1
|
Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
Collapse
Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
| |
Collapse
|
2
|
Mazuca LG, Mohl JE. ISOGlyP: O-Glycosylation Site Prediction Using Peptide Sequences and GALNTs. Methods Mol Biol 2024; 2763:237-247. [PMID: 38347415 DOI: 10.1007/978-1-0716-3670-1_20] [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: 02/15/2024]
Abstract
Mucin-type O-glycosylation is one of the most common posttranslational modifications of proteins. The abnormal expression of various polypeptide GalNAc-transferases (GALNTs) which initiate and define sites of O-glycosylation is linked to many cancers and other diseases. Many current O-glycosylation prediction programs utilize O-glycoproteomics data obtained without using the transferase isoform(s) responsible for the glycosylation. With 20 different GALNTs in humans, having the ability to predict and interpret O-glycosylation sites in terms of specific GALNT isoforms is invaluable.To fill this gap, ISOGlyP (isoform-specific O-glycosylation prediction) has been developed. Using position-specific enhancement values generated based on GalNAc-T isoform-specific amino acid preferences, ISOGlyP predicts the propensity that a site would be glycosylated by a specific transferase. ISOGlyP gave an overall prediction accuracy of 70% against in vivo data, which is comparable to that of the NetOGlyc4.0 predictor. Additionally, ISOGlyP can identify the known effects of long- and short-range prior glycosylation and can generate potential peptide sequences selectively glycosylated by specific isoforms. ISOGlyP is freely available for use at https://ISOGlyP.utep.edu . The code is also available on GitHub ( https://github.com/jonmohl/ISOGlyP ).
Collapse
|
3
|
Ballard CJ, Paserba MR, Paul Daniel EJ, Hurtado-Guerrero R, Gerken TA. Polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) isozyme surface charge governs charge substrate preferences to modulate mucin type O-glycosylation. Glycobiology 2023; 33:817-836. [PMID: 37555669 PMCID: PMC10629720 DOI: 10.1093/glycob/cwad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023] Open
Abstract
A large family of polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) initiate mucin type O-glycosylation transferring α-GalNAc from a UDP-GalNAc donor to the hydroxyl groups of Ser and Thr residues of peptides and proteins, thereby defining sites of O-glycosylation. Mutations and differential expression of several GalNAc-Ts are associated with many disease states including cancers. The mechanisms by which these isozymes choose their targets and their roles in disease are not fully understood. We previously showed that the GalNAc-Ts possess common and unique specificities for acceptor type, peptide sequence and prior neighboring, and/or remote substrate GalNAc glycosylation. In the present study, the role of flanking charged residues was investigated using a library of charged peptide substrates containing the central -YAVTPGP- acceptor sequence. Eleven human and one bird GalNAc-T were initially characterized revealing a range of preferences for net positive, net negative, or unique combinations of flanking N- and/or C-terminal charge, correlating to each isozyme's different electrostatic surface potential. It was further found that isoforms with high sequence identity (>70%) within a subfamily can possess vastly different charge specificities. Enzyme kinetics, activities obtained at elevated ionic strength, and molecular dynamics simulations confirm that the GalNAc-Ts differently recognize substrate charge outside the common +/-3 residue binding site. These electrostatic interactions impact how charged peptide substrates bind/orient on the transferase surface, thus modulating their activities. In summary, we show the GalNAc-Ts utilize more extended surfaces than initially thought for binding substrates based on electrostatic, and likely other hydrophobic/hydrophilic interactions, furthering our understanding of how these transferases select their target.
Collapse
Affiliation(s)
- Collin J Ballard
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Miya R Paserba
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Ramón Hurtado-Guerrero
- Department of Biomedical Engineering, The Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
- Fundación ARAID, Zaragoza 50018, Spain
| | - Thomas A Gerken
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| |
Collapse
|
4
|
Barchi JJ, Strain CN. The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation. Front Mol Biosci 2023; 10:1117850. [PMID: 36845552 PMCID: PMC9950641 DOI: 10.3389/fmolb.2023.1117850] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
A variety of glycan structures cover the surface of all cells and are involved in myriad biological processes, including but not limited to, cell adhesion and communication, protein quality control, signal transduction and metabolism, while also being intimately involved in innate and adaptive immune functions. Immune surveillance and responses to foreign carbohydrate antigens, such as capsular polysaccharides on bacteria and surface protein glycosylation of viruses, are the basis of microbial clearance, and most antimicrobial vaccines target these structures. In addition, aberrant glycans on tumors called Tumor-Associated Carbohydrate Antigens (TACAs) elicit immune responses to cancer, and TACAs have been used in the design of many antitumor vaccine constructs. A majority of mammalian TACAs are derived from what are referred to as mucin-type O-linked glycans on cell-surface proteins and are linked to the protein backbone through the hydroxyl group of either serine or threonine residues. A small group of structural studies that have compared mono- and oligosaccharides attached to each of these residues have shown that there are distinct differences in conformational preferences assumed by glycans attached to either "unmethylated" serine or ß-methylated threonine. This suggests that the linkage point of antigenic glycans will affect their presentation to the immune system as well as to various carbohydrate binding molecules (e.g., lectins). This short review, followed by our hypothesis, will examine this possibility and extend the concept to the presentation of glycans on surfaces and in assay systems where recognition of glycans by proteins and other binding partners can be defined by different attachment points that allow for a range of conformational presentations.
Collapse
Affiliation(s)
| | - Caitlin N. Strain
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute at Frederick, Frederick, MD, United States
| |
Collapse
|
5
|
Syed ZA, Zhang L, Ten Hagen KG. In vivo models of mucin biosynthesis and function. Adv Drug Deliv Rev 2022; 184:114182. [PMID: 35278522 PMCID: PMC9068269 DOI: 10.1016/j.addr.2022.114182] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 12/22/2022]
Abstract
The secreted mucus layer that lines and protects epithelial cells is conserved across diverse species. While the exact composition of this protective layer varies between organisms, certain elements are conserved, including proteins that are heavily decorated with N-acetylgalactosamine-based sugars linked to serines or threonines (O-linked glycosylation). These heavily O-glycosylated proteins, known as mucins, exist in many forms and are able to form hydrated gel-like structures that coat epithelial surfaces. In vivo studies in diverse organisms have highlighted the importance of both the mucin proteins as well as their constituent O-glycans in the protection and health of internal epithelia. Here, we summarize in vivo approaches that have shed light on the synthesis and function of these essential components of mucus.
Collapse
Affiliation(s)
- Zulfeqhar A Syed
- Developmental Glycobiology Section, NIDCR, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892-4370, United States
| | - Liping Zhang
- Developmental Glycobiology Section, NIDCR, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892-4370, United States
| | - Kelly G Ten Hagen
- Developmental Glycobiology Section, NIDCR, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892-4370, United States.
| |
Collapse
|
6
|
Thompson NK, LeClaire LTN, Rodriguez Perez S, Wakarchuk WW. Investigation of sequon engineering for improved O-glycosylation by the human polypeptide N-acetylgalactosaminyl transferase T2 isozyme and two orthologues. Biochem J 2021; 478:3527-3537. [PMID: 34523671 DOI: 10.1042/bcj20210382] [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: 05/26/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
We have been developing bacterial expression systems for human mucin-type O-glycosylation on therapeutic proteins, which is initiated by the addition of α-linked GalNAc to serine or threonine residues by enzymes in the GT-27 family of glycosyltransferases. Substrate preference across different isoforms of this enzyme is influenced by isoform-specific amino acid sequences at the site of glycosylation, which we have exploited to engineer production of Core 1 glycan structures in bacteria on human therapeutic proteins. Using RP-HPLC with a novel phenyl bonded phase to resolve intact protein glycoforms, the effect of sequon mutation on O-glycosylation initiation was examined through in vitro modification of the naturally O-glycosylated human interferon α-2b, and a sequon engineered human growth hormone. As part of the development of our glycan engineering in the bacterial expression system we are surveying various orthologues of critical enzymes to ensure complete glycosylation. Here we present an in vitro enzyme kinetic profile of three related GT-27 orthologues on natural and engineered sequons in recombinant human interferon α2b and human growth hormone where we show a significant change in kinetic properties with the amino acid changes. It was found that optimizing the protein substrate amino acid sequence using Isoform Specific O-Glycosylation Prediction (ISOGlyP, http://isoglyp.utep.edu/index.php) resulted in a measurable increase in kcat/KM, thus improving glycosylation efficiency. We showed that the Drosophila orthologue showed superior activity with our human growth hormone designed sequons compared with the human enzyme.
Collapse
Affiliation(s)
- Nicole K Thompson
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G2E9, Canada
| | - Leif T N LeClaire
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G2E9, Canada
| | | | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G2E9, Canada
| |
Collapse
|
7
|
Belkina EG, Lazebny OE, Gornostaev NG, Mikhailov V, Danilenkova LV, Besedina NG, Bragina JV, Kamyshev NG, Sokolov VV, Kravchuk OI. Influence of the quick-to-court gene deletion on courtship behaviour of Drosophila melanogaster. J Genet 2021. [DOI: 10.1007/s12041-021-01284-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
8
|
Mahajan SP, Srinivasan Y, Labonte JW, DeLisa MP, Gray JJ. Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2. ACS Catal 2021; 11:2977-2991. [PMID: 34322281 DOI: 10.1021/acscatal.0c04609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The polypeptide N-acetylgalactosaminyl transferase (GalNAc-T) enzyme family initiates O-linked mucin-type glycosylation. The family constitutes 20 isoenzymes in humans. GalNAc-Ts exhibit both redundancy and finely tuned specificity for a wide range of peptide substrates. In this work, we deciphered the sequence and structural motifs that determine the peptide substrate preferences for the GalNAc-T2 isoform. Our approach involved sampling and characterization of peptide-enzyme conformations obtained from Rosetta Monte Carlo-minimization-based flexible docking. We computationally scanned 19 amino acid residues at positions -1 and +1 of an eight-residue peptide substrate, which comprised a dataset of 361 (19x19) peptides with previously characterized experimental GalNAc-T2 glycosylation efficiencies. The calculations recapitulated experimental specificity data, successfully discriminating between glycosylatable and non-glycosylatable peptides with a probability of 96.5% (ROC-AUC score), a balanced accuracy of 85.5% and a false positive rate of 7.3%. The glycosylatable peptide substrates viz. peptides with proline, serine, threonine, and alanine at the -1 position of the peptide preferentially exhibited cognate sequon-like conformations. The preference for specific residues at the -1 position of the peptide was regulated by enzyme residues R362, K363, Q364, H365 and W331, which modulate the pocket size and specific enzyme-peptide interactions. For the +1 position of the peptide, enzyme residues K281 and K363 formed gating interactions with aromatics and glutamines at the +1 position of the peptide, leading to modes of peptide-binding sub-optimal for catalysis. Overall, our work revealed enzyme features that lead to the finely tuned specificity observed for a broad range of peptide substrates for the GalNAc-T2 enzyme. We anticipate that the key sequence and structural motifs can be extended to analyze specificities of other isoforms of the GalNAc-T family and can be used to guide design of variants with tailored specificity.
