1
|
Pyle JD, Lund SR, O'Toole KH, Saleh L. Virus-encoded glycosyltransferases hypermodify DNA with diverse glycans. Cell Rep 2024; 43:114631. [PMID: 39154342 DOI: 10.1016/j.celrep.2024.114631] [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: 02/01/2024] [Revised: 07/08/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Enzymatic modification of DNA nucleobases can coordinate gene expression, nuclease protection, or mutagenesis. We recently discovered a clade of phage-specific cytosine methyltransferase (MT) and 5-methylpyrimidine dioxygenase (5mYOX) enzymes that produce 5-hydroxymethylcytosine (5hmC) as a precursor for enzymatic hypermodifications on viral genomes. Here, we identify phage MT- and 5mYOX-associated glycosyltransferases (GTs) that catalyze linkage of diverse sugars to 5hmC nucleobase substrates. Metavirome mining revealed thousands of biosynthetic gene clusters containing enzymes with predicted roles in cytosine sugar hypermodification. We developed a platform for high-throughput screening of GT-containing pathways, relying on the Escherichia coli metabolome as a substrate pool. We successfully reconstituted several pathways and isolated diverse sugar modifications appended to cytosine, including mono-, di-, or tri-saccharides comprised of hexoses, N-acetylhexosamines, or heptose. These findings expand our knowledge of hypermodifications on nucleic acids and the origins of corresponding sugar-installing enzymes.
Collapse
Affiliation(s)
- Jesse D Pyle
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Sean R Lund
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Katherine H O'Toole
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Lana Saleh
- Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
| |
Collapse
|
2
|
Wen X, Liu C, Yang F, Wei Z, Li L, Chen H, Han X, Jiao C, Sha A. Accurate Long-Read RNA Sequencing Analysis Reveals the Key Pathways and Candidate Genes under Drought Stress in the Seed Germination Stage in Faba Bean. Int J Mol Sci 2024; 25:8875. [PMID: 39201560 PMCID: PMC11354372 DOI: 10.3390/ijms25168875] [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: 07/08/2024] [Revised: 07/26/2024] [Accepted: 08/11/2024] [Indexed: 09/02/2024] Open
Abstract
Faba bean is an important pulse. It provides proteins for the human diet and is used in industrial foodstuffs, such as flours. Drought stress severely reduces the yield of faba bean, and this can be efficiently overcome through the identification and application of key genes in response to drought. In this study, PacBio and Illumina RNA sequencing techniques were used to identify the key pathways and candidate genes involved in drought stress response. During seed germination, a total of 17,927 full-length transcripts and 12,760 protein-coding genes were obtained. There were 1676 and 811 differentially expressed genes (DEGs) between the varieties E1 and C105 at 16 h and 64 h under drought stress, respectively. Six and nine KEGG pathways were significantly enriched at 16 h and 64 h under drought stress, which produced 40 and 184 nodes through protein-protein interaction (PPI) analysis, respectively. The DEGs of the PPI nodes were involved in the ABA (abscisic acid) and MAPK (mitogen-activated protein kinase) pathways, N-glycosylation, sulfur metabolism, and sugar metabolism. Furthermore, the ectopic overexpression of a key gene, AAT, encoding aspartate aminotransferase (AAT), in tobacco, enhanced drought tolerance. The activities of AAT and peroxidase (POD), the contents of cysteine and isoleucine, were increased, and the contents of malonaldehyde (MDA) and water loss decreased in the overexpressed plants. This study provides a novel insight into genetic response to drought stress and some candidate genes for drought tolerance genetic improvements in this plant.
Collapse
Affiliation(s)
- Xin Wen
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province)/Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China; (X.W.); (Z.W.)
| | - Changyan Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan 430064, China; (C.L.); (L.L.); (H.C.); (X.H.)
| | - Fangwen Yang
- Shanghai Agrobiological Gene Center, Shanghai 201106, China;
| | - Zhengxin Wei
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province)/Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China; (X.W.); (Z.W.)
| | - Li Li
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan 430064, China; (C.L.); (L.L.); (H.C.); (X.H.)
| | - Hongwei Chen
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan 430064, China; (C.L.); (L.L.); (H.C.); (X.H.)
| | - Xuesong Han
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan 430064, China; (C.L.); (L.L.); (H.C.); (X.H.)
| | - Chunhai Jiao
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan 430064, China; (C.L.); (L.L.); (H.C.); (X.H.)
| | - Aihua Sha
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province)/Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China; (X.W.); (Z.W.)
| |
Collapse
|
3
|
Chen S, Pei CX, Xu S, Li H, Liu YS, Wang Y, Jin C, Dean N, Gao XD. Rft1 catalyzes lipid-linked oligosaccharide translocation across the ER membrane. Nat Commun 2024; 15:5157. [PMID: 38886340 PMCID: PMC11182771 DOI: 10.1038/s41467-024-48999-3] [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: 08/06/2023] [Accepted: 05/20/2024] [Indexed: 06/20/2024] Open
Abstract
The eukaryotic asparagine (N)-linked glycan is pre-assembled as a fourteen-sugar oligosaccharide on a lipid carrier in the endoplasmic reticulum (ER). Seven sugars are first added to dolichol pyrophosphate (PP-Dol) on the cytoplasmic face of the ER, generating Man5GlcNAc2-PP-Dol (M5GN2-PP-Dol). M5GN2-PP-Dol is then flipped across the bilayer into the lumen by an ER translocator. Genetic studies identified Rft1 as the M5GN2-PP-Dol flippase in vivo but are at odds with biochemical data suggesting Rft1 is dispensable for flipping in vitro. Thus, the question of whether Rft1 plays a direct or an indirect role during M5GN2-PP-Dol translocation has been controversial for over two decades. We describe a completely reconstituted in vitro assay for M5GN2-PP-Dol translocation and demonstrate that purified Rft1 catalyzes the translocation of M5GN2-PP-Dol across the lipid bilayer. These data, combined with in vitro results demonstrating substrate selectivity and rft1∆ phenotypes, confirm the molecular identity of Rft1 as the M5GN2-PP-Dol ER flippase.
Collapse
Affiliation(s)
- Shuai Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, China
| | - Cai-Xia Pei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Si Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hanjie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yicheng Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, China
| | - Cheng Jin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Neta Dean
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA.
