1
|
Bao W, Yamasaki T, Nakano M, Nagae M, Kizuka Y. Functions of unique middle loop and C-terminal tail in GnT-III activity and secretion. Biochim Biophys Acta Gen Subj 2025; 1869:130734. [PMID: 39653250 DOI: 10.1016/j.bbagen.2024.130734] [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: 09/03/2024] [Revised: 11/11/2024] [Accepted: 12/05/2024] [Indexed: 12/13/2024]
Abstract
BACKGROUND N-Glycan branching modulates the diversity of protein functions. β1,4-N-acetylglucosaminyltransferase III (GnT-III or MGAT3) produces a unique GlcNAc branch, "bisecting GlcNAc", in N-glycans, and is involved in Alzheimer's disease and cancer. However, the 3D structure and catalytic mechanism of GnT-III are unclear. According to AlphaFold-based structure prediction, GnT-III likely contains two putative disordered segments, a long middle loop (Loop) and a C-terminal tail (Tail). We hypothesized that these segments play important roles in regulating the activity or intracellular behaviors of GnT-III. METHODS We expressed wild-type GnT-III (GnT-III-WT), GnT-III-Loop- and -Tail-deletion mutants in cells. Their in vitro catalytic activity and glycan biosynthesis in cells were examined using high-performance liquid chromatography, UDP-Glo glycosyltransferase assays, and glycomic analysis. Subcellular localization of WT and GnT-III mutants was investigated by immunostaining, and degradation rate and secretion were also examined. RESULTS The Loop-deletion mutant had higher in vitro and in cellulo activity than GnT-III-WT, indicating that Loop suppresses catalytic activity. In contrast, the Tail-deletion mutant showed weaker activity, increased ER localization, and faster degradation than GnT-III-WT, indicating that Tail is required for proper folding. In addition, deletion of Loop led to aberrant shedding of GnT-III, indicating that Loop contains the cleavage site or regulates GnT-III shedding. CONCLUSIONS Loop and Tail of GnT-III play important roles in catalytic activity, folding and shedding. GENERAL SIGNIFICANCE Our results provide further understanding of the catalysis and shedding mechanisms of GnT-III and can help in the development of methods for modifying the levels of bisecting GlcNAc on glycoproteins and in cells.
Collapse
Affiliation(s)
- WanXue Bao
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Takahiro Yamasaki
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Miyako Nakano
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan
| | - Masamichi Nagae
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
| |
Collapse
|
2
|
Wang Y, Lei K, Zhao L, Zhang Y. Clinical glycoproteomics: methods and diseases. MedComm (Beijing) 2024; 5:e760. [PMID: 39372389 PMCID: PMC11450256 DOI: 10.1002/mco2.760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 09/08/2024] [Accepted: 09/10/2024] [Indexed: 10/08/2024] Open
Abstract
Glycoproteins, representing a significant proportion of posttranslational products, play pivotal roles in various biological processes, such as signal transduction and immune response. Abnormal glycosylation may lead to structural and functional changes of glycoprotein, which is closely related to the occurrence and development of various diseases. Consequently, exploring protein glycosylation can shed light on the mechanisms behind disease manifestation and pave the way for innovative diagnostic and therapeutic strategies. Nonetheless, the study of clinical glycoproteomics is fraught with challenges due to the low abundance and intricate structures of glycosylation. Recent advancements in mass spectrometry-based clinical glycoproteomics have improved our ability to identify abnormal glycoproteins in clinical samples. In this review, we aim to provide a comprehensive overview of the foundational principles and recent advancements in clinical glycoproteomic methodologies and applications. Furthermore, we discussed the typical characteristics, underlying functions, and mechanisms of glycoproteins in various diseases, such as brain diseases, cardiovascular diseases, cancers, kidney diseases, and metabolic diseases. Additionally, we highlighted potential avenues for future development in clinical glycoproteomics. These insights provided in this review will enhance the comprehension of clinical glycoproteomic methods and diseases and promote the elucidation of pathogenesis and the discovery of novel diagnostic biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Yujia Wang
- Department of General Practice Ward/International Medical Center WardGeneral Practice Medical Center and Institutes for Systems GeneticsWest China HospitalSichuan UniversityChengduChina
| | - Kaixin Lei
- Department of General Practice Ward/International Medical Center WardGeneral Practice Medical Center and Institutes for Systems GeneticsWest China HospitalSichuan UniversityChengduChina
| | - Lijun Zhao
- Department of General Practice Ward/International Medical Center WardGeneral Practice Medical Center and Institutes for Systems GeneticsWest China HospitalSichuan UniversityChengduChina
| | - Yong Zhang
- Department of General Practice Ward/International Medical Center WardGeneral Practice Medical Center and Institutes for Systems GeneticsWest China HospitalSichuan UniversityChengduChina
| |
Collapse
|
3
|