Collapse
Affiliation(s)
- Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yashes Srinivasan
- Department of Bioengineering, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604, United States
| | - Matthew P. DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Department of Microbiology, and Nancy E. and Peter C. Meinig School of Biomedical Engineering, Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland 21224, United States
| |
Collapse
|
9
|
G Belkina E, E Lazebny O, G Gornostaev N, S Mikhailov V, V Danilenkova L, G Besedina N, V Bragina J, G Kamyshev N, V Sokolov V, I Kravchuk O. Influence of the quick-to-court gene deletion on courtship behaviour of Drosophila melanogaster. J Genet 2021; 100:37. [PMID: 34238777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Using an original method, we have received Drosophila melanogaster with a deficiency including a complete sequence of quick-to-court gene. In this report, we describe the behavioural features of this new deletion mutant. There were no serious deviations from the normal mating behaviour in flies with the deletion, but the behaviour of deletion mutants still had some features. Of all the elements, only the frequency of licking significantly increased in mutants. The duration of mating elements did not change in flies with deletion, and the latent period decreased only for following the female and licking. We have found that mutant males produce more courtship song than control males when courting Oregon R females as estimated by the pulse song index. In our experiment, mutant females provoked much less pulse song production by Oregon R males than control females do. Moreover, Oregon R males initiate courtship song towards mutant females later than towards control females. In other words, the study of pulse song production showed that the deficiency in females leads to a decrease in the intensity of courtship of wild-type males, whereas the deficiency in males leads to more intensive care for wild-type females.
Collapse
Affiliation(s)
- Elena G Belkina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Akasaka-Manya K, Manya H. The Role of APP O-Glycosylation in Alzheimer's Disease. Biomolecules 2020; 10:biom10111569. [PMID: 33218200 PMCID: PMC7699271 DOI: 10.3390/biom10111569] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
The number of people with dementia is increasing rapidly due to the increase in the aging population. Alzheimer’s disease (AD) is a type of neurodegenerative dementia caused by the accumulation of abnormal proteins. Genetic mutations, smoking, and several other factors have been reported as causes of AD, but alterations in glycans have recently been demonstrated to play a role in AD. Amyloid-β (Aβ), a cleaved fragment of APP, is the source of senile plaque, a pathological feature of AD. APP has been reported to undergo N- and O-glycosylation, and several Polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts) have been shown to have catalytic activity for the transfer of GalNAc to APP. Since O-glycosylation in the proximity of a cleavage site in many proteins has been reported to be involved in protein processing, O-glycans may affect the cleavage of APP during the Aβ production process. In this report, we describe new findings on the O-glycosylation of APP and Aβ production.
Collapse
|
11
|
Daniel EJP, las Rivas M, Lira-Navarrete E, García-García A, Hurtado-Guerrero R, Clausen H, Gerken TA. Ser and Thr acceptor preferences of the GalNAc-Ts vary among isoenzymes to modulate mucin-type O-glycosylation. Glycobiology 2020; 30:910-922. [PMID: 32304323 PMCID: PMC7581654 DOI: 10.1093/glycob/cwaa036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/30/2020] [Accepted: 04/12/2020] [Indexed: 12/12/2022] Open
Abstract
A family of polypeptide GalNAc-transferases (GalNAc-Ts) initiates mucin-type O-glycosylation, transferring GalNAc onto hydroxyl groups of Ser and Thr residues of target substrates. The 20 GalNAc-T isoenzymes in humans are classified into nine subfamilies according to sequence similarity. GalNAc-Ts select their sites of glycosylation based on weak and overlapping peptide sequence motifs, as well prior substrate O-GalNAc glycosylation at sites both remote (long-range) and neighboring (short-range) the acceptor. Together, these preferences vary among GalNAc-Ts imparting each isoenzyme with its own unique specificity. Studies on the first identified GalNAc-Ts showed Thr acceptors were preferred over Ser acceptors; however studies comparing Thr vs. Ser glycosylation across the GalNAc-T family are lacking. Using a series of identical random peptide substrates, with single Thr or Ser acceptor sites, we determined the rate differences (Thr/Ser rate ratio) between Thr and Ser substrate glycosylation for 12 isoenzymes (representing 7 GalNAc-T subfamilies). These Thr/Ser rate ratios varied across subfamilies, ranging from ~2 to ~18 (for GalNAc-T4/GalNAc-T12 and GalNAc-T3/GalNAc-T6, respectively), while nearly identical Thr/Ser rate ratios were observed for isoenzymes within subfamilies. Furthermore, the Thr/Ser rate ratios did not appreciably vary over a series of fixed sequence substrates of different relative activities, suggesting the ratio is a constant for each isoenzyme against single acceptor substrates. Finally, based on GalNAc-T structures, the different Thr/Ser rate ratios likely reflect differences in the strengths of the Thr acceptor methyl group binding to the active site pocket. With this work, another activity that further differentiates substrate specificity among the GalNAc-Ts has been identified.
Collapse
Affiliation(s)
| | - Matilde las Rivas
- BIFI and Laboratorio de Microscopías Avanzada (LMA), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain
| | - Erandi Lira-Navarrete
- BIFI and Laboratorio de Microscopías Avanzada (LMA), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain
| | - Ana García-García
- BIFI and Laboratorio de Microscopías Avanzada (LMA), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain
| | - Ramon Hurtado-Guerrero
- BIFI and Laboratorio de Microscopías Avanzada (LMA), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics (CCG), University of Copenhagen, Copenhagen N DK-2200, Denmark
- Department of Dentistry, Faculty of Health Sciences, Copenhagen Center for Glycomics (CCG), University of Copenhagen, Copenhagen N DK-2200, Denmark
- Fundación ARAID, Zaragoza, 50018, Spain
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics (CCG), University of Copenhagen, Copenhagen N DK-2200, Denmark
- Department of Dentistry, Faculty of Health Sciences, Copenhagen Center for Glycomics (CCG), University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Thomas A Gerken
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA
| |
Collapse
|
12
|
Mohl JE, Gerken TA, Leung MY. ISOGlyP: de novo prediction of isoform-specific mucin-type O-glycosylation. Glycobiology 2020; 31:168-172. [PMID: 32681163 DOI: 10.1093/glycob/cwaa067] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/09/2020] [Accepted: 07/12/2020] [Indexed: 02/07/2023] Open
Abstract
Mucin-type O-glycosylation is one of the most common posttranslational modifications of proteins. The abnormal expression of various polypeptide GalNAc-transferases (GalNAc-Ts) which initiate and define sites of O-glycosylation are linked to many cancers and other diseases. Current O-glycosyation prediction programs utilize O-glycoproteomics data obtained without regard to the transferase isoform (s) responsible for the glycosylation. With 20 different GalNAc-Ts in humans, having an ability to predict and interpret O-glycosylation sites in terms of specific GalNAc-T isoforms is invaluable. To fill this gap, ISOGlyP (Isoform-Specific O-Glycosylation Prediction) has been developed. Using position-specific enhancement values generated based on GalNAc-T isoform-specific amino acid preferences, ISOGlyP predicts the propensity that a site would be glycosylated by a specific transferase. ISOGlyP gave an overall prediction accuracy of 70% against in vivo data, which is comparable to that of the NetOGlyc4.0 predictor. Additionally, ISOGlyP can identify the known effects of long- and short-range prior glycosylation and can generate potential peptide sequences selectively glycosylated by specific isoforms. ISOGlyP is freely available for use at ISOGlyP.utep.edu. The code is also available on GitHub (https://github.com/jonmohl/ISOGlyP).
Collapse
Affiliation(s)
- Jonathon E Mohl
- Department of Mathematical Sciences and Border Biomedical Research Center, The University of Texas at El Paso, W University, El Paso, TX 79968, USA
| | - Thomas A Gerken
- Departments of Biochemistry and Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ming-Ying Leung
- Department of Mathematical Sciences and Border Biomedical Research Center, The University of Texas at El Paso, W University, El Paso, TX 79968, USA
| |
Collapse
|
13
|
MOHL JONATHONE, GERKEN THOMAS, LEUNG MINGYING. Predicting mucin-type O-Glycosylation using enhancement value products from derived protein features. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020; 19:2040003. [PMID: 33208985 PMCID: PMC7671581 DOI: 10.1142/s0219633620400039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mucin-type O-glycosylation is one of the most common post-translational modifications of proteins. This glycosylation is initiated in the Golgi by the addition of the sugar N-acetylgalactosamine (GalNAc) onto protein Ser and Thr residues by a family of polypeptide GalNAc transferases. In humans there are 20 isoforms that are differentially expressed across tissues that serve multiple important biological roles. Using random peptide substrates, isoform specific amino acid preferences have been obtained in the form of enhancement values (EV). These EVs alone have previously been used to predict O-glycosylation sites via the web based ISOGlyP (Isoform Specific O-Glycosylation Prediction) tool. Here we explore additional protein features to determine whether these can complement the random peptide derived enhancement values and increase the predictive power of ISOGlyP. The inclusion of additional protein substrate features (such as secondary structure and surface accessibility) was found to increase sensitivity with minimal loss of specificity, when tested with three different published in vivo O-glycoproteomics data sets, thus increasing the overall accuracy of the ISOGlyP predictions.