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
4
|
Quintana JI, Delgado S, Rábano M, Azkargorta M, Florencio-Zabaleta M, Unione L, Vivanco MDM, Elortza F, Jiménez-Barbero J, Ardá A. The impact of glycosylation on the structure, function, and interactions of CD14. Glycobiology 2024; 34:cwae002. [PMID: 38227775 PMCID: PMC10987292 DOI: 10.1093/glycob/cwae002] [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: 10/02/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/18/2024] Open
Abstract
CD14 is an innate immune receptor that senses pathogen-associated molecular patterns, such as lipopolysaccharide, to activate the innate immune response. Although CD14 is known to be glycosylated, detailed understanding about the structural and functional significance of this modification is still missing. Herein, an NMR and MS-based study, assisted by MD simulations, has provided a 3D-structural model of glycosylated CD14. Our results reveal the existence of a key N-glycosylation site at Asn282 that exclusively contains unprocessed oligomannnose N-glycans that perfectly fit the concave cavity of the bent-solenoid shaped protein. This site is not accessible to glycosidases and is fundamental for protein folding and secretion. A second N-site at Asn151 displays mostly complex N-glycans, with the typical terminal epitopes of the host cell-line expression system (i.e. βGal, α2,3 and α2,6 sialylated βGal, here), but also particularities, such as the lack of core fucosylation. The glycan at this site points outside the protein surface, resulting in N-glycoforms fully exposed and available for interactions with lectins. In fact, NMR experiments show that galectin-4, proposed as a binder of CD14 on monocytes to induce their differentiation into macrophages-like cells, interacts in vitro with CD14 through the recognition of the terminal glycoepitopes on Asn151. This work provides key information about CD14 glycosylation, which helps to better understand its functional roles and significance. Although protein glycosylation is known to be dynamic and influenced by many factors, some of the features found herein (presence of unprocessed N-glycans and lack of core Fuc) are likely to be protein specific.
Collapse
Affiliation(s)
- Jon Imanol Quintana
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Sandra Delgado
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Miriam Rábano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mirane Florencio-Zabaleta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Luca Unione
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
| | - Maria dM Vivanco
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Félix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Bizkaia 48940, Spain
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Carlos III Health Institute, C. de Melchor Fernández Almagro, 3, Fuencarral-El Pardo, Madrid 28029, Spain
| | - Ana Ardá
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
| |
Collapse
|
5
|
Duran-Romaña R, Houben B, De Vleeschouwer M, Louros N, Wilson MP, Matthijs G, Schymkowitz J, Rousseau F. N-glycosylation as a eukaryotic protective mechanism against protein aggregation. SCIENCE ADVANCES 2024; 10:eadk8173. [PMID: 38295165 PMCID: PMC10830103 DOI: 10.1126/sciadv.adk8173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
The tendency for proteins to form aggregates is an inherent part of every proteome and arises from the self-assembly of short protein segments called aggregation-prone regions (APRs). While posttranslational modifications (PTMs) have been implicated in modulating protein aggregation, their direct role in APRs remains poorly understood. In this study, we used a combination of proteome-wide computational analyses and biophysical techniques to investigate the potential involvement of PTMs in aggregation regulation. Our findings reveal that while most PTM types are disfavored near APRs, N-glycosylation is enriched and evolutionarily selected, especially in proteins prone to misfolding. Experimentally, we show that N-glycosylation inhibits the aggregation of peptides in vitro through steric hindrance. Moreover, mining existing proteomics data, we find that the loss of N-glycans at the flanks of APRs leads to specific protein aggregation in Neuro2a cells. Our findings indicate that, among its many molecular functions, N-glycosylation directly prevents protein aggregation in higher eukaryotes.
Collapse
Affiliation(s)
- Ramon Duran-Romaña
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Matthias De Vleeschouwer
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Matthew P. Wilson
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Gert Matthijs
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
6
|
Raval PK, Garg SG, Gould SB. Endosymbiotic selective pressure at the origin of eukaryotic cell biology. eLife 2022; 11:e81033. [PMID: 36355038 PMCID: PMC9648965 DOI: 10.7554/elife.81033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
The dichotomy that separates prokaryotic from eukaryotic cells runs deep. The transition from pro- to eukaryote evolution is poorly understood due to a lack of reliable intermediate forms and definitions regarding the nature of the first host that could no longer be considered a prokaryote, the first eukaryotic common ancestor, FECA. The last eukaryotic common ancestor, LECA, was a complex cell that united all traits characterising eukaryotic biology including a mitochondrion. The role of the endosymbiotic organelle in this radical transition towards complex life forms is, however, sometimes questioned. In particular the discovery of the asgard archaea has stimulated discussions regarding the pre-endosymbiotic complexity of FECA. Here we review differences and similarities among models that view eukaryotic traits as isolated coincidental events in asgard archaeal evolution or, on the contrary, as a result of and in response to endosymbiosis. Inspecting eukaryotic traits from the perspective of the endosymbiont uncovers that eukaryotic cell biology can be explained as having evolved as a solution to housing a semi-autonomous organelle and why the addition of another endosymbiont, the plastid, added no extra compartments. Mitochondria provided the selective pressures for the origin (and continued maintenance) of eukaryotic cell complexity. Moreover, they also provided the energetic benefit throughout eukaryogenesis for evolving thousands of gene families unique to eukaryotes. Hence, a synthesis of the current data lets us conclude that traits such as the Golgi apparatus, the nucleus, autophagosomes, and meiosis and sex evolved as a response to the selective pressures an endosymbiont imposes.
Collapse
Affiliation(s)
- Parth K Raval
- Institute for Molecular Evolution, Heinrich-Heine-University DüsseldorfDusseldorfGermany
| | - Sriram G Garg
- Evolutionary Biochemistry Group, Max-Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine-University DüsseldorfDusseldorfGermany
| |
Collapse
|
7
|
Burchill L, Males A, Kaur A, Davies GJ, Williams SJ. Structure, Function and Mechanism of N‐Glycan Processing Enzymes:
endo
‐α‐1,2‐Mannanase and
endo
‐α‐1,2‐Mannosidase. Isr J Chem 2022. [DOI: 10.1002/ijch.202200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura Burchill
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Alexandra Males
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Arashdeep Kaur
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Gideon J. Davies
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| |
Collapse
|
8
|
Kontou A, Herman EK, Field MC, Dacks JB, Koumandou VL. Evolution of factors shaping the endoplasmic reticulum. Traffic 2022; 23:462-473. [PMID: 36040076 PMCID: PMC9804665 DOI: 10.1111/tra.12863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/30/2022] [Accepted: 07/24/2022] [Indexed: 01/09/2023]
Abstract
Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post-translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organelle and the nature of lineage-specific modifications remain poorly studied. To understand the evolution of factors mediating ER morphology and function we report a comparative genomics analysis of experimentally characterized ER-associated proteins involved in maintaining ER structure. We find that reticulons, REEPs, atlastins, Ufe1p, Use1p, Dsl1p, TBC1D20, Yip3p and VAPs are highly conserved, suggesting an origin at least as early as the last eukaryotic common ancestor (LECA), although many of these proteins possess additional non-ER functions in modern eukaryotes. Secondary losses are common in individual species and in certain lineages, for example lunapark is missing from the Stramenopiles and the Alveolata. Lineage-specific innovations include protrudin, Caspr1, Arl6IP1, p180, NogoR, kinectin and CLIMP-63, which are restricted to the Opisthokonta. Hence, much of the machinery required to build and maintain the ER predates the LECA, but alternative strategies for the maintenance and elaboration of ER shape and function are present in modern eukaryotes. Moreover, experimental investigations for ER maintenance factors in diverse eukaryotes are expected to uncover novel mechanisms.
