51
|
Smith DF, Cummings RD. Application of microarrays for deciphering the structure and function of the human glycome. Mol Cell Proteomics 2013; 12:902-12. [PMID: 23412570 DOI: 10.1074/mcp.r112.027110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Glycan structures were defined historically using multiple methods to determine composition, sequence, linkage, and anomericity of component monosaccharides. Such approaches have been replaced by more sensitive MS methods to profile or predict glycan structures, but these methods are limited in their ability to completely define glycan structures. Glycan-binding proteins, including lectins and antibodies, have been found to have exquisite binding specificities that can provide information about glycan structures. Here, we show glycan-binding proteins can be used along with MS to help define glycan linkages and other determinants in unknown glycans printed as shotgun glycan microarrays.
Collapse
Affiliation(s)
- David F Smith
- Department of Biochemistry and Glycomics Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
| | | |
Collapse
|
52
|
Kuzmanov U, Kosanam H, Diamandis EP. The sweet and sour of serological glycoprotein tumor biomarker quantification. BMC Med 2013; 11:31. [PMID: 23390961 PMCID: PMC3751898 DOI: 10.1186/1741-7015-11-31] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 12/25/2022] Open
Abstract
Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.
Collapse
Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, 6th floor, 60 Murray Street, Box 32, Toronto, ON M5T 3L9, Canada
| | | | | |
Collapse
|
53
|
Li F, Glinskii OV, Glinsky VV. Glycobioinformatics: Current strategies and tools for data mining in MS-based glycoproteomics. Proteomics 2012; 13:341-54. [DOI: 10.1002/pmic.201200149] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 10/06/2012] [Accepted: 11/06/2012] [Indexed: 12/18/2022]
|
54
|
Dani N, Nahm M, Lee S, Broadie K. A targeted glycan-related gene screen reveals heparan sulfate proteoglycan sulfation regulates WNT and BMP trans-synaptic signaling. PLoS Genet 2012; 8:e1003031. [PMID: 23144627 PMCID: PMC3493450 DOI: 10.1371/journal.pgen.1003031] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/26/2012] [Indexed: 12/14/2022] Open
Abstract
A Drosophila transgenic RNAi screen targeting the glycan genome, including all N/O/GAG-glycan biosynthesis/modification enzymes and glycan-binding lectins, was conducted to discover novel glycan functions in synaptogenesis. As proof-of-product, we characterized functionally paired heparan sulfate (HS) 6-O-sulfotransferase (hs6st) and sulfatase (sulf1), which bidirectionally control HS proteoglycan (HSPG) sulfation. RNAi knockdown of hs6st and sulf1 causes opposite effects on functional synapse development, with decreased (hs6st) and increased (sulf1) neurotransmission strength confirmed in null mutants. HSPG co-receptors for WNT and BMP intercellular signaling, Dally-like Protein and Syndecan, are differentially misregulated in the synaptomatrix of these mutants. Consistently, hs6st and sulf1 nulls differentially elevate both WNT (Wingless; Wg) and BMP (Glass Bottom Boat; Gbb) ligand abundance in the synaptomatrix. Anterograde Wg signaling via Wg receptor dFrizzled2 C-terminus nuclear import and retrograde Gbb signaling via synaptic MAD phosphorylation and nuclear import are differentially activated in hs6st and sulf1 mutants. Consequently, transcriptional control of presynaptic glutamate release machinery and postsynaptic glutamate receptors is bidirectionally altered in hs6st and sulf1 mutants, explaining the bidirectional change in synaptic functional strength. Genetic correction of the altered WNT/BMP signaling restores normal synaptic development in both mutant conditions, proving that altered trans-synaptic signaling causes functional differentiation defects.