Collapse
Affiliation(s)
- JONATHON E. MOHL
- Department of Mathematical Sciences and Border Biomedical Research
Center, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - THOMAS GERKEN
- Departments of Biochemistry and Chemistry, Case Western Reserve
University, Cleveland, OH, 44106, USA
| | - MING-YING LEUNG
- Department of Mathematical Sciences and Border Biomedical Research
Center, The University of Texas at El Paso, El Paso, TX 79968, USA
| |
Collapse
|
14
|
Stewart TJ, Takahashi K, Whitaker RH, Raska M, Placzek WJ, Novak J, Renfrow MB. IgA1 hinge-region clustered glycan fidelity is established early during semi-ordered glycosylation by GalNAc-T2. Glycobiology 2019; 29:543-556. [PMID: 30759204 PMCID: PMC6583770 DOI: 10.1093/glycob/cwz007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 01/13/2019] [Accepted: 02/04/2019] [Indexed: 01/03/2023] Open
Abstract
GalNAc-type O-glycans are often added to proteins post-translationally in a clustered manner in repeat regions of proteins, such as mucins and IgA1. Observed IgA1 glycosylation patterns show that glycans occur at similar sites with similar structures. It is not clear how the sites and number of glycans added to IgA1, or other proteins, can follow a conservative process. GalNAc-transferases initiate GalNAc-type glycosylation. In IgA nephropathy, an autoimmune disease, the sites and O-glycan structures of IgA1 hinge-region are altered, giving rise to a glycan autoantigen. To better understand how GalNAc-transferases determine sites and densities of clustered O-glycans, we used IgA1 hinge-region (HR) segment as a probe. Using LC-MS, we demonstrated a semi-ordered process of glycosylation by GalNAc-T2 towards the IgA1 HR. The catalytic domain was responsible for selection of four initial sites based on amino-acid sequence recognition. Both catalytic and lectin domains were involved in multiple second site-selections, each dependent on initial site-selection. Our data demonstrated that multiple start-sites and follow-up pathways were key to increasing the number of glycans added. The lectin domain predominately enhanced IgA1 HR glycan density by increasing synthesis pathway exploration by GalNAc-T2. Our data indicated a link between site-specific glycan addition and clustered glycan density that defines a mechanism of how conserved clustered O-glycosylation patterns and glycoform populations of IgA1 can be controlled by GalNAc-T2. Together, these findings characterized a correlation between glycosylation pathway diversity and glycosylation density, revealing mechanisms by which a single GalNAc-T isozyme can limit and define glycan heterogeneity in a disease-relevant context.
Collapse
Affiliation(s)
- Tyler J Stewart
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kazuo Takahashi
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Nephrology, Fujita Health University, Toyoake, Japan
| | - Robert H Whitaker
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Milan Raska
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Immunology, Palacky University and University Hospital, Olomouc, Czech Republic
| | - William J Placzek
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|
15
|
Du T, Buenbrazo N, Kell L, Rahmani S, Sim L, Withers SG, DeFrees S, Wakarchuk W. A Bacterial Expression Platform for Production of Therapeutic Proteins Containing Human-like O-Linked Glycans. Cell Chem Biol 2019; 26:203-212.e5. [PMID: 30503285 DOI: 10.1016/j.chembiol.2018.10.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/07/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022]
Abstract
We have developed an Escherichia coli strain for the in vivo production of O-glycosylated proteins. This was achieved using a dual plasmid approach: one encoding a therapeutic protein target, and a second encoding the enzymatic machinery required for O-glycosylation. The latter plasmid encodes human polypeptide N-acetylgalactosaminyl transferase as well as a β1,3-galactosyl transferase and UDP-Glc(NAc)-4-epimerase, both from Campylobacter jejuni, and a disulfide bond isomerase of bacterial or human origin. The effectiveness of this two-plasmid synthetic operon system has been tested on three proteins with therapeutic potential: the native and an engineered version of the naturally O-glycosylated human interferon α-2b, as well as human growth hormone with one engineered site of glycosylation. Having established proof of principle for the addition of the core-1 glycan onto proteins, we are now developing this system as a platform for producing and modifying human protein therapeutics with more complex O-glycan structures in E. coli.
Collapse
Affiliation(s)
- Ting Du
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Nakita Buenbrazo
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Laura Kell
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Sadia Rahmani
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Lyann Sim
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Shawn DeFrees
- La Jolla Pharmaceutical Company, San Diego, CA 92121, USA
| | - Warren Wakarchuk
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada.
| |
Collapse
|
16
|
de las Rivas M, Paul Daniel EJ, Coelho H, Lira-Navarrete E, Raich L, Compañón I, Diniz A, Lagartera L, Jiménez-Barbero J, Clausen H, Rovira C, Marcelo F, Corzana F, Gerken TA, Hurtado-Guerrero R. Structural and Mechanistic Insights into the Catalytic-Domain-Mediated Short-Range Glycosylation Preferences of GalNAc-T4. ACS CENTRAL SCIENCE 2018; 4:1274-1290. [PMID: 30276263 PMCID: PMC6161044 DOI: 10.1021/acscentsci.8b00488] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 05/03/2023]
Abstract
Mucin-type O-glycosylation is initiated by a family of polypeptide GalNAc-transferases (GalNAc-Ts) which are type-II transmembrane proteins that contain Golgi luminal catalytic and lectin domains that are connected by a flexible linker. Several GalNAc-Ts, including GalNAc-T4, show both long-range and short-range prior glycosylation specificity, governed by their lectin and catalytic domains, respectively. While the mechanism of the lectin-domain-dependent glycosylation is well-known, the molecular basis for the catalytic-domain-dependent glycosylation of glycopeptides is unclear. Herein, we report the crystal structure of GalNAc-T4 bound to the diglycopeptide GAT*GAGAGAGT*TPGPG (containing two α-GalNAc glycosylated Thr (T*), the PXP motif and a "naked" Thr acceptor site) that describes its catalytic domain glycopeptide GalNAc binding site. Kinetic studies of wild-type and GalNAc binding site mutant enzymes show the lectin domain GalNAc binding activity dominates over the catalytic domain GalNAc binding activity and that these activities can be independently eliminated. Surprisingly, a flexible loop protruding from the lectin domain was found essential for the optimal activity of the catalytic domain. This work provides the first structural basis for the short-range glycosylation preferences of a GalNAc-T.
Collapse
Affiliation(s)
- Matilde de las Rivas
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit,
Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Earnest James Paul Daniel
- Departments
of Biochemistry, Pediatrics and Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Helena Coelho
- UCIBIO,
REQUIMTE, Departamento de Química, Faculdade de Ciências
e Tecnologia, Universidade de Nova de Lisboa, Caparica 2825-149, Portugal
- CIC
bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
- Departament
of Organic Chemistry II, Faculty of Science
& Technology, University of the Basque
Country, Leioa, 48940 Bizkaia, Spain
| | - Erandi Lira-Navarrete
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine,
School of Dentistry, University of Copenhagen, Copenhagen 1165, Denmark
| | - Lluis Raich
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Ismael Compañón
- Departamento
de Química, Universidad de La Rioja,
Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Ana Diniz
- UCIBIO,
REQUIMTE, Departamento de Química, Faculdade de Ciências
e Tecnologia, Universidade de Nova de Lisboa, Caparica 2825-149, Portugal
| | | | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
- Departament
of Organic Chemistry II, Faculty of Science
& Technology, University of the Basque
Country, Leioa, 48940 Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
| | - Henrik Clausen
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine,
School of Dentistry, University of Copenhagen, Copenhagen 1165, Denmark
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| | - Filipa Marcelo
- UCIBIO,
REQUIMTE, Departamento de Química, Faculdade de Ciências
e Tecnologia, Universidade de Nova de Lisboa, Caparica 2825-149, Portugal
| | - Francisco Corzana
- Departamento
de Química, Universidad de La Rioja,
Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Thomas A. Gerken
- Departments
of Biochemistry, Pediatrics and Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
- E-mail:
| | - Ramon Hurtado-Guerrero
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit,
Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
- E-mail:
| |
Collapse
|
17
|
Corfield AP. The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human. Microorganisms 2018; 6:microorganisms6030078. [PMID: 30072673 PMCID: PMC6163557 DOI: 10.3390/microorganisms6030078] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023] Open
Abstract
Glycoproteins are major players in the mucus protective barrier in the gastrointestinal and other mucosal surfaces. In particular the mucus glycoproteins, or mucins, are responsible for the protective gel barrier. They are characterized by their high carbohydrate content, present in their variable number, tandem repeat domains. Throughout evolution the mucins have been maintained as integral components of the mucosal barrier, emphasizing their essential biological status. The glycosylation of the mucins is achieved through a series of biosynthetic pathways processes, which generate the wide range of glycans found in these molecules. Thus mucins are decorated with molecules having information in the form of a glycocode. The enteric microbiota interacts with the mucosal mucus barrier in a variety of ways in order to fulfill its many normal processes. How bacteria read the glycocode and link to normal and pathological processes is outlined in the review.
Collapse
Affiliation(s)
- Anthony P Corfield
- Mucin Research Group, School of Clinical Sciences, Bristol Royal Infirmary, Level 7, Marlborough Street, Bristol BS2 8HW, UK.
| |
Collapse
|
18
|
Altered protein glycosylation predicts Alzheimer's disease and modulates its pathology in disease model Drosophila. Neurobiol Aging 2017; 56:159-171. [PMID: 28552182 DOI: 10.1016/j.neurobiolaging.2017.04.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 03/06/2017] [Accepted: 04/23/2017] [Indexed: 12/21/2022]
Abstract
The pathological hallmarks of Alzheimer's disease (AD) are pathogenic oligomers and fibrils of misfolded amyloidogenic proteins (e.g., β-amyloid and hyper-phosphorylated tau in AD), which cause progressive loss of neurons in the brain and nervous system. Although deviations from normal protein glycosylation have been documented in AD, their role in disease pathology has been barely explored. Here our analysis of available expression data sets indicates that many glycosylation-related genes are differentially expressed in brains of AD patients compared with healthy controls. The robust differences found enabled us to predict the occurrence of AD with remarkable accuracy in a test cohort and identify a set of key genes whose expression determines this classification. We then studied in vivo the effect of reducing expression of homologs of 6 of these genes in transgenic Drosophila overexpressing human tau, a well-established invertebrate AD model. These experiments have led to the identification of glycosylation genes that may augment or ameliorate tauopathy phenotypes. Our results indicate that OstDelta, l(2)not and beta4GalT7 are tauopathy suppressors, whereas pgnat5 and CG33303 are enhancers, of tauopathy. These results suggest that specific alterations in protein glycosylation may play a causal role in AD etiology.