Collapse
Affiliation(s)
- Aspasia Kontou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
| | - Emily K. Herman
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Present address:
Department of Agricultural, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Mark C. Field
- School of Life SciencesUniversity of DundeeDundeeUK,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and EnvironmentUniversity College of LondonLondonUK
| | - V. Lila Koumandou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
| |
Collapse
|
9
|
Cao X, Shao Y, Meng P, Cao Z, Yan G, Yao J, Zhou X, Liu C, Zhang L, Shu H, Lu H. Nascent Proteome and Glycoproteome Reveal the Inhibition Role of ALG1 in Hepatocellular Carcinoma Cell Migration. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:230-241. [PMID: 36939752 PMCID: PMC9590484 DOI: 10.1007/s43657-022-00050-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/14/2022] [Accepted: 03/20/2022] [Indexed: 12/09/2022]
Abstract
Asparagine-linked glycosylation protein 1 homolog (ALG1) participates in the initial stage of protein N-glycosylation and N-glycosylation has been implicated in the process of hepatocellular carcinoma (HCC) progression. However, whether ALG1 plays a role in human HCC remains unknown. In this study, the expression profile of ALG1 in tumorous and corresponding adjacent non-tumor tissues was analyzed. The relationship of ALG1 expression with clinical features and prognosis of HCC patients was also evaluated using immuno-histochemical method. Here we found ALG1 decreased in HCC tissues compared with adjacent normal liver tissues, which predicted an unfavorable prognosis. Combined with RNA interference, nascent proteome and glycoproteome were determined systematically in Huh7 cell line. Bioinformatics analysis indicated that the differentially expressed proteins participating in the response of ALG1 knockdown were most significantly associated with cell-cell adhesion. Functional studies confirmed that knockdown of ALG1 reduced cell adhesion capacity, and promoted cell migration. Furthermore, down-regulation of H8N2 (on N-glycosite N651) and H5N4S2F1 (on N-glycosite N692) from N-cadherin was identified as a feature of ALG1 knockdown. Our findings revealed that ALG1 controlled the expression of glycosylated N-cadherin and played a role in HCC migration, with implications for prognosis. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00050-5.
Collapse
Affiliation(s)
- Xinyi Cao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Yuyin Shao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Peiyi Meng
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200433 China
| | - Zhao Cao
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Guoquan Yan
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Jun Yao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Xinwen Zhou
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Chao Liu
- Beijing Advanced Innovation Center for Precision Medicine, Beihang University, Beijing, 100083 China
| | - Lei Zhang
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Hong Shu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021 China
| | - Haojie Lu
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200433 China
| |
Collapse
|
10
|
Concerted Regulation of Glycosylation Factors Sustains Tissue Identity and Function. Biomedicines 2022; 10:biomedicines10081805. [PMID: 36009354 PMCID: PMC9404854 DOI: 10.3390/biomedicines10081805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022] Open
Abstract
Glycosylation is a fundamental cellular process affecting human development and health. Complex machinery establishes the glycan structures whose heterogeneity provides greater structural diversity than other post-translational modifications. Although known to present spatial and temporal diversity, the evolution of glycosylation and its role at the tissue-specific level is poorly understood. In this study, we combined genome and transcriptome profiles of healthy and diseased tissues to uncover novel insights into the complex role of glycosylation in humans. We constructed a catalogue of human glycosylation factors, including transferases, hydrolases and other genes directly involved in glycosylation. These were categorized as involved in N-, O- and lipid-linked glycosylation, glypiation, and glycosaminoglycan synthesis. Our data showed that these glycosylation factors constitute an ancient family of genes, where evolutionary constraints suppressed large gene duplications, except for genes involved in O-linked and lipid glycosylation. The transcriptome profiles of 30 healthy human tissues revealed tissue-specific expression patterns preserved across mammals. In addition, clusters of tightly co-expressed genes suggest a glycosylation code underlying tissue identity. Interestingly, several glycosylation factors showed tissue-specific profiles varying with age, suggesting a role in ageing-related disorders. In cancer, our analysis revealed that glycosylation factors are highly perturbed, at the genome and transcriptome levels, with a strong predominance of copy number alterations. Moreover, glycosylation factor dysregulation was associated with distinct cellular compositions of the tumor microenvironment, reinforcing the impact of glycosylation in modulating the immune system. Overall, this work provides genome-wide evidence that the glycosylation machinery is tightly regulated in healthy tissues and impaired in ageing and tumorigenesis, unveiling novel potential roles as prognostic biomarkers or therapeutic targets.
Collapse
|
11
|
Meyer BH, Adam PS, Wagstaff BA, Kolyfetis GE, Probst AJ, Albers SV, Dorfmueller HC. Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes. eLife 2022; 11:e67448. [PMID: 35394422 PMCID: PMC8993221 DOI: 10.7554/elife.67448] [Citation(s) in RCA: 1] [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: 02/11/2021] [Accepted: 03/13/2022] [Indexed: 11/13/2022] Open
Abstract
Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.
Collapse
Affiliation(s)
- Benjamin H Meyer
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbial Ecology, University of Duisburg-EssenEssenGermany
- Division of Molecular Microbiology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
- Molecular Biology of Archaea, Faculty of Biology, University of FreiburgFreiburgGermany
| | - Panagiotis S Adam
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry University Duisburg-EssenEssenGermany
| | - Ben A Wagstaff
- Division of Molecular Microbiology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - George E Kolyfetis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of AthensAthensGreece
| | - Alexander J Probst
- Centre of Water and Environmental Research (ZWU), University of Duisburg-EssenEssenGermany
| | - Sonja V Albers
- Molecular Biology of Archaea, Faculty of Biology, University of FreiburgFreiburgGermany
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| |
Collapse
|
12
|
(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants. Life (Basel) 2022; 12:life12020324. [PMID: 35207610 PMCID: PMC8874572 DOI: 10.3390/life12020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.
Collapse
|
13
|
Barbosa EA, Alves GSC, Coura MDMA, Silva HDLE, Rocha FSD, Nunes JB, Watanabe MDS, Andrade AC, Brand GD. A first look at the N- and O-glycosylation landscape in anuran skin secretions. Biochimie 2022; 197:19-37. [DOI: 10.1016/j.biochi.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/08/2022] [Accepted: 01/17/2022] [Indexed: 11/26/2022]
|
14
|
Toustou C, Walet-Balieu ML, Kiefer-Meyer MC, Houdou M, Lerouge P, Foulquier F, Bardor M. Towards understanding the extensive diversity of protein N-glycan structures in eukaryotes. Biol Rev Camb Philos Soc 2021; 97:732-748. [PMID: 34873817 PMCID: PMC9300197 DOI: 10.1111/brv.12820] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 11/04/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022]
Abstract
N‐glycosylation is an important post‐translational modification of proteins that has been highly conserved during evolution and is found in Eukaryota, Bacteria and Archaea. In eukaryotes, N‐glycan processing is sequential, involving multiple specific steps within the secretory pathway as proteins travel through the endoplasmic reticulum and the Golgi apparatus. In this review, we first summarize the different steps of the N‐glycan processing and further describe recent findings regarding the diversity of N‐glycan structures in eukaryotic clades. This comparison allows us to explore the different regulation mechanisms of N‐glycan processing among eukaryotic clades. Recent findings regarding the regulation of protein N‐glycosylation are highlighted, especially the regulation of the biosynthesis of complex‐type N‐glycans through manganese and calcium homeostasis and the specific role of transmembrane protein 165 (TMEM165) for which homologous sequences have been identified in several eukaryotic clades. Further research will be required to characterize the function of TMEM165 homologous sequences in different eukaryotic clades.