Collapse
Affiliation(s)
- Neil Dani
- Department of Biological Sciences and Department of Cell and Developmental Biology, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Minyeop Nahm
- Department of Cell and Developmental Biology, Seoul National University, Seoul, Republic of Korea
| | - Seungbok Lee
- Department of Cell and Developmental Biology, Seoul National University, Seoul, Republic of Korea
| | - Kendal Broadie
- Department of Biological Sciences and Department of Cell and Developmental Biology, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee, United States of America
| |
Collapse
|
55
|
Therapies and therapeutic approaches in Congenital Disorders of Glycosylation. Glycoconj J 2012; 30:77-84. [DOI: 10.1007/s10719-012-9447-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 09/03/2012] [Indexed: 01/05/2023]
|
56
|
Nilsson J, Halim A, Grahn A, Larson G. Targeting the glycoproteome. Glycoconj J 2012; 30:119-36. [PMID: 22886069 PMCID: PMC3552370 DOI: 10.1007/s10719-012-9438-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/06/2012] [Accepted: 07/26/2012] [Indexed: 12/12/2022]
Abstract
Despite numerous original publications describing the structural complexity of N- and O-linked glycans on glycoproteins, only very few answer the basic question of which particular glycans are linked to which amino acid residues along the polypeptide chain. Such structural information is of fundamental importance for understanding the biological roles of complex glycosylations as well as deciphering their non-template driven biosynthesis. This review focuses on presenting and commenting on recent strategies, specifically aimed at identifying the glycoproteome of cultured cells and biological samples, using targeted and global enrichment procedures and utilizing the high resolution power, high through-put capacity and complementary fragmentation techniques of tandem mass spectrometry. The goal is to give an update of this emerging field of protein and glyco-sciences and suggest routes to bridge the data gap between the two aspects of glycoprotein characteristics, i.e. glycan structures and their attachment sites.
Collapse
Affiliation(s)
- Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
| | | | | | | |
Collapse
|
57
|
Foulquier F, Amyere M, Jaeken J, Zeevaert R, Schollen E, Race V, Bammens R, Morelle W, Rosnoblet C, Legrand D, Demaegd D, Buist N, Cheillan D, Guffon N, Morsomme P, Annaert W, Freeze H, Van Schaftingen E, Vikkula M, Matthijs G. TMEM165 deficiency causes a congenital disorder of glycosylation. Am J Hum Genet 2012; 91:15-26. [PMID: 22683087 DOI: 10.1016/j.ajhg.2012.05.002] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/02/2012] [Accepted: 05/01/2012] [Indexed: 11/25/2022] Open
Abstract
Protein glycosylation is a complex process that depends not only on the activities of several enzymes and transporters but also on a subtle balance between vesicular Golgi trafficking, compartmental pH, and ion homeostasis. Through a combination of autozygosity mapping and expression analysis in two siblings with an abnormal serum-transferrin isoelectric focusing test (type 2) and a peculiar skeletal phenotype with epiphyseal, metaphyseal, and diaphyseal dysplasia, we identified TMEM165 (also named TPARL) as a gene involved in congenital disorders of glycosylation (CDG). The affected individuals are homozygous for a deep intronic splice mutation in TMEM165. In our cohort of unsolved CDG-II cases, we found another individual with the same mutation and two unrelated individuals with missense mutations in TMEM165. TMEM165 encodes a putative transmembrane 324 amino acid protein whose cellular functions are unknown. Using a siRNA strategy, we showed that TMEM165 deficiency causes Golgi glycosylation defects in HEK cells.
Collapse
|
58
|
Bennett EP, Mandel U, Clausen H, Gerken TA, Fritz TA, Tabak LA. Control of mucin-type O-glycosylation: a classification of the polypeptide GalNAc-transferase gene family. Glycobiology 2012; 22:736-56. [PMID: 22183981 PMCID: PMC3409716 DOI: 10.1093/glycob/cwr182] [Citation(s) in RCA: 612] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 12/14/2011] [Accepted: 12/14/2011] [Indexed: 12/15/2022] Open
Abstract
Glycosylation of proteins is an essential process in all eukaryotes and a great diversity in types of protein glycosylation exists in animals, plants and microorganisms. Mucin-type O-glycosylation, consisting of glycans attached via O-linked N-acetylgalactosamine (GalNAc) to serine and threonine residues, is one of the most abundant forms of protein glycosylation in animals. Although most protein glycosylation is controlled by one or two genes encoding the enzymes responsible for the initiation of glycosylation, i.e. the step where the first glycan is attached to the relevant amino acid residue in the protein, mucin-type O-glycosylation is controlled by a large family of up to 20 homologous genes encoding UDP-GalNAc:polypeptide GalNAc-transferases (GalNAc-Ts) (EC 2.4.1.41). Therefore, mucin-type O-glycosylation has the greatest potential for differential regulation in cells and tissues. The GalNAc-T family is the largest glycosyltransferase enzyme family covering a single known glycosidic linkage and it is highly conserved throughout animal evolution, although absent in bacteria, yeast and plants. Emerging studies have shown that the large number of genes (GALNTs) in the GalNAc-T family do not provide full functional redundancy and single GalNAc-T genes have been shown to be important in both animals and human. Here, we present an overview of the GalNAc-T gene family in animals and propose a classification of the genes into subfamilies, which appear to be conserved in evolution structurally as well as functionally.