Collapse
|
19
|
Corfield A. Eukaryotic protein glycosylation: a primer for histochemists and cell biologists. Histochem Cell Biol 2017; 147:119-147. [PMID: 28012131 PMCID: PMC5306191 DOI: 10.1007/s00418-016-1526-4] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2016] [Indexed: 12/21/2022]
Abstract
Proteins undergo co- and posttranslational modifications, and their glycosylation is the most frequent and structurally variegated type. Histochemically, the detection of glycan presence has first been performed by stains. The availability of carbohydrate-specific tools (lectins, monoclonal antibodies) has revolutionized glycophenotyping, allowing monitoring of distinct structures. The different types of protein glycosylation in Eukaryotes are described. Following this educational survey, examples where known biological function is related to the glycan structures carried by proteins are given. In particular, mucins and their glycosylation patterns are considered as instructive proof-of-principle case. The tissue and cellular location of glycoprotein biosynthesis and metabolism is reviewed, with attention to new findings in goblet cells. Finally, protein glycosylation in disease is documented, with selected examples, where aberrant glycan expression impacts on normal function to let disease pathology become manifest. The histological applications adopted in these studies are emphasized throughout the text.
Collapse
Affiliation(s)
- Anthony Corfield
- Mucin Research Group, School of Clinical Sciences, Bristol Royal Infirmary, University of Bristol, Bristol, BS2 8HW, UK.
| |
Collapse
|
20
|
Festari MF, Trajtenberg F, Berois N, Pantano S, Revoredo L, Kong Y, Solari-Saquieres P, Narimatsu Y, Freire T, Bay S, Robello C, Bénard J, Gerken TA, Clausen H, Osinaga E. Revisiting the human polypeptide GalNAc-T1 and T13 paralogs. Glycobiology 2017; 27:140-153. [PMID: 27913570 PMCID: PMC5224595 DOI: 10.1093/glycob/cww111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/30/2016] [Accepted: 11/02/2016] [Indexed: 11/13/2022] Open
Abstract
Polypeptide GalNAc-transferases (GalNAc-Ts) constitute a family of 20 human glycosyltransferases (comprising 9 subfamilies), which initiate mucin-type O-glycosylation. The O-glycoproteome is thought to be differentially regulated via the different substrate specificities and expression patterns of each GalNAc-T isoforms. Here, we present a comprehensive in vitro analysis of the peptide substrate specificity of GalNAc-T13, showing that it essentially overlaps with the ubiquitous expressed GalNAc-T1 isoform found in the same subfamily as T13. We have also identified and partially characterized nine splice variants of GalNAc-T13, which add further complexity to the GalNAc-T family. Two variants with changes in their lectin domains were characterized by in vitro glycosylation assays, and one (Δ39Ex9) was inactive while the second one (Ex10b) had essentially unaltered activity. We used reverse transcription-polymerase chain reaction analysis of human neuroblastoma cell lines, normal brain and a small panel of neuroblastoma tumors to demonstrate that several splice variants (Ex10b, ΔEx9, ΔEx2-7 and ΔEx6/8-39bpEx9) were highly expressed in tumor cell lines compared with normal brain, although the functional implications remain to be unveiled. In summary, the GalNAc-T13 isoform is predicted to function similarly to GalNAc-T1 against peptide substrates in vivo, in contrast to a prior report, but is unique by being selectively expressed in the brain.
Collapse
Affiliation(s)
- María Florencia Festari
- Laboratory of Tumor Immunology and Glycobiology, Institut Pasteur de Montevideo, Mataojo 2020 (C.P. 11400), Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Avenida General Flores 2125 (C.P. 11800), Montevideo, Uruguay
| | | | - Nora Berois
- Laboratory of Tumor Immunology and Glycobiology, Institut Pasteur de Montevideo, Mataojo 2020 (C.P. 11400), Montevideo, Uruguay
| | - Sergio Pantano
- Grupo de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Mataojo 2020 (C.P. 11400), Montevideo, Uruguay
| | - Leslie Revoredo
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yun Kong
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Patricia Solari-Saquieres
- Laboratory of Tumor Immunology and Glycobiology, Institut Pasteur de Montevideo, Mataojo 2020 (C.P. 11400), Montevideo, Uruguay
| | - Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Teresa Freire
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Avenida General Flores 2125 (C.P. 11800), Montevideo, Uruguay
| | - Sylvie Bay
- Unité de Chimie de Biomoleculares, CNRS UMR 3523 Institut Pasteur, Paris, France
| | - Carlos Robello
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Mataojo 2020 (C.P. 11400), Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avenida General Flores 2125 (C.P. 11800), Montevideo, Uruguay
| | - Jean Bénard
- CNRS UMR 8126, Université Paris-Sud 11, and Département de Biologie et Pathologie Médicales Institut Gustave Roussy, Villejuif Cedex, France
| | - Thomas A Gerken
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
- Departments of Pediatrics and Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Henrik Clausen
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Eduardo Osinaga
- Laboratory of Tumor Immunology and Glycobiology, Institut Pasteur de Montevideo, Mataojo 2020 (C.P. 11400), Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Avenida General Flores 2125 (C.P. 11800), Montevideo, Uruguay
| |
Collapse
|
21
|
Nagai-Okatani C, Minamino N. Aberrant Glycosylation in the Left Ventricle and Plasma of Rats with Cardiac Hypertrophy and Heart Failure. PLoS One 2016; 11:e0150210. [PMID: 27281159 PMCID: PMC4900630 DOI: 10.1371/journal.pone.0150210] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/20/2016] [Indexed: 11/21/2022] Open
Abstract
Targeted proteomics focusing on post-translational modifications, including glycosylation, is a useful strategy for discovering novel biomarkers. To apply this strategy effectively to cardiac hypertrophy and resultant heart failure, we aimed to characterize glycosylation profiles in the left ventricle and plasma of rats with cardiac hypertrophy. Dahl salt-sensitive hypertensive rats, a model of hypertension-induced cardiac hypertrophy, were fed a high-salt (8% NaCl) diet starting at 6 weeks. As a result, they exhibited cardiac hypertrophy at 12 weeks and partially impaired cardiac function at 16 weeks compared with control rats fed a low-salt (0.3% NaCl) diet. Gene expression analysis revealed significant changes in the expression of genes encoding glycosyltransferases and glycosidases. Glycoproteome profiling using lectin microarrays indicated upregulation of mucin-type O-glycosylation, especially disialyl-T, and downregulation of core fucosylation on N-glycans, detected by specific interactions with Amaranthus caudatus and Aspergillus oryzae lectins, respectively. Upregulation of plasma α-l-fucosidase activity was identified as a biomarker candidate for cardiac hypertrophy, which is expected to support the existing marker, atrial natriuretic peptide and its related peptides. Proteomic analysis identified cysteine and glycine-rich protein 3, a master regulator of cardiac muscle function, as an O-glycosylated protein with altered glycosylation in the rats with cardiac hypertrophy, suggesting that alternations in O-glycosylation affect its oligomerization and function. In conclusion, our data provide evidence of significant changes in glycosylation pattern, specifically mucin-type O-glycosylation and core defucosylation, in the pathogenesis of cardiac hypertrophy and heart failure, suggesting that they are potential biomarkers for these diseases.
Collapse
Affiliation(s)
- Chiaki Nagai-Okatani
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Naoto Minamino
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
- * E-mail:
| |
Collapse
|
22
|
Chia J, Goh G, Bard F. Short O-GalNAc glycans: regulation and role in tumor development and clinical perspectives. Biochim Biophys Acta Gen Subj 2016; 1860:1623-39. [PMID: 26968459 DOI: 10.1016/j.bbagen.2016.03.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/03/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND While the underlying causes of cancer are genetic modifications, changes in cellular states mediate cancer development. Tumor cells display markedly changed glycosylation states, of which the O-GalNAc glycans called the Tn and TF antigens are particularly common. How these antigens get over-expressed is not clear. The expression levels of glycosylation enzymes fail to explain it. SCOPE OF REVIEW We describe the regulation of O-GalNAc glycosylation initiation and extension with emphasis on the initiating enzymes ppGalNAcTs (GALNTs), and introduce the GALA pathway--a change in GALNTs compartmentation within the secretory pathway that regulates Tn levels. We discuss the roles of O-GalNAc glycans and GALNTs in tumorigenic processes and finally consider diagnostic and therapeutic perspectives. MAJOR CONCLUSIONS Contrary to a common hypothesis, short O-glycans in tumors are not the result of an incomplete glycosylation process but rather reveal the activation of regulatory pathways. Surprisingly, high Tn levels reveal a major shift in the O-glycoproteome rather than a shortening of O-glycans. These changes are driven by membrane trafficking events. GENERAL SIGNIFICANCE Many attempts to use O-glycans for biomarker, antibody and therapeutic vaccine development have been made, but suffer limitations including poor sensitivity and/or specificity that may in part derive from lack of a mechanistic understanding. Deciphering how short O-GalNAc glycans are regulated would open new perspectives to exploit this biology for therapeutic usage. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
Collapse
Affiliation(s)
- Joanne Chia
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Germaine Goh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Frederic Bard
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore; Department of Biochemistry, National University of Singapore, 21 Lower Kent Ridge, Road, 119077, Singapore.
| |
Collapse
|
23
|
Mucin-Type O-Glycosylation in Invertebrates. Molecules 2015; 20:10622-40. [PMID: 26065637 PMCID: PMC6272458 DOI: 10.3390/molecules200610622] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 12/12/2022] Open
Abstract
O-Glycosylation is one of the most important posttranslational modifications of proteins. It takes part in protein conformation, protein sorting, developmental processes and the modulation of enzymatic activities. In vertebrates, the basics of the biosynthetic pathway of O-glycans are already well understood. However, the regulation of the processes and the molecular aspects of defects, especially in correlation with cancer or developmental abnormalities, are still under investigation. The knowledge of the correlating invertebrate systems and evolutionary aspects of these highly conserved biosynthetic events may help improve the understanding of the regulatory factors of this pathway. Invertebrates display a broad spectrum of glycosylation varieties, providing an enormous potential for glycan modifications which may be used for the design of new pharmaceutically active substances. Here, overviews of the present knowledge of invertebrate mucin-type O-glycan structures and the currently identified enzymes responsible for the biosynthesis of these oligosaccharides are presented, and the few data dealing with functional aspects of O-glycans are summarised.