Hashimoto Y, Kawade H, Bao W, Morii S, Nakano M, Nagae M, Murakami R, Tokoro Y, Nakashima M, Cai Z, Isaji T, Gu J, Nakajima K, Kizuka Y. The K346T mutant of GnT-III bearing weak in vitro and potent intracellular activity. Biochim Biophys Acta Gen Subj 2024; 1868:130663. [PMID: 38936637 DOI: 10.1016/j.bbagen.2024.130663] [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: 05/04/2024] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND N-Acetylglucosaminyltransferase-III (GnT-III, also designated MGAT3) catalyzes the formation of a specific N-glycan branch, bisecting GlcNAc, in the Golgi apparatus. Bisecting GlcNAc is a key residue that suppresses N-glycan maturation and is associated with the pathogenesis of cancer and Alzheimer's disease. However, it remains unclear how GnT-III recognizes its substrates and how GnT-III activity is regulated in cells. METHODS Using AlphaFold2 and structural comparisons, we predicted the key amino acid residues in GnT-III that interact with substrates in the catalytic pocket. We also performed in vitro activity assay, lectin blotting analysis and N-glycomic analysis using point mutants to assess their activity. RESULTS Our data suggested that E320 of human GnT-III is the catalytic center. More interestingly, we found a unique mutant, K346T, that exhibited lower in vitro activity and higher intracellular activity than wild-type GnT-III. The enzyme assays using various substrates showed that the substrate specificity of K346T was unchanged, whereas cycloheximide chase experiments revealed that the K346T mutant has a slightly shorter half-life, suggesting that the mutant is unstable possibly due to a partial misfolding. Furthermore, TurboID-based proximity labeling showed that the localization of the K346T mutant is shifted slightly to the cis side of the Golgi, probably allowing for prior action to competing galactosyltransferases. CONCLUSIONS The slight difference in K346T localization may be responsible for the higher biosynthetic activity despite the reduced activity. GENERAL SIGNIFICANCE Our findings underscore the importance of fine intra-Golgi localization and reaction orders of glycosyltransferases for the biosynthesis of complex glycan structures in cells.
Collapse
Affiliation(s)
- Yuta Hashimoto
- Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan
| | - Haruka Kawade
- Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan
| | - WanXue Bao
- Glyco-Biochemistry Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Sayaka Morii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan
| | - Miyako Nakano
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan
| | - Masamichi Nagae
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan
| | - Reiko Murakami
- Glycoanalytical Chemistry Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Yuko Tokoro
- Glyco-Biochemistry Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Misaki Nakashima
- Glyco-Biochemistry Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Zixuan Cai
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, Japan
| | - Tomoya Isaji
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, Japan
| | - Jianguo Gu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, Japan
| | - Kazuki Nakajima
- Glycoanalytical Chemistry Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Yasuhiko Kizuka
- Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan; Glyco-Biochemistry Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
| |
Collapse
|
4
|
Kizuka Y. Regulation of intracellular activity of N-glycan branching enzymes in mammals. J Biol Chem 2024; 300:107471. [PMID: 38879010 PMCID: PMC11328876 DOI: 10.1016/j.jbc.2024.107471] [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: 03/27/2024] [Revised: 06/01/2024] [Accepted: 06/06/2024] [Indexed: 07/07/2024] Open
Abstract
Most proteins in the secretory pathway are glycosylated, and N-glycans are estimated to be attached to over 7000 proteins in humans. As structural variation of N-glycans critically regulates the functions of a particular glycoprotein, it is pivotal to understand how structural diversity of N-glycans is generated in cells. One of the major factors conferring structural variation of N-glycans is the variable number of N-acetylglucosamine branches. These branch structures are biosynthesized by dedicated glycosyltransferases, including GnT-III (MGAT3), GnT-IVa (MGAT4A), GnT-IVb (MGAT4B), GnT-V (MGAT5), and GnT-IX (GnT-Vb, MGAT5B). In addition, the presence or absence of core modification of N-glycans, namely, core fucose (included as an N-glycan branch in this manuscript), synthesized by FUT8, also confers large structural variation on N-glycans, thereby crucially regulating many protein-protein interactions. Numerous biochemical and medical studies have revealed that these branch structures are involved in a wide range of physiological and pathological processes. However, the mechanisms regulating the activity of the biosynthetic glycosyltransferases are yet to be fully elucidated. In this review, we summarize the previous findings and recent updates regarding regulation of the activity of these N-glycan branching enzymes. We hope that such information will help readers to develop a comprehensive overview of the complex system regulating mammalian N-glycan maturation.