Collapse
Affiliation(s)
- Eric P Bennett
- Department of Odontology, Copenhagen Center for Glycomics, University of Copenhagen, Nørre Alle 20, DK-2200 Copenhagen N, Denmark.
| | | | | | | | | | | |
Collapse
|
59
|
Markiv A, Rambaruth NDS, Dwek MV. Beyond the genome and proteome: targeting protein modifications in cancer. Curr Opin Pharmacol 2012; 12:408-13. [PMID: 22560919 DOI: 10.1016/j.coph.2012.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/30/2012] [Accepted: 04/11/2012] [Indexed: 12/31/2022]
Abstract
Nearly all proteins are modified in post translational events, indeed, understanding the control and function of post translational modifications (PTMs) is arguably the 'next frontier' for cancer cell biologists. The most well understood PTMs include glycosylation, phosphorylation, ubiquitination, methylation and palmitylation. Each of these modifications has been observed to be altered in cancer, affecting key cellular pathways including signal transduction, cell membrane receptor function, and protein-protein interactions. A number of strategies have been proposed that aim to target the modified proteins themselves, the enzymes that construct them, or that boost host-cellular immunity against modified residues aberrantly expressed in cancer.
Collapse
Affiliation(s)
- Anatoliy Markiv
- Department of Molecular and Applied Biosciences, School of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
| | | | | |
Collapse
|
60
|
Dani N, Broadie K. Glycosylated synaptomatrix regulation of trans-synaptic signaling. Dev Neurobiol 2012; 72:2-21. [PMID: 21509945 DOI: 10.1002/dneu.20891] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Synapse formation is driven by precisely orchestrated intercellular communication between the presynaptic and the postsynaptic cell, involving a cascade of anterograde and retrograde signals. At the neuromuscular junction (NMJ), both neuron and muscle secrete signals into the heavily glycosylated synaptic cleft matrix sandwiched between the two synapsing cells. These signals must necessarily traverse and interact with the extracellular environment, for the ligand-receptor interactions mediating communication to occur. This complex synaptomatrix, rich in glycoproteins and proteoglycans, comprises heterogeneous, compartmentalized domains where specialized glycans modulate trans-synaptic signaling during synaptogenesis and subsequent synapse modulation. The general importance of glycans during development, homeostasis and disease is well established, but this important molecular class has received less study in the nervous system. Glycan modifications are now understood to play functional and modulatory roles as ligands and co-receptors in numerous tissues; however, roles at the synapse are relatively unexplored. We highlight here properties of synaptomatrix glycans and glycan-interacting proteins with key roles in synaptogenesis, with a particular focus on recent advances made in the Drosophila NMJ genetic system. We discuss open questions and interesting new findings driving this investigation of complex, diverse, and largely understudied glycan mechanisms at the synapse.
Collapse
Affiliation(s)
- Neil Dani
- Department of Biological Sciences, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee 37232, USA
| | | |
Collapse
|
61
|
Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genet Med 2012; 13:921-32. [PMID: 21811164 DOI: 10.1097/gim.0b013e318226fbf2] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Congenital disorders of glycosylation are a heterogeneous group of disorders caused by deficient glycosylation, primarily affecting the N-linked pathway. It is estimated that more than 40% of congenital disorders of glycosylation patients lack a confirmatory molecular diagnosis. The purpose of this study was to improve molecular diagnosis for congenital disorders of glycosylation by developing and validating a next generation sequencing panel for comprehensive mutation detection in 24 genes known to cause congenital disorders of glycosylation. METHODS Next generation sequencing validation was performed on 12 positive control congenital disorders of glycosylation patients. These samples were blinded as to the disease-causing mutations. Both RainDance and Fluidigm platforms were used for sequence enrichment and targeted amplification. The SOLiD platform was used for sequencing the amplified products. Bioinformatic analysis was performed using NextGENe® software. RESULTS The disease-causing mutations were identified by next generation sequencing for all 12 positive controls. Additional variants were also detected in three controls that are known or predicted to impair gene function and may contribute to the clinical phenotype. CONCLUSIONS We conclude that development of next generation sequencing panels in the diagnostic laboratory where multiple genes are implicated in a disorder is more cost-effective and will result in improved and faster patient diagnosis compared with a gene-by-gene approach. Recommendations are also provided for data analysis from the next generation sequencing-derived data in the clinical laboratory, which will be important for the widespread use of this technology.