Collapse
Affiliation(s)
- Charlotte Toustou
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - Marie-Laure Walet-Balieu
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - Marie-Christine Kiefer-Meyer
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - Marine Houdou
- Univ Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, F-59000, France.,Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, Box 802, Leuven, 3000, Belgium
| | - Patrice Lerouge
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France
| | - François Foulquier
- Univ Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, F-59000, France
| | - Muriel Bardor
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, Mont-Saint-Aignan, 76821, France.,Univ Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, F-59000, France
| |
Collapse
|
15
|
De Coninck T, Gistelinck K, Janse van Rensburg HC, Van den Ende W, Van Damme EJM. Sweet Modifications Modulate Plant Development. Biomolecules 2021; 11:756. [PMID: 34070047 PMCID: PMC8158104 DOI: 10.3390/biom11050756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
Collapse
Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Koen Gistelinck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Henry C. Janse van Rensburg
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Els J. M. Van Damme
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| |
Collapse
|
16
|
Alzan HF, Bastos RG, Ueti MW, Laughery JM, Rathinasamy VA, Cooke BM, Suarez CE. Assessment of Babesia bovis 6cys A and 6cys B as components of transmission blocking vaccines for babesiosis. Parasit Vectors 2021; 14:210. [PMID: 33879245 PMCID: PMC8056569 DOI: 10.1186/s13071-021-04712-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Background Babesia bovis reproduces sexually in the gut of its tick vector Rhipicephalus microplus, which involves expression of 6cys A and 6cys B proteins. Members of the widely conserved 6cys superfamily are candidates for transmission blocking vaccines (TBV), but intricacies in the immunogenicity of the 6cys proteins in the related Plasmodium parasites required the identification of transmission blocking domains in these molecules for vaccine design. Hereby, the immunogenic efficacy of recombinant (r) B. bovis 6cys A and B proteins as a TBV formulation was studied. Methods The immunogenicity of r6cys A and 6cys B proteins expressed in a eukaryotic system was evaluated in a cattle immunization trial (3 immunized and 3 control calves). A B. bovis sexual stage induction in vitro inhibition assay to assess the ability of antibodies to block the production of sexual forms by the parasite was developed. Results Immunized cattle generated antibodies against r6cys A and r6cys B that were unable to block sexual reproduction of the parasite in ticks. Additionally, these antibodies also failed in recognizing native 6cys A and 6cys B and peptides representing 6cys A and 6cys B functional domains and in inhibiting the development of sexual forms in an in vitro induction system. In contrast, rabbit antibodies generated against synthetic peptides representing predicted B-cell epitopes of 6cys A and 6cys B recognized recombinant and native forms of both 6cys proteins as well as peptides representing 6cys A and 6cys B functional domains and were able to neutralize development of sexual forms of the parasite in vitro. Conclusions These data, combined with similar work performed on Plasmodium 6cys proteins, indicate that an effective 6cys protein-based TBV against B. bovis will require identifying and targeting selected regions of proteins containing epitopes able to reduce transmission. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04712-7.
Collapse
Affiliation(s)
- Heba F Alzan
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA. .,Parasitology and Animal Diseases Department, National Research Center, Dokki, Giza, Egypt. .,Tick and Tick-Borne Disease Research Unit, National Research Center, Dokki, Giza, 12622, Egypt.
| | - Reginaldo G Bastos
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Massaro W Ueti
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.,Animal Disease Research Unit, United States Department of Agricultural - Agricultural Research Service, Pullman, WA, USA
| | - Jacob M Laughery
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Vignesh A Rathinasamy
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Brian M Cooke
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Carlos E Suarez
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA. .,Animal Disease Research Unit, United States Department of Agricultural - Agricultural Research Service, Pullman, WA, USA.
| |
Collapse
|
17
|
García-Carnero LC, Martínez-Álvarez JA, Salazar-García LM, Lozoya-Pérez NE, González-Hernández SE, Tamez-Castrellón AK. Recognition of Fungal Components by the Host Immune System. Curr Protein Pept Sci 2021; 21:245-264. [PMID: 31889486 DOI: 10.2174/1389203721666191231105546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/08/2019] [Accepted: 10/15/2019] [Indexed: 11/22/2022]
Abstract
By being the first point of contact of the fungus with the host, the cell wall plays an important role in the pathogenesis, having many molecules that participate as antigens that are recognized by immune cells, and also that help the fungus to establish infection. The main molecules reported to trigger an immune response are chitin, glucans, oligosaccharides, proteins, melanin, phospholipids, and others, being present in the principal pathogenic fungi with clinical importance worldwide, such as Histoplasma capsulatum, Paracoccidioides brasiliensis, Aspergillus fumigatus, Candida albicans, Cryptococcus neoformans, Blastomyces dermatitidis, and Sporothrix schenckii. Knowledge and understanding of how the immune system recognizes and responds to fungal antigens are relevant for the future research and development of new diagnostic tools and treatments for the control of mycosis caused by these fungi.
Collapse
Affiliation(s)
- Laura C García-Carnero
- Department of Biology, Exact and Natural Sciences Division, Universidad de Guanajuato, Guanajuato, Mexico
| | - José A Martínez-Álvarez
- Department of Biology, Exact and Natural Sciences Division, Universidad de Guanajuato, Guanajuato, Mexico
| | - Luis M Salazar-García
- Department of Biology, Exact and Natural Sciences Division, Universidad de Guanajuato, Guanajuato, Mexico
| | - Nancy E Lozoya-Pérez
- Department of Biology, Exact and Natural Sciences Division, Universidad de Guanajuato, Guanajuato, Mexico
| | | | - Alma K Tamez-Castrellón
- Department of Biology, Exact and Natural Sciences Division, Universidad de Guanajuato, Guanajuato, Mexico
| |
Collapse
|
18
|
Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target. Proc Natl Acad Sci U S A 2020; 117:29595-29601. [PMID: 33154157 PMCID: PMC7703563 DOI: 10.1073/pnas.2013620117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from Glc3Man9GlcNAc2 precursors that are trimmed and modified in the endoplasmic reticulum (ER) and Golgi apparatus by glycoside hydrolases and glycosyltransferases. Endo-α-1,2-mannosidase (MANEA) is the sole endo-acting glycoside hydrolase involved in N-glycan trimming and is located within the Golgi, where it allows ER-escaped glycoproteins to bypass the classical N-glycosylation trimming pathway involving ER glucosidases I and II. There is considerable interest in the use of small molecules that disrupt N-linked glycosylation as therapeutic agents for diseases such as cancer and viral infection. Here we report the structure of the catalytic domain of human MANEA and complexes with substrate-derived inhibitors, which provide insight into dynamic loop movements that occur on substrate binding. We reveal structural features of the human enzyme that explain its substrate preference and the mechanistic basis for catalysis. These structures have inspired the development of new inhibitors that disrupt host protein N-glycan processing of viral glycans and reduce the infectivity of bovine viral diarrhea and dengue viruses in cellular models. These results may contribute to efforts aimed at developing broad-spectrum antiviral agents and help provide a more in-depth understanding of the biology of mammalian glycosylation.