Collapse
Affiliation(s)
- Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan.
| |
Collapse
|
5
|
Suttapitugsakul S, Stavenhagen K, Donskaya S, Bennett DA, Mealer RG, Seyfried NT, Cummings RD. Glycoproteomics Landscape of Asymptomatic and Symptomatic Human Alzheimer's Disease Brain. Mol Cell Proteomics 2022; 21:100433. [PMID: 36309312 PMCID: PMC9706167 DOI: 10.1016/j.mcpro.2022.100433] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/27/2022] Open
Abstract
Molecular changes in the brain of individuals afflicted with Alzheimer's disease (AD) are an intense area of study. Little is known about the role of protein abundance and posttranslational modifications in AD progression and treatment, in particular large-scale intact N-linked glycoproteomics analysis. To elucidate the N-glycoproteome landscape, we developed an approach based on multi-lectin affinity enrichment, hydrophilic interaction chromatography, and LC-MS-based glycoproteomics. We analyzed brain tissue from 10 persons with no cognitive impairment or AD, 10 with asymptomatic AD, and 10 with symptomatic AD, detecting over 300 glycoproteins and 1900 glycoforms across the samples. The majority of glycoproteins have N-glycans that are high-mannosidic or complex chains that are fucosylated and bisected. The Man5 N-glycan was found to occur most frequently at >20% of the total glycoforms. Unlike the glycoproteomes of other tissues, sialylation is a minor feature of the brain N-glycoproteome, occurring at <9% among the glycoforms. We observed AD-associated differences in the number of antennae, frequency of fucosylation, bisection, and other monosaccharides at individual glycosylation sites among samples from our three groups. Further analysis revealed glycosylation differences in subcellular compartments across disease stage, including glycoproteins in the lysosome frequently modified with paucimannosidic glycans. These results illustrate the N-glycoproteomics landscape across the spectrum of AD clinical and pathologic severity and will facilitate a deeper understanding of progression and treatment development.
Collapse
Affiliation(s)
- Suttipong Suttapitugsakul
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathrin Stavenhagen
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Sofia Donskaya
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Robert G Mealer
- Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
6
|
Klarić TS, Lauc G. The dynamic brain N-glycome. Glycoconj J 2022; 39:443-471. [PMID: 35334027 DOI: 10.1007/s10719-022-10055-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 01/17/2023]
Abstract
The attachment of carbohydrates to other macromolecules, such as proteins or lipids, is an important regulatory mechanism termed glycosylation. One subtype of protein glycosylation is asparagine-linked glycosylation (N-glycosylation) which plays a key role in the development and normal functioning of the vertebrate brain. To better understand the role of N-glycans in neurobiology, it's imperative we analyse not only the functional roles of individual structures, but also the collective impact of large-scale changes in the brain N-glycome. The systematic study of the brain N-glycome is still in its infancy and data are relatively scarce. Nevertheless, the prevailing view has been that the neuroglycome is inherently restricted with limited capacity for variation. The development of improved methods for N-glycomics analysis of brain tissue has facilitated comprehensive characterisation of the complete brain N-glycome under various experimental conditions on a larger scale. Consequently, accumulating data suggest that it's more dynamic than previously recognised and that, within a general framework, it has a given capacity to change in response to both intrinsic and extrinsic stimuli. Here, we provide an overview of the many factors that can alter the brain N-glycome, including neurodevelopment, ageing, diet, stress, neuroinflammation, injury, and disease. Given this emerging evidence, we propose that the neuroglycome has a hitherto underappreciated plasticity and we discuss the therapeutic implications of this regarding the possible reversal of pathological changes via interventions. We also briefly review the merits and limitations of N-glycomics as an analytical method before reflecting on some of the outstanding questions in the field.
