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2.
Glycoconj J ; 39(1): 83-97, 2022 02.
Article in English | MEDLINE | ID: covidwho-1813733

ABSTRACT

Plants contain an extended group of lectins differing from each other in their molecular structures, biochemical properties and carbohydrate-binding specificities. The heterogeneous group of plant lectins can be classified in several families based on the primary structure of the lectin domain. All proteins composed of one or more lectin domains, or having a domain architecture including one or more lectin domains in combination with other protein domains can be defined as lectins. Plant lectins reside in different cell compartments, and depending on their location will encounter a large variety carbohydrate structures, allowing them to be involved in multiple biological functions. Over the years lectins have been studied intensively for their carbohydrate-binding properties and biological activities, which also resulted in diverse applications. The present overview on plant lectins especially focuses on the structural and functional characteristics of plant lectins and their applications for crop improvement, glycobiology and biomedical research.


Subject(s)
Lectins , Plant Lectins , Agriculture , Glycomics , Humans , Lectins/metabolism , Plant Lectins/chemistry , Protein Domains
3.
Anal Bioanal Chem ; 413(29): 7305-7318, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1460297

ABSTRACT

The spike protein of SARS-CoV-2, the virus responsible for the global pandemic of COVID-19, is an abundant, heavily glycosylated surface protein that plays a key role in receptor binding and host cell fusion, and is the focus of all current vaccine development efforts. Variants of concern are now circulating worldwide that exhibit mutations in the spike protein. Protein sequence and glycosylation variations of the spike may affect viral fitness, antigenicity, and immune evasion. Global surveillance of the virus currently involves genome sequencing, but tracking emerging variants should include quantitative measurement of changes in site-specific glycosylation as well. In this work, we used data-dependent acquisition (DDA) and data-independent acquisition (DIA) mass spectrometry to quantitatively characterize the five N-linked glycosylation sites of the glycoprotein standard alpha-1-acid glycoprotein (AGP), as well as the 22 sites of the SARS-CoV-2 spike protein. We found that DIA compared favorably to DDA in sensitivity, resulting in more assignments of low-abundance glycopeptides. However, the reproducibility across replicates of DIA-identified glycopeptides was lower than that of DDA, possibly due to the difficulty of reliably assigning low-abundance glycopeptides confidently. The differences in the data acquired between the two methods suggest that DIA outperforms DDA in terms of glycoprotein coverage but that overall performance is a balance of sensitivity, selectivity, and statistical confidence in glycoproteomics. We assert that these analytical and bioinformatics methods for assigning and quantifying glycoforms would benefit the process of tracking viral variants as well as for vaccine development.


Subject(s)
Glycomics/methods , Mass Spectrometry/methods , Proteomics/methods , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , COVID-19/virology , Glycosylation , Humans , Limit of Detection , Reproducibility of Results , Spike Glycoprotein, Coronavirus/metabolism
5.
STAR Protoc ; 1(3): 100214, 2020 12 18.
Article in English | MEDLINE | ID: covidwho-1386744

ABSTRACT

This protocol describes an integrated approach for analyzing site-specific N- and O-linked glycosylation of SARS-CoV-2 spike protein by mass spectrometry. Glycoproteomics analyzes intact glycopeptides to examine site-specific microheterogeneity of glycoproteins. Glycomics provides structural characterization on any glycan assignments by glycoproteomics. This procedure can be modified and applied to a variety of N- and/or O-linked glycoproteins. Combined with bioinformatics, the glycomics-informed glycoproteomics may be useful in generating 3D molecular dynamics simulations of certain glycoproteins alone or interacting with one another. For complete details on the use and execution of this protocol, please refer to Zhao et al. (2020).


Subject(s)
Glycomics/methods , Glycoproteins , Proteomics/methods , Spike Glycoprotein, Coronavirus , COVID-19/virology , Glycoproteins/analysis , Glycoproteins/chemistry , Glycoproteins/metabolism , Glycosylation , Humans , Spike Glycoprotein, Coronavirus/analysis , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
6.
Int J Mol Sci ; 22(15)2021 Jul 28.
Article in English | MEDLINE | ID: covidwho-1346499