Collapse
|
24
|
Kong Y, Joshi HJ, Schjoldager KTBG, Madsen TD, Gerken TA, Vester-Christensen MB, Wandall HH, Bennett EP, Levery SB, Vakhrushev SY, Clausen H. Probing polypeptide GalNAc-transferase isoform substrate specificities by in vitro analysis. Glycobiology 2015; 25:55-65. [PMID: 25155433 PMCID: PMC4245906 DOI: 10.1093/glycob/cwu089] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 08/13/2014] [Accepted: 08/19/2014] [Indexed: 12/16/2022] Open
Abstract
N-acetylgalactosaminyltransferase (GalNAc)-type (mucin-type) O-glycosylation is an abundant and highly diverse modification of proteins. This type of O-glycosylation is initiated in the Golgi by a large family of up to 20 homologous polypeptide GalNAc-T isoenzymes that transfer GalNAc to Ser, Thr and possibly Tyr residues. These GalNAc residues are then further elongated by a large set of glycosyltransferases to build a variety of complex O-glycan structures. What determines O-glycan site occupancy is still poorly understood, although it is clear that the substrate specificities of individual isoenzymes and the repertoire of GalNAc-Ts in cells are key parameters. The GalNAc-T isoenzymes are differentially expressed in cells and tissues in principle allowing cells to produce unique O-glycoproteomes dependent on the specific subset of isoforms present. In vitro analysis of acceptor peptide substrate specificities using recombinant expressed GalNAc-Ts has been the method of choice for probing activities of individual isoforms, but these studies have been hampered by biological validation of actual O-glycosylation sites in proteins and number of substrate testable. Here, we present a systematic analysis of the activity of 10 human GalNAc-T isoenzymes with 195 peptide substrates covering known O-glycosylation sites and provide a comprehensive dataset for evaluating isoform-specific contributions to the O-glycoproteome.
Collapse
Affiliation(s)
- Yun Kong
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Katrine Ter-Borch Gram Schjoldager
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Thomas Daugbjerg Madsen
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Thomas A Gerken
- Department of Pediatrics Department of Biochemistry and Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Malene B Vester-Christensen
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Eric Paul Bennett
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Steven B Levery
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| |
Collapse
|
25
|
Taus C, Windwarder M, Altmann F, Grabherr R, Staudacher E. UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyl-transferase from the snail Biomphalaria glabrata - substrate specificity and preference of glycosylation sites. Glycoconj J 2014; 31:661-70. [PMID: 25338825 PMCID: PMC4245494 DOI: 10.1007/s10719-014-9565-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/11/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022]
Abstract
O-glycosylation is a widely occurring posttranslational modification of proteins. The glycosylation status of a specific site may influence the location, activity and function of a protein. The initiating enzyme of mucin-type O-glycosylation is UDP-GalNAc:polypeptide GalNAc transferase (ppGalNAcT; EC 2.4.1.41). Using electron-transfer dissociation mass spectrometry, ppGalNAcT from the snail Biomphalaria glabrata was characterized regarding its ability to glycosylate threonine and serine residues in different peptide sequence environments. The preferences of the snail enzyme for flanking amino acids of the potential glycosylation site were very similar to vertebrate and insect members of the family. Acceptor sites with adjacent proline residues were highly preferred, while other residues caused less pronounced effects. No specific O-glycosylation consensus sequence was found. The results obtained from synthetic peptides were in good correlation with the observed glycosylation patterns of native peptides and with the order of attachment in a multi-glycosylated peptide. The snail enzyme clearly preferred threonine over serine in the in vitro assays. No significant differences of transfer speed or efficiency could be detected using a mutant of the enzyme lacking the lectin domain. This is the first characterisation of the substrate specificity of a member of the ppGalNAcT family from mollusc origin.
Collapse
Affiliation(s)
- Christopher Taus
- Department of Chemistry, Glycobiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Present Address: Institute of Urology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Markus Windwarder
- Department of Chemistry, Glycobiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, Glycobiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Erika Staudacher
- Department of Chemistry, Glycobiology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|
26
|
Mathias DK, Jardim JG, Parish LA, Armistead JS, Trinh HV, Kumpitak C, Sattabongkot J, Dinglasan RR. Differential roles of an Anopheline midgut GPI-anchored protein in mediating Plasmodium falciparum and Plasmodium vivax ookinete invasion. INFECTION GENETICS AND EVOLUTION 2014; 28:635-47. [PMID: 24929123 DOI: 10.1016/j.meegid.2014.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/19/2014] [Accepted: 05/23/2014] [Indexed: 12/14/2022]
Abstract
Novel strategies to directly thwart malaria transmission are needed to maintain the gains achieved by current control measures. Transmission-blocking interventions (TBIs), namely vaccines and drugs targeting parasite or mosquito molecules required for vector-stage parasite development, have been recognized as promising approaches for preventing malaria transmission. However, the number of TBI targets is limited and their degree of conservation among the major vector-parasite systems causing human disease is unclear. Therefore, discovery and characterization of novel proteins involved in vector-stage parasite development of Plasmodium falciparum and Plasmodium vivax is paramount. We mined the recent Anopheles gambiae midgut lipid raft proteome for putative mosquito-derived TBI targets and characterized a secreted glycoconjugate of unknown function, AgSGU. We analyzed molecular variation in this protein among a range of anopheline mosquitoes, determined its transcriptomic and proteomic profiles, and conducted both standard and direct membrane feeding assays with P. falciparum (lab/field) and P. vivax (field) in An. gambiae and Anopheles dirus. We observed that α-AgSGU antibodies significantly reduced midgut infection intensity for both lab and field isolates of P. falciparum in An. gambiae and An. dirus. However, no transmission-reducing effects were noted when comparable concentrations of antibodies were included in P. vivax-infected blood meals. Although antibodies against AgSGU exhibit transmission-reducing activity, the high antibody titer required for achieving 80% reduction in oocyst intensity precludes its consideration as a malaria mosquito-based TBI candidate. However, our results suggest that P. falciparum and P. vivax ookinetes use a different repertoire of midgut surface glycoproteins for invasion and that α-AgSGU antibodies, as well as antibodies to other mosquito-midgut microvillar surface proteins, may prove useful as tools for interrogating Plasmodium-mosquito interactions.
Collapse
Affiliation(s)
- Derrick K Mathias
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Juliette G Jardim
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Lindsay A Parish
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Jennifer S Armistead
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Hung V Trinh
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | | | | | - Rhoel R Dinglasan
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| |
Collapse
|
27
|
Pedersen NB, Wang S, Narimatsu Y, Yang Z, Halim A, Schjoldager KTBG, Madsen TD, Seidah NG, Bennett EP, Levery SB, Clausen H. Low density lipoprotein receptor class A repeats are O-glycosylated in linker regions. J Biol Chem 2014; 289:17312-24. [PMID: 24798328 DOI: 10.1074/jbc.m113.545053] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The low density lipoprotein receptor (LDLR) is crucial for cholesterol homeostasis and deficiency in LDLR functions cause hypercholesterolemia. LDLR is a type I transmembrane protein that requires O-glycosylation for stable expression at the cell surface. It has previously been suggested that LDLR O-glycosylation is found N-terminal to the juxtamembrane region. Recently we identified O-glycosylation sites in the linker regions between the characteristic LDLR class A repeats in several LDLR-related receptors using the "SimpleCell" O-glycoproteome shotgun strategy. Herein, we have systematically characterized O-glycosylation sites on recombinant LDLR shed from HEK293 SimpleCells and CHO wild-type cells. We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position -1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. The glycosites in linker regions of LDLR class A repeats are conserved in LDLR from man to Xenopus and found in other homologous receptors. O-Glycosylation is controlled by a large family of polypeptide GalNAc transferases. Probing into which isoform(s) contributed to glycosylation of the linker regions of the LDLR class A repeats by in vitro enzyme assays suggested a major role of GalNAc-T11. This was supported by expression of LDLR in HEK293 cells, where knock-out of the GalNAc-T11 isoform resulted in the loss of glycosylation of three of four linker regions.