Collapse
|
19
|
Illiano A, Pinto G, Melchiorre C, Carpentieri A, Faraco V, Amoresano A. Protein Glycosylation Investigated by Mass Spectrometry: An Overview. Cells 2020; 9:E1986. [PMID: 32872358 PMCID: PMC7564411 DOI: 10.3390/cells9091986] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
The protein glycosylation is a post-translational modification of crucial importance for its involvement in molecular recognition, protein trafficking, regulation, and inflammation. Indeed, abnormalities in protein glycosylation are correlated with several disease states such as cancer, inflammatory diseases, and congenial disorders. The understanding of cellular mechanisms through the elucidation of glycan composition encourages researchers to find analytical solutions for their detection. Actually, the multiplicity and diversity of glycan structures bond to the proteins, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies make their detection much trickier than other kinds of biopolymers. An overview of the most prominent techniques based on mass spectrometry (MS) for protein glycosylation (glycoproteomics) studies is here presented. The tricks and pre-treatments of samples are discussed as a crucial step prodromal to the MS analysis to improve the glycan ionization efficiency. Therefore, the different instrumental MS mode is also explored for the qualitative and quantitative analysis of glycopeptides and the glycans structural composition, thus contributing to the elucidation of biological mechanisms.
Collapse
Affiliation(s)
- Anna Illiano
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
- CEINGE Advanced Biotechnology, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Chiara Melchiorre
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Andrea Carpentieri
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
- Istituto Nazionale Biostrutture e Biosistemi—Consorzio Interuniversitario, Viale delle Medaglie d’Oro, 305, 00136 Rome, Italy
| |
Collapse
|
20
|
Computational Chemogenomics Drug Repositioning Strategy Enables the Discovery of Epirubicin as a New Repurposed Hit for Plasmodium falciparum and P. vivax. Antimicrob Agents Chemother 2020; 64:AAC.02041-19. [PMID: 32601162 PMCID: PMC7449180 DOI: 10.1128/aac.02041-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Widespread resistance against antimalarial drugs thwarts current efforts for controlling the disease and urges the discovery of new effective treatments. Drug repositioning is increasingly becoming an attractive strategy since it can reduce costs, risks, and time-to-market. Herein, we have used this strategy to identify novel antimalarial hits. We used a comparative in silico chemogenomics approach to select Plasmodium falciparum and Plasmodium vivax proteins as potential drug targets and analyzed them using a computer-assisted drug repositioning pipeline to identify approved drugs with potential antimalarial activity. Widespread resistance against antimalarial drugs thwarts current efforts for controlling the disease and urges the discovery of new effective treatments. Drug repositioning is increasingly becoming an attractive strategy since it can reduce costs, risks, and time-to-market. Herein, we have used this strategy to identify novel antimalarial hits. We used a comparative in silico chemogenomics approach to select Plasmodium falciparum and Plasmodium vivax proteins as potential drug targets and analyzed them using a computer-assisted drug repositioning pipeline to identify approved drugs with potential antimalarial activity. Among the seven drugs identified as promising antimalarial candidates, the anthracycline epirubicin was selected for further experimental validation. Epirubicin was shown to be potent in vitro against sensitive and multidrug-resistant P. falciparum strains and P. vivax field isolates in the nanomolar range, as well as being effective against an in vivo murine model of Plasmodium yoelii. Transmission-blocking activity was observed for epirubicin in vitro and in vivo. Finally, using yeast-based haploinsufficiency chemical genomic profiling, we aimed to get insights into the mechanism of action of epirubicin. Beyond the target predicted in silico (a DNA gyrase in the apicoplast), functional assays suggested a GlcNac-1-P-transferase (GPT) enzyme as a potential target. Docking calculations predicted the binding mode of epirubicin with DNA gyrase and GPT proteins. Epirubicin is originally an antitumoral agent and presents associated toxicity. However, its antiplasmodial activity against not only P. falciparum but also P. vivax in different stages of the parasite life cycle supports the use of this drug as a scaffold for hit-to-lead optimization in malaria drug discovery.
Collapse
|
21
|
Eichler J. N-glycosylation in Archaea-New roles for an ancient posttranslational modification. Mol Microbiol 2020; 114:735-741. [PMID: 32633872 DOI: 10.1111/mmi.14569] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/27/2020] [Indexed: 12/26/2022]
Abstract
Genome analysis points to N-glycosylation as being an almost universal posttranslational modification in Archaea. Although such predictions have been confirmed in only a limited number of species, such studies are making it increasingly clear that the N-linked glycans which decorate archaeal glycoproteins present diversity in terms of both glycan composition and architecture far beyond what is seen in the other two domains of life. In addition to continuing to decipher pathways of N-glycosylation, recent efforts have revealed how Archaea exploit this variability in novel roles. As well as encouraging glycoprotein synthesis, folding and assembly into properly functioning higher ordered complexes, N-glycosylation also provides Archaea with a strategy to cope with changing environments. Archaea can, moreover, exploit the apparent species-specific nature of N-glycosylation for selectivity in mating, and hence, to maintain species boundaries, and in other events where cell-selective interactions are required. At the same time, addressing components of N-glycosylation pathways across archaeal phylogeny offers support for the concept of an archaeal origin for eukaryotes. In this MicroReview, these and other recent discoveries related to N-glycosylation in Archaea are considered.
