for the functional analysis of these interactions. Although it is relatively easy to purify galectins via affinity to Galβ1-4GlcNAc using affinity adsorbents such as asialofetuin-Sepharose, it could be difficult to do so with mutated galectins, which may have reduced affinity towards their endogenous ligands. However, this is not the case with Caenorhabditis elegans galectin LEC-6; binding to its endogenous recognition unit Galβ1-4Fuc, a unique disaccharide found only in invertebrates, is not necessarily affected by point mutations of the eight well-conserved amino acids. In this study, we constructed mutants of mouse galectin-1 carrying substitutions of each of the eight conserved amino acid residues (H44F, N46D, R48H, V59A, N61D, W68F, E71Q, and R73H) and examined their affinity for Galβ1-4GlcNAc and Galβ1-4Fuc. These mutants, except W68F, had very low affinity for asialofetuin-Sepharose; however, most of them (with the exception of H44F and R48H) could be purified using Galβ1-4Fuc-Sepharose. The affinity of the purified mutant galectins for glycans containing Galβ1-4Fuc or Galβ1-4GlcNAc moieties was quantitatively examined by frontal affinity chromatography, and the results indicated that the mutants retained the affinity only for Galβ1-4Fuc. Given that other mammalian galectins are known to bind Galβ1-4Fuc, our data suggest that immobilized Galβ1-4Fuc ligands could be generally used for easy one-step affinity purification of mutant galectins.
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Affiliation(s)
- Tomoharu Takeuchi
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan.
| | - Mayumi Tamura
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Nobuaki Ishii
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Hiroki Ishikida
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Saori Sugimoto
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Daichi Suzuki
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Kazusa Nishiyama
- Laboratory of Synthetic Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
| | - Hideyo Takahashi
- Laboratory of Synthetic Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
| | - Hideaki Natsugari
- Laboratory of Synthetic Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
| | - Yoichiro Arata
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
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