Collapse
|
62
|
Jones MA, Ng BG, Bhide S, Chin E, Rhodenizer D, He P, Losfeld ME, He M, Raymond K, Berry G, Freeze HH, Hegde MR. DDOST mutations identified by whole-exome sequencing are implicated in congenital disorders of glycosylation. Am J Hum Genet 2012; 90:363-8. [PMID: 22305527 DOI: 10.1016/j.ajhg.2011.12.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 12/12/2011] [Accepted: 12/30/2011] [Indexed: 01/16/2023] Open
Abstract
Congenital disorders of glycosylation (CDG) are inherited autosomal-recessive diseases that impair N-glycosylation. Approximately 20% of patients do not survive beyond the age of 5 years old as a result of widespread organ dysfunction. Although most patients receive a CDG diagnosis based on abnormal glycosylation of transferrin, this test cannot provide a genetic diagnosis; indeed, many patients with abnormal transferrin do not have mutations in any known CDG genes. Here, we combined biochemical analysis with whole-exome sequencing (WES) to identify the genetic defect in an untyped CDG patient, and we found a 22 bp deletion and a missense mutation in DDOST, whose product is a component of the oligosaccharyltransferase complex that transfers the glycan chain from a lipid carrier to nascent proteins in the endoplasmic reticulum lumen. Biochemical analysis with three biomarkers revealed that N-glycosylation was decreased in the patient's fibroblasts. Complementation with wild-type-DDOST cDNA in patient fibroblasts restored glycosylation, indicating that the mutations were pathological. Our results highlight the power of combining WES and biochemical studies, including a glyco-complementation system, for identifying and confirming the defective gene in an untyped CDG patient. This approach will be very useful for uncovering other types of CDG as well.
Collapse
Affiliation(s)
- Melanie A Jones
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
63
|
Glycomics: An Overview of the Complex Glycocode. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 749:1-13. [DOI: 10.1007/978-1-4614-3381-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
64
|
Goreta SS, Dabelic S, Pavlinic D, Lauc G, Dumic J. Frequency Determination of α-1,3 Glucosyltransferase p.Y131H and p.F304S Polymorphisms in the Croatian Population Revealed Five Novel Single Nucleotide Polymorphisms in the hALG6 Gene. Genet Test Mol Biomarkers 2011; 16:50-3. [PMID: 21899441 DOI: 10.1089/gtmb.2011.0093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The congenital disorder of glycosylation (CDG)-Ic (ALG6-CDG, CDG-Ic) is caused by mutations in the hALG6 gene that encodes the N-glycosylation pathway enzyme, α-1,3-glucosyltransferase (NP_037471.2). The aim of our study was to estimate the frequencies of ALG6-CDG related p.Y131H and p.F304S polymorphisms in the Croatian population. Genomic DNA was isolated from blood samples collected from 600 healthy individuals. Functional single-nucleotide polymorphisms rs35383149 and rs17856039 causing p.Y131H and p.F304S, respectively, were genotyped by the TaqMan method and direct sequencing. The frequency of p.F304S polymorphism in the studied cohort was shown to be similar to the frequencies found in other tested populations (27%), whereas the frequency of p.Y131H was found to be three times higher (6.7%). Five novel base substitutions in the hALG6 gene were also found: three in exon 5 (c.383T>C, c.390G>A, and c.429G>C) and two in a downstream intervening sequence (IVS5+17C/T and IVS5+34G/A).