Collapse
Affiliation(s)
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
7
|
Towards Mapping of the Human Brain N-Glycome with Standardized Graphitic Carbon Chromatography. Biomolecules 2022; 12:biom12010085. [PMID: 35053234 PMCID: PMC8774104 DOI: 10.3390/biom12010085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/21/2022] Open
Abstract
The brain N-glycome is known to be crucial for many biological functions, including its involvement in neuronal diseases. Although large structural studies of brain N-glycans were recently carried out, a comprehensive isomer-specific structural analysis has still not been achieved, as indicated by the recent discovery of novel structures with galactosylated bisecting GlcNAc. Here, we present a detailed, isomer-specific analysis of the human brain N-glycome based on standardized porous graphitic carbon (PGC)-LC-MS/MS. To achieve this goal, we biosynthesized glycans with substitutions typically occurring in the brain N-glycome and acquired their normalized retention times. Comparison of these values with the standardized retention times of neutral and desialylated N-glycan fractions of the human brain led to unambiguous isomer specific assignment of most major peaks. Profound differences in the glycan structures between naturally neutral and desialylated glycans were found. The neutral and sialylated N-glycans derive from diverging biosynthetic pathways and are biosynthetically finished end products, rather than just partially processed intermediates. The focus on structural glycomics defined the structure of human brain N-glycans, amongst these are HNK-1 containing glycans, a bisecting sialyl-lactose and structures with fucose and N-acetylgalactosamine on the same arm, the so-called LDNF epitope often associated with parasitic worms.
Collapse
|
8
|
Helm J, Grünwald-Gruber C, Thader A, Urteil J, Führer J, Stenitzer D, Maresch D, Neumann L, Pabst M, Altmann F. Bisecting Lewis X in Hybrid-Type N-Glycans of Human Brain Revealed by Deep Structural Glycomics. Anal Chem 2021; 93:15175-15182. [PMID: 34723506 PMCID: PMC8600501 DOI: 10.1021/acs.analchem.1c03793] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The importance of
protein glycosylation in the biomedical field
requires methods that not only quantitate structures by their monosaccharide
composition, but also resolve and identify the many isomers expressed
by mammalian cells. The art of unambiguous identification of isomeric
structures in complex mixtures, however, did not yet catch up with
the fast pace of advance of high-throughput glycomics. Here, we present
a strategy for deducing structures with the help of a deci-minute
accurate retention time library for porous graphitic carbon chromatography
with mass spectrometric detection. We implemented the concept for
the fundamental N-glycan type consisting of five
hexoses, four N-acetylhexosamines and one fucose
residue. Nearly all of the 40 biosynthetized isomers occupied unique
elution positions. This result demonstrates the unique isomer selectivity
of porous graphitic carbon. With the help of a rather tightly spaced
grid of isotope-labeled internal N-glycan, standard
retention times were transposed to a standard chromatogram. Application
of this approach to animal and human brain N-glycans
immediately identified the majority of structures as being of the
bisected type. Most notably, it exposed hybrid-type glycans with galactosylated
and even Lewis X containing bisected N-acetylglucosamine,
which have not yet been discovered in a natural source. Thus, the
time grid approach implemented herein facilitated discovery of the
still missing pieces of the N-glycome in our most
noble organ and suggests itself—in conjunction with collision
induced dissociation—as a starting point for the overdue development
of isomer-specific deep structural glycomics.
Collapse
Affiliation(s)
- Johannes Helm
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Andreas Thader
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Jonathan Urteil
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Johannes Führer
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - David Stenitzer
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Laura Neumann
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Martin Pabst
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|