Collapse
Affiliation(s)
- Nis Borbye Pedersen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Shengjun Wang
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Yoshiki Narimatsu
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Zhang Yang
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Adnan Halim
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Katrine Ter-Borch Gram Schjoldager
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Thomas Daugbjerg Madsen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Nabil G Seidah
- the Clinical Research Institute of Montreal, University of Montreal, Montreal, Quebec H2W 1R7, Canada
| | - Eric Paul Bennett
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Steven B Levery
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Henrik Clausen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| |
Collapse
|
28
|
Gerken TA, Revoredo L, Thome JJC, Tabak LA, Vester-Christensen MB, Clausen H, Gahlay GK, Jarvis DL, Johnson RW, Moniz HA, Moremen K. The lectin domain of the polypeptide GalNAc transferase family of glycosyltransferases (ppGalNAc Ts) acts as a switch directing glycopeptide substrate glycosylation in an N- or C-terminal direction, further controlling mucin type O-glycosylation. J Biol Chem 2013; 288:19900-14. [PMID: 23689369 PMCID: PMC3707691 DOI: 10.1074/jbc.m113.477877] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/17/2013] [Indexed: 01/22/2023] Open
Abstract
Mucin type O-glycosylation is initiated by a large family of polypeptide GalNAc transferases (ppGalNAc Ts) that add α-GalNAc to the Ser and Thr residues of peptides. Of the 20 human isoforms, all but one are composed of two globular domains linked by a short flexible linker: a catalytic domain and a ricin-like lectin carbohydrate binding domain. Presently, the roles of the catalytic and lectin domains in peptide and glycopeptide recognition and specificity remain unclear. To systematically study the role of the lectin domain in ppGalNAc T glycopeptide substrate utilization, we have developed a series of novel random glycopeptide substrates containing a single GalNAc-O-Thr residue placed near either the N or C terminus of the glycopeptide substrate. Our results reveal that the presence and N- or C-terminal placement of the GalNAc-O-Thr can be important determinants of overall catalytic activity and specificity that differ between transferase isoforms. For example, ppGalNAc T1, T2, and T14 prefer C-terminally placed GalNAc-O-Thr, whereas ppGalNAc T3 and T6 prefer N-terminally placed GalNAc-O-Thr. Several transferase isoforms, ppGalNAc T5, T13, and T16, display equally enhanced N- or C-terminal activities relative to the nonglycosylated control peptides. This N- and/or C-terminal selectivity is presumably due to weak glycopeptide binding to the lectin domain, whose orientation relative to the catalytic domain is dynamic and isoform-dependent. Such N- or C-terminal glycopeptide selectivity provides an additional level of control or fidelity for the O-glycosylation of biologically significant sites and suggests that O-glycosylation may in some instances be exquisitely controlled.
Collapse
Affiliation(s)
- Thomas A. Gerken
- From the Departments of Pediatrics (W. A. Bernbaum Center for Cystic Fibrosis Research)
- Biochemistry, and
- Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Leslie Revoredo
- Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Joseph J. C. Thome
- From the Departments of Pediatrics (W. A. Bernbaum Center for Cystic Fibrosis Research)
| | - Lawrence A. Tabak
- the Section on Biological Chemistry, NIDCR, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892
| | - Malene Bech Vester-Christensen
- the Copenhagen Center for Glycomics (CCG), Departments of Cellular and Molecular Medicine and Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- the Copenhagen Center for Glycomics (CCG), Departments of Cellular and Molecular Medicine and Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Gagandeep K. Gahlay
- the Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, and
| | - Donald L. Jarvis
- the Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, and
| | - Roy W. Johnson
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Heather A. Moniz
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Kelley Moremen
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| |
Collapse
|
29
|
Abstract
Mucin-type O-glycosylation is an evolutionarily conserved protein modification present on membrane-bound and secreted proteins. Aberrations in O-glycosylation are responsible for certain human diseases and are associated with disease risk factors. Recent studies have demonstrated essential roles for mucin-type O-glycosylation in protein secretion, stability, processing, and function. Here, we summarize our current understanding of the diverse roles of mucin-type O-glycosylation during eukaryotic development. Appreciating how this conserved modification operates in developmental processes will provide insight into its roles in human disease and disease susceptibilities.
Collapse
Affiliation(s)
- Duy T Tran
- Developmental Glycobiology Section, NIDCR, National Institutes of Health, Bethesda, Maryland 20892-4370, USA
| | | |
Collapse
|
30
|
Schjoldager KTBG, Clausen H. Site-specific protein O-glycosylation modulates proprotein processing - deciphering specific functions of the large polypeptide GalNAc-transferase gene family. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1820:2079-94. [PMID: 23022508 DOI: 10.1016/j.bbagen.2012.09.014] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 01/18/2023]
Abstract
BACKGROUND Posttranslational modifications (PTMs) greatly expand the function and regulation of proteins, and glycosylation is the most abundant and diverse PTM. Of the many different types of protein glycosylation, one is quite unique; GalNAc-type (or mucin-type) O-glycosylation, where biosynthesis is initiated in the Golgi by up to twenty distinct UDP-N-acetyl-α-d-galactosamine:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts). These GalNAc-Ts are differentially expressed in cells and have different (although partly overlapping) substrate specificities, which provide for both unique functions and considerable redundancy. Recently we have begun to uncover human diseases associated with deficiencies in GalNAc-T genes (GALNTs). Thus deficiencies in individual GALNTs produce cell and protein specific effects and subtle distinct phenotypes such as hyperphosphatemia with hyperostosis (GALNT3) and dysregulated lipid metabolism (GALNT2). These phenotypes appear to be caused by deficient site-specific O-glycosylation that co-regulates proprotein convertase (PC) processing of FGF23 and ANGPTL3, respectively. SCOPE OF REVIEW Here we summarize recent progress in uncovering the interplay between human O-glycosylation and protease regulated processing and describes other important functions of site-specific O-glycosylation in health and disease. MAJOR CONCLUSIONS Site-specific O-glycosylation modifies pro-protein processing and other proteolytic events such as ADAM processing and thus emerges as an important co-regulator of limited proteolytic processing events. GENERAL SIGNIFICANCE Our appreciation of this function may have been hampered by our sparse knowledge of the O-glycoproteome and in particular sites of O-glycosylation. New strategies for identification of O-glycoproteins have emerged and recently the concept of SimpleCells, i.e. human cell lines made deficient in O-glycan extension by zinc finger nuclease gene targeting, was introduced for broad O-glycoproteome analysis.
Collapse
|
31
|
Cruz-Cano R, Lee MLT, Leung MY. Logic minimization and rule extraction for identification of functional sites in molecular sequences. BioData Min 2012; 5:10. [PMID: 22897894 PMCID: PMC3492099 DOI: 10.1186/1756-0381-5-10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 07/24/2012] [Indexed: 12/16/2022] Open
Abstract
Background Logic minimization is the application of algebraic axioms to a binary dataset with the purpose of reducing the number of digital variables and/or rules needed to express it. Although logic minimization techniques have been applied to bioinformatics datasets before, they have not been used in classification and rule discovery problems. In this paper, we propose a method based on logic minimization to extract predictive rules for two bioinformatics problems involving the identification of functional sites in molecular sequences: transcription factor binding sites (TFBS) in DNA and O-glycosylation sites in proteins. TFBS are important in various developmental processes and glycosylation is a posttranslational modification critical to protein functions. Methods In the present study, we first transformed the original biological dataset into a suitable binary form. Logic minimization was then applied to generate sets of simple rules to describe the transformed dataset. These rules were used to predict TFBS and O-glycosylation sites. The TFBS dataset is obtained from the TRANSFAC database, while the glycosylation dataset was compiled using information from OGLYCBASE and the Swiss-Prot Database. We performed the same predictions using two standard classification techniques, Artificial Neural Networks (ANN) and Support Vector Machines (SVM), and used their sensitivities and positive predictive values as benchmarks for the performance of our proposed algorithm. SVM were also used to reduce the number of variables included in the logic minimization approach. Results For both TFBS and O-glycosylation sites, the prediction performance of the proposed logic minimization method was generally comparable and, in some cases, superior to the standard ANN and SVM classification methods with the advantage of providing intelligible rules to describe the datasets. In TFBS prediction, logic minimization produced a very small set of simple rules. In glycosylation site prediction, the rules produced were also interpretable and the most popular rules generated appeared to correlate well with recently reported hydrophilic/hydrophobic enhancement values of amino acids around possible O-glycosylation sites. Experiments with Self-Organizing Neural Networks corroborate the practical worth of the logic minimization method for these case studies. Conclusions The proposed logic minimization algorithm provides sets of rules that can be used to predict TFBS and O-glycosylation sites with sensitivity and positive predictive value comparable to those from ANN and SVM. Moreover, the logic minimization method has the additional capability of generating interpretable rules that allow biological scientists to correlate the predictions with other experimental results and to form new hypotheses for further investigation. Additional experiments with alternative rule-extraction techniques demonstrate that the logic minimization method is able to produce accurate rules from datasets with large numbers of variables and limited numbers of positive examples.
Collapse
Affiliation(s)
- Raul Cruz-Cano
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD, USA.
| | | | | |
Collapse
|
32
|
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: 592] [Impact Index Per Article: 49.3] [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
|
33
|
Gerken TA. O-glycoprotein biosynthesis: site localization by Edman degradation and site prediction based on random peptide substrates. Methods Mol Biol 2012; 842:81-108. [PMID: 22259131 DOI: 10.1007/978-1-61779-513-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The characterization of mucin-type O-glycosylation is fraught with extreme difficulty at almost every level of analysis: from difficulties in obtaining glycopeptides suitable for study, their structural heterogeneity, lack of broad acting glycosidase tools capable of simplifying the glycans, and finally the vast complexity of performing analysis on multiply glycosylated glycopeptides. This, along with a lack of known peptide sequence motif(s) for the transferases that initiate mucin-type O-glycosylation, significantly hinders our understanding of mucin-type O-glycosylation at almost every level from their biosynthesis to their biological and biophysical properties. In this chapter, the use of partial chemical deglycosylation coupled with Edman amino acid sequencing is described to quantify sites of O-glycosylation. In addition, the use of oriented random peptide substrates is described for providing the specificities of the polypeptide α-N-acetylgalactosaminyltransferases, which can be used to estimate transferase-specific sites of O-glycosylation.
Collapse
Affiliation(s)
- Thomas A Gerken
- Department of Pediatrics and Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, OH, USA,
| |
Collapse
|
34
|
Raman J, Guan Y, Perrine CL, Gerken TA, Tabak LA. UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferases: completion of the family tree. Glycobiology 2011; 22:768-77. [PMID: 22186971 DOI: 10.1093/glycob/cwr183] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The formation of mucin-type O-glycans is initiated by an evolutionarily conserved family of enzymes, the UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts). The human genome encodes 20 transferases; 17 of which have been characterized functionally. The complexity of the GalNAc-T family reflects the differential patterns of expression among the individual enzyme isoforms and the unique substrate specificities which are required to form the dense arrays of glycans that are essential for mucin function. We report the expression patterns and enzymatic activity of the remaining three members of the family and the further characterization of a recently reported isoform, GalNAc-T17. One isoform, GalNAcT-16 that is most homologous to GalNAc-T14, is widely expressed (abundantly in the heart) and has robust polypeptide transferase activity. The second isoform GalNAc-T18, most similar to GalNAc-T8, -T9 and -T19, completes a discrete subfamily of GalNAc-Ts. It is widely expressed and has low, albeit detectable, activity. The final isoform, GalNAc-T20, is most homologous to GalNAc-T11 but lacks a lectin domain and has no detectable transferase activity with the panel of substrates tested. We have also identified and characterized enzymatically active splice variants of GalNAc-T13 that differ in the sequence of their lectin domain. The variants differ in their affinities for glycopeptide substrates. Our findings provide a comprehensive view of the complexities of mucin-type O-glycan formation and provide insight into the underlying mechanisms employed to heavily decorate mucins and mucin-like domains with carbohydrate.