Collapse
Affiliation(s)
- Sandra Supraha Goreta
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | | | | | | |
Collapse
|
65
|
Jaffee MB, Imperiali B. Exploiting topological constraints to reveal buried sequence motifs in the membrane-bound N-linked oligosaccharyl transferases. Biochemistry 2011; 50:7557-67. [PMID: 21812456 DOI: 10.1021/bi201018d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The central enzyme in N-linked glycosylation is the oligosaccharyl transferase (OTase), which catalyzes glycan transfer from a polyprenyldiphosphate-linked carrier to select asparagines within acceptor proteins. PglB from Campylobacter jejuni is a single-subunit OTase with homology to the Stt3 subunit of the complex multimeric yeast OTase. Sequence identity between PglB and Stt3 is low (17.9%); however, both have a similar predicted architecture and contain the conserved WWDxG motif. To investigate the relationship between PglB and other Stt3 proteins, sequence analysis was performed using 28 homologues from evolutionarily distant organisms. Since detection of small conserved motifs within large membrane-associated proteins is complicated by divergent sequences surrounding the motifs, we developed a program to parse sequences according to predicted topology and then analyze topologically related regions. This approach identified three conserved motifs that served as the basis for subsequent mutagenesis and functional studies. This work reveals that several inter-transmembrane loop regions of PglB/Stt3 contain strictly conserved motifs that are essential for PglB function. The recent publication of a 3.4 Å resolution structure of full-length C. lari OTase provides clear structural evidence that these loops play a fundamental role in catalysis [ Lizak , C. ; ( 2011 ) Nature 474 , 350 - 355 ]. The current study provides biochemical support for the role of the inter-transmembrane domain loops in OTase catalysis and demonstrates the utility of combining topology prediction and sequence analysis for exposing buried pockets of homology in large membrane proteins. The described approach allowed detection of the catalytic motifs prior to availability of structural data and reveals additional catalytically relevant residues that are not predicted by structural data alone.
Collapse
Affiliation(s)
- Marcie B Jaffee
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | | |
Collapse
|
66
|
Sturiale L, Barone R, Garozzo D. The impact of mass spectrometry in the diagnosis of congenital disorders of glycosylation. J Inherit Metab Dis 2011; 34:891-9. [PMID: 21384227 DOI: 10.1007/s10545-011-9306-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/08/2011] [Accepted: 02/17/2011] [Indexed: 12/29/2022]
Abstract
Contribution of mass spectrometry (MS) in the diagnosis and characterization of congenital disorders of glycosylation (CDG) has long been known. CDG type I diseases are characterized by the under-occupancy of protein N-glycosylation sites. Electrospray (ESI) MS and matrix assisted laser desorption ionization (MALDI) MS are effective for underglycosylation analyses of intact serum Transferrin (Tf) in CDG-I patients by mass determination of individual component glycoforms. Thus, high-throughput methods developed to speed-up analytical times found increasing application in clinical testing for CDG detection. ESI MS recognizable glycoform profiles of serum Tf have been reported in CDG-I different from PMM2-CDG and in individual CDG-II defects. MALDI MS analysis of acidic and neutral N-linked glycans released from total plasma or targeted glycoproteins, is the mainstream tool to explore abnormal oligosaccharide structure and changes in the relative amount of individual oligosaccharides in CDG-II patients. Here we briefly review state-of-the-art and updates of MS-based applications for the diagnosis of CDG with special emphasis to detectable glycosylation profiles reported in different CDG types.
Collapse
Affiliation(s)
- Luisa Sturiale
- CNR - Institute of Chemistry and Technology of Polymers, Via P. Gaifami 18, 95126, Catania, Italy
| | | | | |
Collapse
|
67
|
Goreta SS, Dabelic S, Dumic J. Employment of single-strand conformation polymorphism analysis in screening for α-1,3 glucosyltransferase gene mutation A333V in Croatian population. J Clin Lab Anal 2011; 25:65-70. [PMID: 21437994 DOI: 10.1002/jcla.20425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Congenital disorder of glycosylation type Ic (CDG-Ic) is caused by mutations in hALG6 gene encoding α-1,3 glucosyltransferase (NP_037471.2), an enzyme that catalyzes the addition of the first glucose residue to the growing lipid-linked oligosaccharide precursor in N-glycosylation process. The most frequent mutation in hALG6 gene causing CDG-Ic is c.998C>T that results in p.A333V substitution. Up-to-date, no CDG-Ic patient has been detected in Croatia. However, as a part of the comprehensive project undertaken with the aim to estimate the frequencies of the carriers for specific mutations and polymorphisms related to particular CDGs in Croatian population, we screened genomic DNA samples obtained from 600 healthy nonconsanguineous Croatian residents to determine the frequency of the A333V mutation. For that purpose, we established the conditions for polymerase chain reaction-based single-strand conformation polymorphism analysis that is suitable for primary screening and in population studies, especially when the initial sample volume is small or DNA quantity is limited. None of the analyzed samples carried this mutation, indicating that the frequency of the patients carrying this homozygous mutation in Croatian population would be <1 in 1.4×10(6).