ABSTRACT

Glycosylation is a complex post-translational modification that conveys functional diversity to glycoconjugates. Cell surface glycosylation mediates several biological activities such as induction of the intracellular signaling pathway and pathogen recognition. Red blood cell (RBC) membrane N-glycans determine blood type and influence cell lifespan. Although several proteomic studies have been carried out, the glycosylation of RBC membrane proteins has not been systematically investigated. This work aims at exploring the human RBC N-glycome by high-sensitivity MALDI-MS techniques to outline a fingerprint of RBC N-glycans. To this purpose, the MALDI-TOF spectra of healthy subjects harboring different blood groups were acquired. Results showed the predominant occurrence of neutral and sialylated complex N-glycans with bisected N-acetylglucosamine and core- and/or antennary fucosylation. In the higher mass region, these species presented with multiple N-acetyllactosamine repeating units. Amongst the detected glycoforms, the presence of glycans bearing ABO(H) antigens allowed us to define a distinctive spectrum for each blood group. For the first time, advanced glycomic techniques have been applied to a comprehensive exploration of human RBC N-glycosylation, providing a new tool for the early detection of distinct glycome changes associated with disease conditions as well as for understanding the molecular recognition of pathogens.


Subject(s)
Blood Group Antigens/metabolism , Erythrocytes/metabolism , Glycomics , Polysaccharides/analysis , Protein Processing, Post-Translational , Glycosylation , Humans , Proteomics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
7.
Cells ; 10(7)2021 07 09.
Article in English | MEDLINE | ID: covidwho-1323127

ABSTRACT

Extracellular vesicles (EVs), comprising large microvesicles (MVs) and exosomes (EXs), play a key role in intercellular communication, both in physiological and in a wide variety of pathological conditions. However, the education of EV target cells has so far mainly been investigated as a function of EX cargo, while few studies have focused on the characterization of EV surface membrane molecules and the mechanisms that mediate the addressability of specific EVs to different cell types and tissues. Identifying these mechanisms will help fulfill the diagnostic, prognostic, and therapeutic promises fueled by our growing knowledge of EVs. In this review, we first discuss published studies on the presumed EV "delivery code" and on the combinations of the hypothesized EV surface membrane "sender" and "recipient" molecules that may mediate EV targeting in intercellular communication. Then we briefly review the main experimental approaches and techniques, and the bioinformatic tools that can be used to identify and characterize the structure and functional role of EV surface membrane molecules. In the final part, we present innovative techniques and directions for future research that would improve and deepen our understandings of EV-cell targeting.


Subject(s)
Extracellular Vesicles/metabolism , Animals , Biomarkers/metabolism , Glycomics , Humans , Models, Biological , Proteomics , Vaccines/immunology
9.
Front Immunol ; 12: 686240, 2021.
Article in English | MEDLINE | ID: covidwho-1285294

ABSTRACT

A disruption of the crosstalk between the gut and the lung has been implicated as a driver of severity during respiratory-related diseases. Lung injury causes systemic inflammation, which disrupts gut barrier integrity, increasing the permeability to gut microbes and their products. This exacerbates inflammation, resulting in positive feedback. We aimed to test whether severe Coronavirus disease 2019 (COVID-19) is associated with markers of disrupted gut permeability. We applied a multi-omic systems biology approach to analyze plasma samples from COVID-19 patients with varying disease severity and SARS-CoV-2 negative controls. We investigated the potential links between plasma markers of gut barrier integrity, microbial translocation, systemic inflammation, metabolome, lipidome, and glycome, and COVID-19 severity. We found that severe COVID-19 is associated with high levels of markers of tight junction permeability and translocation of bacterial and fungal products into the blood. These markers of disrupted intestinal barrier integrity and microbial translocation correlate strongly with higher levels of markers of systemic inflammation and immune activation, lower levels of markers of intestinal function, disrupted plasma metabolome and glycome, and higher mortality rate. Our study highlights an underappreciated factor with significant clinical implications, disruption in gut functions, as a potential force that may contribute to COVID-19 severity.


Subject(s)
COVID-19/immunology , Gastrointestinal Microbiome/immunology , Inflammation/immunology , Intestines/physiology , SARS-CoV-2/physiology , Female , Glycomics , Haptoglobins/metabolism , Humans , Lipidomics , Male , Metabolomics , Middle Aged , Permeability , Protein Precursors/metabolism , Tight Junctions/metabolism
10.
Glycobiology ; 31(3): 181-187, 2021 04 01.
Article in English | MEDLINE | ID: covidwho-1169666

ABSTRACT

The novel coronavirus SARS-CoV-2, the infective agent causing COVID-19, is having a global impact both in terms of human disease as well as socially and economically. Its heavily glycosylated spike glycoprotein is fundamental for the infection process, via its receptor-binding domains interaction with the glycoprotein angiotensin-converting enzyme 2 on human cell surfaces. We therefore utilized an integrated glycomic and glycoproteomic analytical strategy to characterize both N- and O- glycan site-specific glycosylation within the receptor-binding domain. We demonstrate the presence of complex-type N-glycans with unusual fucosylated LacdiNAc at both sites N331 and N343 and a single site of O-glycosylation on T323.