Collapse
Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| |
Collapse
|
22
|
Gandini R, Reichenbach T, Spadiut O, Tan TC, Kalyani DC, Divne C. A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays an Unexpected Minimal Cellulose-Synthase-like Fold. J Mol Biol 2020; 432:4658-4672. [PMID: 32569746 DOI: 10.1016/j.jmb.2020.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
Protein glycosylation constitutes a critical post-translational modification that supports a vast number of biological functions in living organisms across all domains of life. A seemingly boundless number of enzymes, glycosyltransferases, are involved in the biosynthesis of these protein-linked glycans. Few glycan-biosynthetic glycosyltransferases have been characterized in vitro, mainly due to the majority being integral membrane proteins and the paucity of relevant acceptor substrates. The crenarchaeote Pyrobaculum calidifontis belongs to the TACK superphylum of archaea (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) that has been proposed as an eukaryotic ancestor. In archaea, N-glycans are mainly found on cell envelope surface-layer proteins, archaeal flagellins and pili. Archaeal N-glycans are distinct from those of eukaryotes, but one noteworthy exception is the high-mannose N-glycan produced by P. calidifontis, which is similar in sugar composition to the eukaryotic counterpart. Here, we present the characterization and crystal structure of the first member of a crenarchaeal membrane glycosyltransferase, PcManGT. We show that the enzyme is a GDP-, dolichylphosphate-, and manganese-dependent mannosyltransferase. The membrane domain of PcManGT includes three transmembrane helices that topologically coincide with "half" of the six-transmembrane helix cellulose-binding tunnel in Rhodobacter spheroides cellulose synthase BcsA. Conceivably, this "half tunnel" would be suitable for binding the dolichylphosphate-linked acceptor substrate. The PcManGT gene (Pcal_0472) is located in a large gene cluster comprising 14 genes of which 6 genes code for glycosyltransferases, and we hypothesize that this cluster may constitute a crenarchaeal N-glycosylation (PNG) gene cluster.
Collapse
Affiliation(s)
- Rosaria Gandini
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Tom Reichenbach
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Oliver Spadiut
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Tien-Chye Tan
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Dayanand C Kalyani
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Christina Divne
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden.
| |
Collapse
|
23
|
Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
Collapse
Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| |
Collapse
|
24
|
Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
Collapse
Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| |
Collapse
|
25
|
López-García P, Moreira D. The Syntrophy hypothesis for the origin of eukaryotes revisited. Nat Microbiol 2020; 5:655-667. [DOI: 10.1038/s41564-020-0710-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/13/2020] [Indexed: 11/10/2022]
|
26
|
Tretina K, Pelle R, Orvis J, Gotia HT, Ifeonu OO, Kumari P, Palmateer NC, Iqbal SBA, Fry LM, Nene VM, Daubenberger CA, Bishop RP, Silva JC. Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms. BMC Genomics 2020; 21:279. [PMID: 32245418 PMCID: PMC7126163 DOI: 10.1186/s12864-020-6683-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/18/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parva. Over a million bovines die each year of ECF, with a tremendous economic burden to pastoralists in endemic countries. Comprehensive, accurate parasite genome annotation can facilitate the discovery of novel chemotherapeutic targets for disease treatment, as well as elucidate the biology of the parasite. However, genome annotation remains a significant challenge because of limitations in the quality and quantity of the data being used to inform the location and function of protein-coding genes and, when RNA data are used, the underlying biological complexity of the processes involved in gene expression. Here, we apply our recently published RNAseq dataset derived from the schizont life-cycle stage of T. parva to update structural and functional gene annotations across the entire nuclear genome. RESULTS The re-annotation effort lead to evidence-supported updates in over half of all protein-coding sequence (CDS) predictions, including exon changes, gene merges and gene splitting, an increase in average CDS length of approximately 50 base pairs, and the identification of 128 new genes. Among the new genes identified were those involved in N-glycosylation, a process previously thought not to exist in this organism and a potentially new chemotherapeutic target pathway for treating ECF. Alternatively-spliced genes were identified, and antisense and multi-gene family transcription were extensively characterized. CONCLUSIONS The process of re-annotation led to novel insights into the organization and expression profiles of protein-coding sequences in this parasite, and uncovered a minimal N-glycosylation pathway that changes our current understanding of the evolution of this post-translational modification in apicomplexan parasites.
Collapse
Affiliation(s)
- Kyle Tretina
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Roger Pelle
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hanzel T Gotia
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Olukemi O Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Priti Kumari
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Nicholas C Palmateer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Shaikh B A Iqbal
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lindsay M Fry
- Animal Disease Research Unit, Agricultural Research Service, USDA, Pullman, WA, 99164, USA
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, 99164, USA
| | | | - Claudia A Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Richard P Bishop
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| |
Collapse
|
27
|
Taujale R, Venkat A, Huang LC, Zhou Z, Yeung W, Rasheed KM, Li S, Edison AS, Moremen KW, Kannan N. Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases. eLife 2020; 9:54532. [PMID: 32234211 PMCID: PMC7185993 DOI: 10.7554/elife.54532] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosyltransferases (GTs) are prevalent across the tree of life and regulate nearly all aspects of cellular functions. The evolutionary basis for their complex and diverse modes of catalytic functions remain enigmatic. Here, based on deep mining of over half million GT-A fold sequences, we define a minimal core component shared among functionally diverse enzymes. We find that variations in the common core and emergence of hypervariable loops extending from the core contributed to GT-A diversity. We provide a phylogenetic framework relating diverse GT-A fold families for the first time and show that inverting and retaining mechanisms emerged multiple times independently during evolution. Using evolutionary information encoded in primary sequences, we trained a machine learning classifier to predict donor specificity with nearly 90% accuracy and deployed it for the annotation of understudied GTs. Our studies provide an evolutionary framework for investigating complex relationships connecting GT-A fold sequence, structure, function and regulation. Carbohydrates are one of the major groups of large biological molecules that regulate nearly all aspects of life. Yet, unlike DNA or proteins, carbohydrates are made without a template to follow. Instead, these molecules are built from a set of sugar-based building blocks by the intricate activities of a large and diverse family of enzymes known as glycosyltransferases. An incomplete understanding of how glycosyltransferases recognize and build diverse carbohydrates presents a major bottleneck in developing therapeutic strategies for diseases associated with abnormalities in these enzymes. It also limits efforts to engineer these enzymes for biotechnology applications and biofuel production. Taujale et al. have now used evolutionary approaches to map the evolution of a major subset of glycosyltransferases from species across the tree of life to understand how these enzymes evolved such precise mechanisms to build diverse carbohydrates. First, a minimal structural unit was defined based on being shared among a group of over half a million unique glycosyltransferase enzymes with different activities. Further analysis then showed that the diverse activities of these enzymes evolved through the accumulation of mutations within this structural unit, as well as in much more variable regions in the enzyme that extend from the minimal unit. Taujale et al. then built an extended family tree for this collection of glycosyltransferases and details of the evolutionary relationships between the enzymes helped them to create a machine learning framework that could predict which sugar-containing molecules were the raw materials for a given glycosyltransferase. This framework could make predictions with nearly 90% accuracy based only on information that can be deciphered from the gene for that enzyme. These findings will provide scientists with new hypotheses for investigating the complex relationships connecting the genetic information about glycosyltransferases with their structures and activities. Further refinement of the machine learning framework may eventually enable the design of enzymes with properties that are desirable for applications in biotechnology.