Collapse
Affiliation(s)
- Sandra Supraha Goreta
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | | |
Collapse
|
68
|
Barker MK, Wilkinson BL, Faridmoayer A, Scaman CH, Fairbanks AJ, Rose DR. Production and crystallization of processing α-glucosidase I: Pichia pastoris expression and a two-step purification toward structural determination. Protein Expr Purif 2011; 79:96-101. [PMID: 21640829 DOI: 10.1016/j.pep.2011.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/19/2011] [Accepted: 05/20/2011] [Indexed: 12/17/2022]
Abstract
Eukaryotic N-glycoprotein processing in the endoplasmic reticulum begins with the catalytic action of processing α-glucosidase I (αGlu). αGlu trims the terminal glucose from nascent glycoproteins in an inverting-mechanism glycoside hydrolysis reaction. αGlu has been studied in terms of kinetic parameters and potential key residues; however, the active site is unknown. A structural model would yield important insights into the reaction mechanism. A model would also be useful in developing specific therapeutics, as αGlu is a viable drug target against viruses with glycosylated envelope proteins. However, due to lack of a high-yielding overexpression and purification scheme, no eukaryotic structural model of αGlu has been determined. To address this issue, we overexpressed the Saccharomyces cerevisiae soluble αGlu, Cwht1p, in the host Pichia pastoris. It was purified in a simple two-step protocol, with a final yield of 4.2mg Cwht1p per liter of growth culture. To test catalytic activity, we developed a modified synthesis of a tetrasaccharide substrate, Glc(3)ManOMe. Cwht1p with Glc(3)ManOMe shows a K(m) of 1.26 mM. Cwht1p crystals were grown and subjected to X-ray irradiation, giving a complete diffraction dataset to 2.04 Å resolution. Work is ongoing to obtain phases so that we may further understand this fundamental member of the N-glycosylation pathway through the discovery of its molecular structure.
Collapse
Affiliation(s)
- Megan K Barker
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | | | | | | | | | | |
Collapse
|
69
|
Park C, Zhang J. Genome-wide evolutionary conservation of N-glycosylation sites. Mol Biol Evol 2011; 28:2351-7. [PMID: 21355035 DOI: 10.1093/molbev/msr055] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Although posttranslational protein modifications are generally thought to perform important cellular functions, recent studies showed that a large fraction of phosphorylation sites are not evolutionarily conserved. Whether the same is true for other protein modifications, such as N-glycosylation is an open question. N-glycosylation is a form of cotranslational and posttranslational modification that occurs by enzymatic addition of a polysaccharide, or glycan, to an asparagine (N) residue of a protein. Examining a large set of experimentally determined mouse N-glycosylation sites, we find that the evolutionary rate of glycosylated asparagines is significantly lower than that of nonglycosylated asparagines of the same proteins. We further confirm that the conservation of glycosylated asparagines is accompanied by the conservation of the canonical motif sequence for glycosylation, suggesting that the above substitution rate difference is related to glycosylation. Interestingly, when solvent accessibility is considered, the substitution rate disparity between glycosylated and nonglycosylated asparagines is highly significant at solvent accessible sites but not at solvent inaccessible sites. Thus, although the solvent inaccessible glycosylation sites were experimentally identified, they are unlikely to be genuine or physiologically important. For solvent accessible asparagines, our analysis reveals a widespread and strong functional constraint on glycosylation, unlike what has been observed for phosphorylation sites in most studies, including our own analysis. Because the majority of N-glycosylation occurs at solvent accessible sites, our results show an overall functional importance for N-glycosylation.
Collapse
Affiliation(s)
- Chungoo Park
- Department of Ecology and Evolutionary Biology, University of Michigan, USA
| | | |
Collapse
|
70
|
Pabst M, Altmann F. Glycan analysis by modern instrumental methods. Proteomics 2011; 11:631-43. [PMID: 21241022 DOI: 10.1002/pmic.201000517] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 12/23/2022]
Abstract
The oligosaccharides attached to proteins or lipids are among the most challenging analytical tasks due to their complexity and variety. Knowing the genes and enzymes responsible for their biosynthesis, a large but not unlimited number of different structures and isomers of such glycans can be imagined. Understanding of the biological role of structural variations requires the ability to unambiguously determine the identity and quantity of all glycan species. Here, we examine, which analytical strategies - with a certain high-throughput potential - may come near this ideal. After an expose of the relevant techniques, we try to depict how analytical raw data are translated into structural assignments using retention times, mass and fragment spectra. A method's ability to discriminate between the many conceivable isomeric structures together with the time, effort and sample amount needed for that purpose is suggested as a criterion for the comparative assessment of approaches and their evolutionary stages.