Subject(s)
COVID-19/virology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/metabolism , Binding Sites/genetics , COVID-19/metabolism , Carbohydrate Conformation , Carbohydrate Sequence , Glycomics , Glycosylation , HEK293 Cells , Host Microbial Interactions , Humans , Pandemics , Protein Binding , Protein Interaction Domains and Motifs , Proteomics , Receptors, Virus/chemistry , Receptors, Virus/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Spike Glycoprotein, Coronavirus/genetics
11.
OMICS ; 25(4): 234-241, 2021 04.
Article in English | MEDLINE | ID: covidwho-1165314

ABSTRACT

A key lesson emerging from COVID-19 is that pandemic proofing planetary health against future ecological crises calls for systems science and preventive medicine innovations. With greater proximity of the human and animal natural habitats in the 21st century, it is also noteworthy that zoonotic infections such as COVID-19 that jump from animals to humans are increasingly plausible in the coming decades. In this context, glycomics technologies and the third alphabet of life, the sugar code, offer veritable prospects to move omics systems science from discovery to diverse applications of relevance to global public health and preventive medicine. In this expert review, we discuss the science of glycomics, its importance in vaccine development, and the recent progress toward discoveries on the sugar code that can help prevent future infectious outbreaks that are looming on the horizon in the 21st century. Glycomics offers veritable prospects to boost planetary health, not to mention the global scientific capacity for vaccine innovation against novel and existing infectious agents.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/epidemiology , Glycomics/organization & administration , Pandemics/prevention & control , SARS-CoV-2/pathogenicity , Zoonoses/epidemiology , Animals , COVID-19/immunology , COVID-19/prevention & control , COVID-19/transmission , COVID-19 Vaccines/biosynthesis , Ecosystem , Global Health/economics , Global Health/trends , Humans , International Cooperation , Mass Vaccination/methods , Preventive Medicine/methods , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology , Vaccines, Synthetic/administration & dosage , Vaccines, Synthetic/biosynthesis , Zoonoses/immunology , Zoonoses/prevention & control , Zoonoses/transmission
12.
Nat Methods ; 18(1): 28, 2021 01.
Article in English | MEDLINE | ID: covidwho-1065919
13.
J Biol Chem ; 296: 100375, 2021.
Article in English | MEDLINE | ID: covidwho-1062444

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged during the last months of 2019, spreading throughout the world as a highly transmissible infectious illness designated as COVID-19. Vaccines have now appeared, but the challenges in producing sufficient material and distributing them around the world means that effective treatments to limit infection and improve recovery are still urgently needed. This review focuses on the relevance of different glycobiological molecules that could potentially serve as or inspire therapeutic tools during SARS-CoV-2 infection. As such, we highlight the glycobiology of the SARS-CoV-2 infection process, where glycans on viral proteins and on host glycosaminoglycans have critical roles in efficient infection. We also take notice of the glycan-binding proteins involved in the infective capacity of virus and in human defense. In addition, we critically evaluate the glycobiological contribution of candidate drugs for COVID-19 therapy such as glycans for vaccines, anti-glycan antibodies, recombinant lectins, lectin inhibitors, glycosidase inhibitors, polysaccharides, and numerous glycosides, emphasizing some opportunities to repurpose FDA-approved drugs. For the next-generation drugs suggested here, biotechnological engineering of new probes to block the SARS-CoV-2 infection might be based on the essential glycobiological insight on glycosyltransferases, glycans, glycan-binding proteins, and glycosidases related to this pathology.


Subject(s)
Antiviral Agents/therapeutic use , COVID-19/prevention & control , Drug Repositioning , Glycoside Hydrolase Inhibitors/therapeutic use , Glycosyltransferases/antagonists & inhibitors , Viral Proteins/antagonists & inhibitors , Antibodies, Neutralizing/therapeutic use , Antiviral Agents/chemistry , COVID-19/epidemiology , COVID-19/immunology , COVID-19/virology , Drug Design , Drug Discovery , Gene Expression , Glycomics/methods , Glycosaminoglycans/chemistry , Glycosaminoglycans/immunology , Glycosaminoglycans/metabolism , Glycosyltransferases/chemistry , Glycosyltransferases/genetics , Glycosyltransferases/immunology , Host-Pathogen Interactions/drug effects , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/immunology , Humans , Lectins/chemistry , Lectins/immunology , Lectins/metabolism , Polysaccharides/chemistry , Polysaccharides/immunology , Polysaccharides/metabolism , SARS-CoV-2/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Signal Transduction , Viral Proteins/chemistry , Viral Proteins/genetics , Viral Proteins/immunology
14.
Glycobiology ; 31(4): 410-424, 2021 05 03.
Article in English | MEDLINE | ID: covidwho-900424