Collapse
Affiliation(s)
- Rahil Taujale
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Zhongliang Zhou
- Department of Computer Science, University of Georgia, Athens, Georgia
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Khaled M Rasheed
- Department of Computer Science, University of Georgia, Athens, Georgia
| | - Sheng Li
- Department of Computer Science, University of Georgia, Athens, Georgia
| | - Arthur S Edison
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| |
Collapse
|
28
|
Tamana S, Promponas VJ. An updated view of the oligosaccharyltransferase complex in Plasmodium. Glycobiology 2019; 29:385-396. [PMID: 30835280 DOI: 10.1093/glycob/cwz011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 01/27/2019] [Accepted: 03/04/2019] [Indexed: 12/18/2022] Open
Abstract
Despite the controversy regarding the importance of protein N-linked glycosylation in species of the genus Plasmodium, genes potentially encoding core subunits of the oligosaccharyltransferase (OST) complex have already been characterized in completely sequenced genomes of malaria parasites. Nevertheless, the currently established notion is that only four out of eight subunits of the OST complex-which is considered conserved across eukaryotes-are present in Plasmodium species. In this study, we carefully conduct computational analysis to provide unequivocal evidence that all components of the OST complex, with the exception of Swp1/Ribophorin II, can be reliably identified within completely sequenced plasmodial genomes. In fact, most of the subunits currently considered as absent from Plasmodium refer to uncharacterized protein sequences already existing in sequence databases. Interestingly, the main reason why the unusually short Ost4 subunit (36 residues long in yeast) has not been identified so far in plasmodia (and possibly other species) is the failure of gene-prediction pipelines to detect such a short coding sequence. We further identify elusive OST subunits in select protist species with completely sequenced genomes. Thus, our work highlights the necessity of a systematic approach towards the characterization of OST subunits across eukaryotes. This is necessary both for obtaining a concrete picture of the evolution of the OST complex but also for elucidating its possible role in eukaryotic pathogens.
Collapse
Affiliation(s)
- Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, CY, Nicosia, Cyprus
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, CY, Nicosia, Cyprus
| |
Collapse
|
29
|
Tjondro HC, Loke I, Chatterjee S, Thaysen-Andersen M. Human protein paucimannosylation: cues from the eukaryotic kingdoms. Biol Rev Camb Philos Soc 2019; 94:2068-2100. [PMID: 31410980 DOI: 10.1111/brv.12548] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022]
Abstract
Paucimannosidic proteins (PMPs) are bioactive glycoproteins carrying truncated α- or β-mannosyl-terminating asparagine (N)-linked glycans widely reported across the eukaryotic domain. Our understanding of human PMPs remains limited, despite findings documenting their existence and association with human disease glycobiology. This review comprehensively surveys the structures, biosynthetic routes and functions of PMPs across the eukaryotic kingdoms with the aim of synthesising an improved understanding on the role of protein paucimannosylation in human health and diseases. Convincing biochemical, glycoanalytical and biological data detail a vast structural heterogeneity and fascinating tissue- and subcellular-specific expression of PMPs within invertebrates and plants, often comprising multi-α1,3/6-fucosylation and β1,2-xylosylation amongst other glycan modifications and non-glycan substitutions e.g. O-methylation. Vertebrates and protists express less-heterogeneous PMPs typically only comprising variable core fucosylation of bi- and trimannosylchitobiose core glycans. In particular, the Manα1,6Manβ1,4GlcNAc(α1,6Fuc)β1,4GlcNAcβAsn glycan (M2F) decorates various human neutrophil proteins reportedly displaying bioactivity and structural integrity demonstrating that they are not degradation products. Less-truncated paucimannosidic glycans (e.g. M3F) are characteristic glycosylation features of proteins expressed by human cancer and stem cells. Concertedly, these observations suggest the involvement of human PMPs in processes related to innate immunity, tumorigenesis and cellular differentiation. The absence of human PMPs in diverse bodily fluids studied under many (patho)physiological conditions suggests extravascular residence and points to localised functions of PMPs in peripheral tissues. Absence of PMPs in Fungi indicates that paucimannosylation is common, but not universally conserved, in eukaryotes. Relative to human PMPs, the expression of PMPs in plants, invertebrates and protists is more tissue-wide and constitutive yet, similar to their human counterparts, PMP expression remains regulated by the physiology of the producing organism and PMPs evidently serve essential functions in development, cell-cell communication and host-pathogen/symbiont interactions. In most PMP-producing organisms, including humans, the N-acetyl-β-hexosaminidase isoenzymes and linkage-specific α-mannosidases are glycoside hydrolases critical for generating PMPs via N-acetylglucosaminyltransferase I (GnT-I)-dependent and GnT-I-independent truncation pathways. However, the identity and structure of many species-specific PMPs in eukaryotes, their biosynthetic routes, strong tissue- and development-specific expression, and diverse functions are still elusive. Deep exploration of these PMP features involving, for example, the characterisation of endogenous PMP-recognising lectins across a variety of healthy and N-acetyl-β-hexosaminidase-deficient human tissue types and identification of microbial adhesins reactive to human PMPs, are amongst the many tasks required for enhanced insight into the glycobiology of human PMPs. In conclusion, the literature supports the notion that PMPs are significant, yet still heavily under-studied biomolecules in human glycobiology that serve essential functions and create structural heterogeneity not dissimilar to other human N-glycoprotein types. Human PMPs should therefore be recognised as bioactive glycoproteins that are distinctly different from the canonical N-glycoprotein classes and which warrant a more dedicated focus in glycobiological research.
Collapse
Affiliation(s)
- Harry C Tjondro
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Ian Loke
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| |
Collapse
|
30
|
Bai L, Kovach A, You Q, Kenny A, Li H. Structure of the eukaryotic protein O-mannosyltransferase Pmt1-Pmt2 complex. Nat Struct Mol Biol 2019; 26:704-711. [PMID: 31285605 PMCID: PMC6684406 DOI: 10.1038/s41594-019-0262-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/29/2019] [Indexed: 12/24/2022]
Abstract
In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61-translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, respectively. While the structure of the eight-protein oligosaccharyltransferase complex has been determined recently, the structures of mannosyltransferases of the PMT family, which are an integral part of ER protein homeostasis, are still unknown. Here we report cryo-EM structures of the S. cerevisiae Pmt1–Pmt2 complex bound to a donor and an acceptor peptide at 3.2-Å resolution, showing that each subunit contains 11 transmembrane helices and a lumenal β-trefoil fold termed the MIR domain. The structures reveal the substrate recognition model and confirm an inverting mannosyl-transferring reaction mechanism by the enzyme complex. Furthermore, we found that the transmembrane domains of Pmt1 and Pmt2 share a structural fold with the catalytic subunits of oligosaccharyltransferases, confirming a previously proposed evolutionary relationship between protein O-mannosylation and protein N-glycosylation.