Collapse
Affiliation(s)
- Martin Pabst
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | | |
Collapse
|
71
|
Hart GW, Copeland RJ. Glycomics hits the big time. Cell 2010; 143:672-6. [PMID: 21111227 DOI: 10.1016/j.cell.2010.11.008] [Citation(s) in RCA: 499] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 10/27/2010] [Accepted: 11/02/2010] [Indexed: 10/18/2022]
Abstract
Cells run on carbohydrates. Glycans, sequences of carbohydrates conjugated to proteins and lipids, are arguably the most abundant and structurally diverse class of molecules in nature. Recent advances in glycomics reveal the scope and scale of their functional roles and their impact on human disease.
Collapse
Affiliation(s)
- Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205-2185, USA.
| | | |
Collapse
|
72
|
Firth SM, Yan X, Baxter RC. D440N mutation in the acid-labile subunit of insulin-like growth factor complexes inhibits secretion and complex formation. Mol Endocrinol 2010; 25:307-14. [PMID: 21177759 DOI: 10.1210/me.2010-0295] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The acid-labile subunit (ALS) regulates IGF bioavailability by forming heterotrimeric complexes with IGFs and IGF-binding protein-3 (IGFBP-3). A homozygous missense mutation (D440N) resulting in undetectable circulating levels of ALS with a concomitant reduction in IGF-I and IGFBP-3 has been reported to cause mild growth retardation. To understand how this particular mutation affects ALS circulating levels and IGF-transport function, we expressed recombinant ALS and its variants, D440N-ALS, T442A-ALS, and D440N/T442A-ALS, using adenovirus vectors. Compared with wild-type ALS, the secretion of D440N-ALS was 80% lower. The D440N mutation was proposed to generate an N-glycosylation site additional to the seven existing motifs in ALS. D440N-ALS appeared larger than ALS, attributable to N-linked glycans because deglycosylation with N-glycosidase F reduced both proteins to the same molecular mass. When ALS was incubated with IGF-I and IGFBP-3, 70-80% of IGF-I was detected by gel-filtration chromatography in forms corresponding to the 150-kDa ternary complex. In contrast, when D440N-ALS was tested, less than 30% of IGF-I was found in high molecular mass complexes. Two other ALS variants mutated in the same putative glycosylation site, D440N/T442A-ALS and T442A-ALS, showed similar chromatographic profiles to wild-type ALS. The D440N mutation in ALS generates a hyperglycosylated form with impaired secretion and complex formation, potentially leading to dysregulation of endocrine IGF, thus contributing to the growth retardation observed in the affected patient. This is the first study to explain how a natural mutation, D440N, in ALS impairs its function.
Collapse
Affiliation(s)
- Sue M Firth
- Kolling Institute of Medical Research, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales 2065, Australia.
| | | | | |
Collapse
|
73
|
Gupta G, Surolia A, Sampathkumar SG. Lectin microarrays for glycomic analysis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:419-36. [PMID: 20726799 DOI: 10.1089/omi.2009.0150] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. Glycocalyx of mammalian cells actively participate in cell-cell, cell-matrix, and cell-pathogen interactions, which impact embryogenesis, growth and development, homeostasis, infection and immunity, signaling, malignancy, and metabolic disorders. Relative to genomics and proteomics, glycomics is just growing out of infancy with great potential in biomedicine for biomarker discovery, diagnosis, and treatment. However, the immense diversity and complexity of glycan structures and their multiple modes of interactions with proteins pose great challenges for development of analytical tools for delineating structure function relationships and understanding glyco-code. Several tools are being developed for glycan profiling based on chromatography, mass spectrometry, glycan microarrays, and glyco-informatics. Lectins, which have long been used in glyco-immunology, printed on a microarray provide a versatile platform for rapid high throughput analysis of glycoforms of biological samples. Herein, we summarize technological advances in lectin microarrays and critically review their impact on glycomics analysis. Challenges remain in terms of expansion to include nonplant derived lectins, standardization for routine clinical use, development of recombinant lectins, and exploration of plant kingdom for discovery of novel lectins.