ABSTRACT

The emergence of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created the need for development of new therapeutic strategies. Understanding the mode of viral attachment, entry and replication has become a key aspect of such interventions. The coronavirus surface features a trimeric spike (S) protein that is essential for viral attachment, entry and membrane fusion. The S protein of SARS-CoV-2 binds to human angiotensin converting enzyme 2 (hACE2) for entry. Herein, we describe glycomic and glycoproteomic analysis of hACE2 expressed in HEK293 cells. We observed high glycan occupancy (73.2 to 100%) at all seven possible N-glycosylation sites and surprisingly detected one novel O-glycosylation site. To deduce the detailed structure of glycan epitopes on hACE2 that may be involved in viral binding, we have characterized the terminal sialic acid linkages, the presence of bisecting GlcNAc and the pattern of N-glycan fucosylation. We have conducted extensive manual interpretation of each glycopeptide and glycan spectrum, in addition to using bioinformatics tools to validate the hACE2 glycosylation. Our elucidation of the site-specific glycosylation and its terminal orientations on the hACE2 receptor, along with the modeling of hACE2 glycosylation sites can aid in understanding the intriguing virus-receptor interactions and assist in the development of novel therapeutics to prevent viral entry. The relevance of studying the role of ACE2 is further increased due to some recent reports about the varying ACE2 dependent complications with regard to age, sex, race and pre-existing conditions of COVID-19 patients.


Subject(s)
Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , Polysaccharides/metabolism , SARS-CoV-2/physiology , COVID-19/virology , Glycomics , Glycosylation , HEK293 Cells , Humans , Protein Binding , Protein Conformation
15.
J Am Soc Mass Spectrom ; 31(10): 2013-2024, 2020 Oct 07.
Article in English | MEDLINE | ID: covidwho-744341

ABSTRACT

As corona virus disease 2019 (COVID-19) is a rapidly growing public health crisis across the world, our knowledge of meaningful diagnostic tests and treatment for severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is still evolving. This novel coronavirus disease COVID-19 can be diagnosed using RT-PCR, but inadequate access to reagents, equipment, and a nonspecific target has slowed disease detection and management. Precision medicine, individualized patient care, requires suitable diagnostics approaches to tackle the challenging aspects of viral outbreaks where many tests are needed in a rapid and deployable approach. Mass spectrometry (MS)-based technologies such as proteomics, glycomics, lipidomics, and metabolomics have been applied in disease outbreaks for identification of infectious disease agents such as virus and bacteria and the molecular phenomena associated with pathogenesis. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) is widely used in clinical diagnostics in the United States and Europe for bacterial pathogen identification. Paper spray ionization mass spectrometry (PSI-MS), a rapid ambient MS technique, has recently open a new opportunity for future clinical investigation to diagnose pathogens. Ultra-high-pressure liquid chromatography coupled high-resolution mass spectrometry (UHPLC-HRMS)-based metabolomics and lipidomics have been employed in large-scale biomedical research to discriminate infectious pathogens and uncover biomarkers associated with pathogenesis. PCR-MS has emerged as a new technology with the capability to directly identify known pathogens from the clinical specimens and the potential to identify genetic evidence of undiscovered pathogens. Moreover, miniaturized MS offers possible applications with relatively fast, highly sensitive, and potentially portable ways to analyze for viral compounds. However, beneficial aspects of these rapidly growing MS technologies in pandemics like COVID-19 outbreaks has been limited. Hence, this perspective gives a brief of the existing knowledge, current challenges, and opportunities for MS-based techniques as a promising avenue in studying emerging pathogen outbreaks such as COVID-19.


Subject(s)
Coronavirus Infections/etiology , Lipidomics/methods , Mass Spectrometry/methods , Metabolomics/methods , Pneumonia, Viral/etiology , Proteomics/methods , COVID-19 , COVID-19 Testing , Chromatography, High Pressure Liquid , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Glycomics/methods , Humans , Pandemics , Polymerase Chain Reaction , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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