Collapse
Affiliation(s)
- Jayalakshmi Raman
- Department of Health and Human Services, Section on Biological Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | |
Collapse
|
35
|
Tran DT, Zhang L, Zhang Y, Tian E, Earl LA, Ten Hagen KG. Multiple members of the UDP-GalNAc: polypeptide N-acetylgalactosaminyltransferase family are essential for viability in Drosophila. J Biol Chem 2011; 287:5243-52. [PMID: 22157008 DOI: 10.1074/jbc.m111.306159] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mucin-type O-glycosylation represents a major form of post-translational modification that is conserved across most eukaryotic species. This type of glycosylation is initiated by a family of enzymes (GalNAc-Ts in mammals and PGANTs in Drosophila) whose members are expressed in distinct spatial and temporal patterns during development. Previous work from our group demonstrated that one member of this family is essential for viability and another member modulates extracellular matrix composition and integrin-mediated cell adhesion during development. To investigate whether other members of this family are essential, we employed RNA interference (RNAi) to each gene in vivo. Using this approach, we identified 4 additional pgant genes that are required for viability. Ubiquitous RNAi to pgant4, pgant5, pgant7, or the putative glycosyltransferase CG30463 resulted in lethality. Tissue-specific RNAi was also used to define the specific organ systems and tissues in which each essential family member is required. Interestingly, each essential pgant had a unique complement of tissues in which it was required. Additionally, certain tissues (mesoderm, digestive system, and tracheal system) required more than one pgant, suggesting unique functions for specific enzymes in these tissues. Expanding upon our RNAi results, we found that conventional mutations in pgant5 resulted in lethality and specific defects in specialized cells of the digestive tract, resulting in loss of proper digestive system acidification. In summary, our results highlight essential roles for O-glycosylation and specific members of the pgant family in many aspects of development and organogenesis.
Collapse
Affiliation(s)
- Duy T Tran
- Developmental Glycobiology Unit, NIDCR, National Institutes of Health, Bethesda, Maryland 20892-4370, USA
| | | | | | | | | | | |
Collapse
|
36
|
Pedersen JW, Bennett EP, Schjoldager KTBG, Meldal M, Holmér AP, Blixt O, Cló E, Levery SB, Clausen H, Wandall HH. Lectin domains of polypeptide GalNAc transferases exhibit glycopeptide binding specificity. J Biol Chem 2011; 286:32684-96. [PMID: 21768105 PMCID: PMC3173194 DOI: 10.1074/jbc.m111.273722] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/09/2011] [Indexed: 11/06/2022] Open
Abstract
UDP-GalNAc:polypeptide α-N-acetylgalactosaminyltransferases (GalNAc-Ts) constitute a family of up to 20 transferases that initiate mucin-type O-glycosylation. The transferases are structurally composed of catalytic and lectin domains. Two modes have been identified for the selection of glycosylation sites by GalNAc-Ts: confined sequence recognition by the catalytic domain alone, and concerted recognition of acceptor sites and adjacent GalNAc-glycosylated sites by the catalytic and lectin domains, respectively. Thus far, only the catalytic domain has been shown to have peptide sequence specificity, whereas the primary function of the lectin domain is to increase affinity to previously glycosylated substrates. Whether the lectin domain also has peptide sequence selectivity has remained unclear. Using a glycopeptide array with a library of synthetic and recombinant glycopeptides based on sequences of mucins MUC1, MUC2, MUC4, MUC5AC, MUC6, and MUC7 as well as a random glycopeptide bead library, we examined the binding properties of four different lectin domains. The lectin domains of GalNAc-T1, -T2, -T3, and -T4 bound different subsets of small glycopeptides. These results indicate an additional level of complexity in the initiation step of O-glycosylation by GalNAc-Ts.
Collapse
Affiliation(s)
| | - Eric P. Bennett
- School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N and
| | | | - Morten Meldal
- the Carlsberg Laboratory and Nano Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | | | - Ola Blixt
- From the Department of Cellular and Molecular Medicine and
| | - Emiliano Cló
- From the Department of Cellular and Molecular Medicine and
| | | | - Henrik Clausen
- From the Department of Cellular and Molecular Medicine and
| | | |
Collapse
|
37
|
Abstract
Glycosylation is a very common modification of protein and lipid, and most glycosylation reactions occur in the Golgi. Although the transfer of initial sugar(s) to glycoproteins or glycolipids occurs in the ER or on the ER membrane, the subsequent addition of the many different sugars that make up a mature glycan is accomplished in the Golgi. Golgi membranes are studded with glycosyltransferases, glycosidases, and nucleotide sugar transporters arrayed in a generally ordered manner from the cis-Golgi to the trans-Golgi network (TGN), such that each activity is able to act on specific substrate(s) generated earlier in the pathway. The spectrum of glycosyltransferases and other activities that effect glycosylation may vary with cell type, and thus the final complement of glycans on glycoconjugates is variable. In addition, glycan synthesis is affected by Golgi pH, the integrity of Golgi peripheral membrane proteins, growth factor signaling, Golgi membrane dynamics, and cellular stress. Knowledge of Golgi glycosylation has fostered the development of assays to identify mechanisms of intracellular vesicular trafficking and facilitated glycosylation engineering of recombinant glycoproteins.
Collapse
Affiliation(s)
- Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York 10461, USA.
| |
Collapse
|
38
|
Gill DJ, Clausen H, Bard F. Location, location, location: new insights into O-GalNAc protein glycosylation. Trends Cell Biol 2011; 21:149-58. [PMID: 21145746 DOI: 10.1016/j.tcb.2010.11.004] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/10/2010] [Accepted: 11/11/2010] [Indexed: 01/04/2023]
Abstract
O-GalNAc glycosylation of proteins confers essential structural, protective and signaling roles in eumetazoans. Addition of O-glycans onto proteins is an extremely complex process that regulates both sites of attachment and the types of oligosaccharides added. Twenty distinct polypeptide GalNAc-transferases (GalNAc-Ts) initiate O-glycosylation and fine-tuning their expression provides a mechanism for regulating this action. Recently, a new mode of regulation has emerged where activation of Src kinase selectively redistributes Golgi-localized GalNAc-Ts to the ER. This relocalization results in a strong increase in the density of O-glycan decoration. In this review, we discuss how different mechanisms can regulate the number and the types of O-glycans decorating proteins. In addition, we speculate how Src-dependent relocation of GalNAc-Ts could play an important role in cancerous cellular transformation.
Collapse
Affiliation(s)
- David J Gill
- Institute of Molecular and Cell Biology (IMCB), Proteos, 61 Biopolis Drive, Singapore, 138673
| | | | | |
Collapse
|
39
|
Gerken TA, Jamison O, Perrine CL, Collette JC, Moinova H, Ravi L, Markowitz SD, Shen W, Patel H, Tabak LA. Emerging paradigms for the initiation of mucin-type protein O-glycosylation by the polypeptide GalNAc transferase family of glycosyltransferases. J Biol Chem 2011; 286:14493-507. [PMID: 21349845 DOI: 10.1074/jbc.m111.218701] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian mucin-type O-glycosylation is initiated by a large family of ∼20 UDP-GalNAc:polypeptide α-N-acetylgalactosaminyltransferases (ppGalNAc Ts) that transfer α-GalNAc from UDP-GalNAc to Ser and Thr residues of polypeptide acceptors. Characterizing the peptide substrate specificity of each isoform is critical to understanding their properties, biological roles, and significance. Presently, only the specificities of ppGalNAc T1, T2, and T10 and the fly orthologues of T1 and T2 have been systematically characterized utilizing random peptide substrates. We now extend these studies to ppGalNAc T3, T5, and T12, transferases variously associated with human disease. Our results reveal several common features; the most striking is the similar pattern of enhancements for the three residues C-terminal to the site of glycosylation for those transferases that contain a common conserved Trp. In contrast, residues N-terminal to the site of glycosylation show a wide range of isoform-specific enhancements, with elevated preferences for Pro, Val, and Tyr being the most common at the -1 position. Further analysis reveals that the ratio of positive (Arg, Lys, and His) to negative (Asp and Glu) charged residue enhancements varied among transferases, thus further modulating substrate preference in an isoform-specific manner. By utilizing the obtained transferase-specific preferences, the glycosylation patterns of the ppGalNAc Ts against a series of peptide substrates could roughly be reproduced, demonstrating the potential for predicting isoform-specific glycosylation. We conclude that each ppGalNAc T isoform may be uniquely sensitive to peptide sequence and overall charge, which together dictates the substrate sites that will be glycosylated.
Collapse
Affiliation(s)
- Thomas A Gerken
- Department of Pediatrics (W. A. Bernbaum Center for Cystic Fibrosis Research), Case Western Reserve University, Cleveland, Ohio 44106, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Ju T, Otto VI, Cummings RD. The Tn antigen-structural simplicity and biological complexity. Angew Chem Int Ed Engl 2011; 50:1770-91. [PMID: 21259410 PMCID: PMC7159538 DOI: 10.1002/anie.201002313] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Indexed: 01/01/2023]
Abstract
Glycoproteins in animal cells contain a variety of glycan structures that are added co- and/or posttranslationally to proteins. Of over 20 different types of sugar-amino acid linkages known, the two major types are N-glycans (Asn-linked) and O-glycans (Ser/Thr-linked). An abnormal mucin-type O-glycan whose expression is associated with cancer and several human disorders is the Tn antigen. It has a relatively simple structure composed of N-acetyl-D-galactosamine with a glycosidic α linkage to serine/threonine residues in glycoproteins (GalNAcα1-O-Ser/Thr), and was one of the first glycoconjugates to be chemically synthesized. The Tn antigen is normally modified by a specific galactosyltransferase (T-synthase) in the Golgi apparatus of cells. Expression of active T-synthase is uniquely dependent on the molecular chaperone Cosmc, which is encoded by a gene on the X chromosome. Expression of the Tn antigen can arise as a consequence of mutations in the genes for T-synthase or Cosmc, or genes affecting other steps of O-glycosylation pathways. Because of the association of the Tn antigen with disease, there is much interest in the development of Tn-based vaccines and other therapeutic approaches based on Tn expression.