Collapse
Affiliation(s)
- Garima Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | |
Collapse
|
74
|
Congenital disorders of glycosylation with emphasis on loss of dermatan-4-sulfotransferase. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010; 93:289-307. [PMID: 20807649 DOI: 10.1016/s1877-1173(10)93012-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The autosomal, recessively inherited, adducted thumb-clubfoot syndrome (ATCS) represents a generalized connective tissue disorder with congenital malformations, contractures of thumbs and feet, and a typical facial appearance. Cognitive development is normal in ATCS patients during childhood. ATCS is caused by homozygous nonsense and missense mutations in CHST14 which encodes an N-acetylgalactosamine 4-O-sulfotransferase 1 (D4ST1) that catalyzes the 4-O-sulfation of N-acetylgalactosamine in the repeating iduronic acid-alpha-1,3-N-acetylgalactosamine disaccharide sequence to form dermatan sulfate (DS). ATCS mutations lead to either a decrease or a loss of D4ST1 activity, as revealed by absence of DS and an excess of chondroitin sulfate (CS) in patient's fibroblasts. Either of these effects or their combination might cause the observed clinical symptoms by altering the physiological pattern of dermatan and CS chains on their corresponding proteoglycans (PGs). ATCS is the only recognized disorder resulting from a defect that is specific to DS biosynthesis, and thus represents another class of the congenital glycosylation disorders. Congenital disorders of glycosylation (CDG) include all genetic diseases that result from defects in the synthesis of glycans. These disorders cause a wide range of human diseases, with examples emanating from all medical subspecialties. ATCS is the first human disorder that emphasizes a role for DS in human development and extracellular matrix maintenance.
Collapse
|
75
|
Lübbehusen J, Thiel C, Rind N, Ungar D, Prinsen BHCMT, de Koning TJ, van Hasselt PM, Körner C. Fatal outcome due to deficiency of subunit 6 of the conserved oligomeric Golgi complex leading to a new type of congenital disorders of glycosylation. Hum Mol Genet 2010; 19:3623-33. [PMID: 20605848 DOI: 10.1093/hmg/ddq278] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Deficiency of subunit 6 of the conserved oligomeric Golgi (COG6) complex causes a new combined N- and O-glycosylation deficiency of the congenital disorders of glycosylation, designated as CDG-IIL (COG6-CDG). The index patient presented with a severe neurologic disease characterized by vitamin K deficiency, vomiting, intractable focal seizures, intracranial bleedings and fatal outcome in early infancy. Analysis of oligosaccharides from serum transferrin by HPLC and mass spectrometry revealed the loss of galactose and sialic acid residues, whereas import and transfer of these sugar residues into Golgi-enriched vesicles or onto proteins, respectively, were normal to slightly reduced. Western blot examinations combined with gel filtration chromatography studies in patient-derived skin fibroblasts showed a severely reduced expression of the mentioned subunit and the occurrence of COG complex fragments at the expense of the integral COG complex. Sequencing of COG6-cDNA and COG6 gene resulted in a homozygous mutation (c.G1646T), leading to amino acid exchange p.G549V in the COG6 protein. Retroviral complementation of the patients' fibroblasts with the wild-type COG6-cDNA led to normalization of the COG complex-depending retrograde protein transport after Brefeldin A treatment, demonstrated by immunofluorescence analysis.
Collapse
Affiliation(s)
- Jürgen Lübbehusen
- Center for Child and Adolescent Medicine, Center for Metabolic Diseases Heidelberg, Department I, Heidelberg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
76
|
Tabak LA. The role of mucin-type O-glycans in eukaryotic development. Semin Cell Dev Biol 2010; 21:616-21. [PMID: 20144722 DOI: 10.1016/j.semcdb.2010.02.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/22/2010] [Accepted: 02/01/2010] [Indexed: 01/09/2023]
Abstract
Newly emerging genetic studies have revealed that a subset of the family of glycosyltransferases responsible for the formation of mucin-type O glycans is essential for normal development. As additional genetic, biochemical and physical tools are developed to interrogate the complex structure and surface location of this under-studied class of carbohydrate, no doubt additional roles will be elucidated.
Collapse
Affiliation(s)
- Lawrence A Tabak
- Section on Biological Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|