Collapse
Affiliation(s)
- Tongzhong Ju
- Department of Biochemistry, Emory University School of Medicine, O. Wayne Rollins Research Center, 1510 Clifton Road, Suite 4001, Atlanta, GA 30322 (USA), Fax: (+1) 404‐727‐2738
| | - Vivianne I. Otto
- Institute of Pharmaceutical Sciences, ETH Zurich, 8093 Zurich (Switzerland)
| | - Richard D. Cummings
- Department of Biochemistry, Emory University School of Medicine, O. Wayne Rollins Research Center, 1510 Clifton Road, Suite 4001, Atlanta, GA 30322 (USA), Fax: (+1) 404‐727‐2738
| |
Collapse
|
41
|
Ju T, Otto VI, Cummings RD. Das Tn-Antigen - strukturell einfach und biologisch komplex. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201002313] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
42
|
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
|
43
|
Miwa HE, Gerken TA, Jamison O, Tabak LA. Isoform-specific O-glycosylation of osteopontin and bone sialoprotein by polypeptide N-acetylgalactosaminyltransferase-1. J Biol Chem 2010; 285:1208-19. [PMID: 19880513 PMCID: PMC2801249 DOI: 10.1074/jbc.m109.035436] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 10/08/2009] [Indexed: 11/06/2022] Open
Abstract
Mucin-type O-glycan biosynthesis is regulated by the family of UDP-GalNAc polypeptide:N-acetylgalactosaminlytransfersases (ppGalNAcTs) that catalyzes the first step in the pathway by transferring GalNAc to Ser or Thr residues in a protein from the sugar donor UDP-GalNAc. Because not all Ser/Thr residues are glycosylated, rules must exist that signal which hydroyxamino acids acquire sugar. To date, no universal consensus signal has emerged. Therefore, strategies to deduce the subset of proteins that will be glycosylated by distinct ppGalNAcTs must be developed. Mucin-type O-glycoproteins are present abundantly in bone, where we found multiple ppGalNAcT isoforms, including ppGalNAcT-1, to be highly expressed. Thus, we compared glycoproteins expressed in wild-type and Galnt1-null mice to identify bone-associated proteins that were glycosylated in a ppGalNAcT-1-dependent manner. A reduction in the apparent molecular masses of two SIBLINGs (small integrin binding ligand N-linked glycoproteins), osteopontin (OPN) and bone sialoprotein (BSP) in the Galnt1-null mice relative to those of the wild-type was observed. Several synthetic peptides derived from OPN and BSP sequences were designed to include either known or predicted (in silico) glycosylation sites. In vitro glycosylation assays of these peptides with recombinant ppGalNAcT-1, ppGalNAcT-2, or ppGalNAcT-3 demonstrated that both SIBLINGs contained Thr/Ser residues that were preferentially glycosylated by ppGalNAcT-1. In addition, lysates prepared from wild-type, but not those from Galnt1-null derived osteoblasts, could glycosylate these peptides efficiently, suggesting that OPN and BSP contain sites that are specific for ppGalNAcT-1. Our study presents a novel and systematic approach for identification of isoform-specific substrates of the ppGalNAcT family and suggests ppGalNAcT-1 to be indispensable for O-glycosylation at specific sites of the bone glycoproteins OPN and BSP.
Collapse
Affiliation(s)
- Hazuki E. Miwa
- From the Section on Biological Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892 and
| | - Thomas A. Gerken
- the Departments of Pediatrics and Biochemistry, W. A. Bernbaum Center for Cystic Fibrosis Research, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Oliver Jamison
- the Departments of Pediatrics and Biochemistry, W. A. Bernbaum Center for Cystic Fibrosis Research, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Lawrence A. Tabak
- From the Section on Biological Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892 and
| |
Collapse
|
44
|
Perrine CL, Ganguli A, Wu P, Bertozzi CR, Fritz TA, Raman J, Tabak LA, Gerken TA. Glycopeptide-preferring polypeptide GalNAc transferase 10 (ppGalNAc T10), involved in mucin-type O-glycosylation, has a unique GalNAc-O-Ser/Thr-binding site in its catalytic domain not found in ppGalNAc T1 or T2. J Biol Chem 2009; 284:20387-97. [PMID: 19460755 PMCID: PMC2740463 DOI: 10.1074/jbc.m109.017236] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 05/05/2009] [Indexed: 02/05/2023] Open
Abstract
Mucin-type O-gly co sy la tion is initiated by a large family of UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferases (ppGalNAc Ts) that transfer GalNAc from UDP-GalNAc to the Ser and Thr residues of polypeptide acceptors. Some members of the family prefer previously gly co sylated peptides (ppGalNAc T7 and T10), whereas others are inhibited by neighboring gly co sy la tion (ppGalNAc T1 and T2). Characterizing their peptide and glycopeptide substrate specificity is critical for understanding the biological role and significance of each isoform. Utilizing a series of random peptide and glycopeptide substrates, we have obtained the peptide and glycopeptide specificities of ppGalNAc T10 for comparison with ppGalNAc T1 and T2. For the glycopeptide substrates, ppGalNAc T10 exhibited a single large preference for Ser/Thr-O-GalNAc at the +1 (C-terminal) position relative to the Ser or Thr acceptor site. ppGalNAc T1 and T2 revealed no significant enhancements suggesting Ser/Thr-O-GalNAc was inhibitory at most positions for these isoforms. Against random peptide substrates, ppGalNAc T10 revealed no significant hydrophobic or hydrophilic residue enhancements, in contrast to what has been reported previously for ppGalNAc T1 and T2. Our results reveal that these transferases have unique peptide and glycopeptide preferences demonstrating their substrate diversity and their likely roles ranging from initiating transferases to filling-in transferases.
Collapse
Affiliation(s)
| | | | - Peng Wu
- the Departments of Chemistry and
| | - Carolyn R. Bertozzi
- the Departments of Chemistry and
- Molecular and Cell Biology and
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and
| | - Timothy A. Fritz
- Section on Biological Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892
| | - Jayalakshmi Raman
- Section on Biological Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892
| | - Lawrence A. Tabak
- Section on Biological Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892
| | - Thomas A. Gerken
- From the Departments ofChemistry
- Biochemistry, and
- Pediatrics and
- the W. A. Bernbaum Center for Cystic Fibrosis Research, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
45
|
Perrine C, Ju T, Cummings RD, Gerken TA. Systematic determination of the peptide acceptor preferences for the human UDP-Gal:glycoprotein-alpha-GalNAc beta 3 galactosyltransferase (T-synthase). Glycobiology 2008; 19:321-8. [PMID: 19073881 DOI: 10.1093/glycob/cwn143] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mucin-type protein O-glycosylation is initiated by the addition of alpha-GalNAc to Ser/Thr residues of a polypeptide chain. The addition of beta-Gal to GalNAc by the UDP-Gal:glycoprotein-alpha-GalNAc beta 3 galactosyltransferase (T-synthase), forming the Core 1 structure (beta-Gal(1-3)-alpha-GalNAc-O-Ser/Thr), is a common and biologically significant subsequent step in O-glycan biosynthesis. What dictates the sites of Core 1 glycosylation is poorly understood; however, the peptide sequence and neighboring glycosylation effects have been implicated. To systematically address the role of the peptide sequence on the specificity of T-synthase, we used the oriented random glycopeptide: GAGAXXXX(T-O-GalNAc)XXXXAGAG (where X = G, A, P, V, I, F, Y, S, N, D, E, H, R, and K) as a substrate. The Core 1 glycosylated product was isolated on immobilized PNA (Arachis hypogaea) lectin and its composition determined by Edman amino acid sequencing for comparison with the initial substrate composition, from which transferase preferences were obtained. From these studies, elevated preferences for Gly at the +1 position with moderately high preferences for Phe and Tyr in the +3 position relative to the acceptor Thr-O-GalNAc were found. A number of smaller Pro enhancements were also observed. Basic residues, i.e., Lys, Arg, and His, in any position were disfavored, suggesting electrostatic interactions as an additional important component modulating transferase specificity. This work suggests that there are indeed subtle specific and nonspecific protein-targeting sequence motifs for this transferase.
Collapse
Affiliation(s)
- Cynthia Perrine
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | | |
Collapse
|
46
|
ten Hagen KG, Zhang L, Tian E, Zhang Y. Glycobiology on the fly: developmental and mechanistic insights from Drosophila. Glycobiology 2008; 19:102-11. [PMID: 18824561 DOI: 10.1093/glycob/cwn096] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Drosophila melanogaster offers many unique advantages for deciphering the complexities of glycan biosynthesis and function. The completion of the Drosophila genome sequencing project as well as the comprehensive catalogue of existing mutations and phenotypes have lead to a prolific database where many of the genes involved in glycan synthesis, assembly, modification, and recognition have been identified and characterized. Recent biochemical and molecular studies have elucidated the structure of the glycans present in Drosophila. Powerful genetic approaches have uncovered a number of critical biological roles for glycans during development that impact on our understanding of their function during mammalian development. Here, we summarize key recent findings and provide evidence for the usefulness of this model organism in unraveling the complexities of glycobiology across many species.
Collapse
Affiliation(s)
- Kelly G ten Hagen
- Developmental Glycobiology Unit, NIDCR, National Institutes of Health, Building 30, 30 Convent Drive, MSC 4370, Bethesda, MD 20892-4370, USA.
| | | | | | | |
Collapse
|