Collapse
Affiliation(s)
- Lin Bai
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Amanda Kovach
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Qinglong You
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Alanna Kenny
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Huilin Li
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.
| |
Collapse
|
31
|
Gill S, Catchpole R, Forterre P. Extracellular membrane vesicles in the three domains of life and beyond. FEMS Microbiol Rev 2019; 43:273-303. [PMID: 30476045 PMCID: PMC6524685 DOI: 10.1093/femsre/fuy042] [Citation(s) in RCA: 268] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Cells from all three domains of life, Archaea, Bacteria and Eukarya, produce extracellular vesicles (EVs) which are sometimes associated with filamentous structures known as nanopods or nanotubes. The mechanisms of EV biogenesis in the three domains remain poorly understood, although studies in Bacteria and Eukarya indicate that the regulation of lipid composition plays a major role in initiating membrane curvature. EVs are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. They have been implicated in many aspects of cell physiology such as stress response, intercellular competition, lateral gene transfer (via RNA or DNA), pathogenicity and detoxification. Their role in various human pathologies and aging has aroused much interest in recent years. EVs can be used as decoys against viral attack but virus-infected cells also produce EVs that boost viral infection. Here, we review current knowledge on EVs in the three domains of life and their interactions with the viral world.
Collapse
Affiliation(s)
- Sukhvinder Gill
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
| | - Ryan Catchpole
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
| |
Collapse
|
32
|
Elton CM, Rodriguez M, Ben Mamoun C, Lobo CA, Wright GJ. A library of recombinant Babesia microti cell surface and secreted proteins for diagnostics discovery and reverse vaccinology. Int J Parasitol 2019; 49:115-125. [PMID: 30367868 PMCID: PMC6406021 DOI: 10.1016/j.ijpara.2018.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 01/03/2023]
Abstract
Human babesiosis is an emerging tick-borne parasitic disease and blood transfusion-transmitted infection primarily caused by the apicomplexan parasite, Babesia microti. There is no licensed vaccine for B. microti and the development of a reliable serological screening test would contribute to ensuring the safety of the donated blood supply. The recent sequencing of the B. microti genome has revealed many novel genes encoding proteins that can now be tested for their suitability as subunit vaccine candidates and diagnostic serological markers. Extracellular proteins are considered excellent vaccine candidates and serological markers because they are directly exposed to the host humoral immune system, but can be challenging to express as soluble recombinant proteins. We have recently developed an approach based on a mammalian expression system that can produce large panels of functional recombinant cell surface and secreted parasite proteins. Here, we use the B. microti genome sequence to identify 54 genes that are predicted to encode surface-displayed and secreted proteins expressed during the blood stages, and show that 41 (76%) are expressed using our method at detectable levels. We demonstrate that the proteins contain conformational, heat-labile, epitopes and use them to serologically profile the kinetics of the humoral immune responses to two strains of B. microti in a murine infection model. Using sera from validated human infections, we show a concordance in the host antibody responses to B. microti infections in mouse and human hosts. Finally, we show that BmSA1 expressed in mammalian cells can elicit high antibody titres in vaccinated mice using a human-compatible adjuvant but these antibodies did not affect the pathology of infection in vivo. Our library of recombinant B. microti cell surface and secreted antigens constitutes a valuable resource that could contribute to the development of a serological diagnostic test, vaccines, and elucidate the molecular basis of host-parasite interactions.
Collapse
Affiliation(s)
- Catherine M Elton
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Marilis Rodriguez
- New York Blood Center, Blood Borne Parasites, 310 E. 67th Street, New York, NY 10065, USA
| | - Choukri Ben Mamoun
- Infectious Diseases, PO Box 208056, 333 Cedar Street, New Haven, CT 06520-8056, USA
| | - Cheryl A Lobo
- New York Blood Center, Blood Borne Parasites, 310 E. 67th Street, New York, NY 10065, USA
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom.
| |
Collapse
|
33
|
A Defective Undecaprenyl Pyrophosphate Synthase Induces Growth and Morphological Defects That Are Suppressed by Mutations in the Isoprenoid Pathway of Escherichia coli. J Bacteriol 2018; 200:JB.00255-18. [PMID: 29986944 DOI: 10.1128/jb.00255-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
The peptidoglycan exoskeleton shapes bacteria and protects them against osmotic forces, making its synthesis the target of many current antibiotics. Peptidoglycan precursors are attached to a lipid carrier and flipped from the cytoplasm into the periplasm to be incorporated into the cell wall. In Escherichia coli, this carrier is undecaprenyl phosphate (Und-P), which is synthesized as a diphosphate by the enzyme undecaprenyl pyrophosphate synthase (UppS). E. coli MG1655 exhibits wild-type morphology at all temperatures, but one of our laboratory strains (CS109) was highly aberrant when grown at 42°C. This strain contained mutations affecting the Und-P synthetic pathway genes uppS, ispH, and idi Normal morphology was restored by overexpressing uppS or by replacing the mutant (uppS31) with the wild-type allele. Importantly, moving uppS31 into MG1655 was lethal even at 30°C, indicating that the altered enzyme was highly deleterious, but growth was restored by adding the CS109 versions of ispH and idi Purified UppSW31R was enzymatically defective at all temperatures, suggesting that it could not supply enough Und-P during rapid growth unless suppressor mutations were present. We conclude that cell wall synthesis is profoundly sensitive to changes in the pool of polyisoprenoids and that isoprenoid homeostasis exerts a particularly strong evolutionary pressure.IMPORTANCE Bacterial morphology is determined primarily by the overall structure of the semirigid macromolecule peptidoglycan. Not only does peptidoglycan contribute to cell shape, but it also protects cells against lysis caused by excess osmotic pressure. Because it is critical for bacterial survival, it is no surprise that many antibiotics target peptidoglycan biosynthesis. However, important gaps remain in our understanding about how this process is affected by peptidoglycan precursor availability. Here, we report that a mutation altering the enzyme that synthesizes Und-P prevents cells from growing at high temperatures and that compensatory mutations in enzymes functioning upstream of uppS can reverse this phenotype. The results highlight the importance of Und-P metabolism for maintaining normal cell wall synthesis and shape.
Collapse
|
34
|
Ruiz-May E, Sørensen I, Fei Z, Zhang S, Domozych DS, Rose JKC. The Secretome and N-Glycosylation Profiles of the Charophycean Green Alga, Penium margaritaceum, Resemble Those of Embryophytes. Proteomes 2018; 6:E14. [PMID: 29561781 PMCID: PMC6027541 DOI: 10.3390/proteomes6020014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 11/16/2022] Open
Abstract
The secretome can be defined as the population of proteins that are secreted into the extracellular environment. Many proteins that are secreted by eukaryotes are N-glycosylated. However, there are striking differences in the diversity and conservation of N-glycosylation patterns between taxa. For example, the secretome and N-glycosylation structures differ between land plants and chlorophyte green algae, but it is not clear when this divergence took place during plant evolution. A potentially valuable system to study this issue is provided by the charophycean green algae (CGA), which is the immediate ancestors of land plants. In this study, we used lectin affinity chromatography (LAC) coupled with mass spectrometry to characterize the secretome including secreted N-glycoproteins of Penium margaritaceum, which is a member of the CGA. The identified secreted proteins and N-glycans were compared to those known from the chlorophyte green alga Chlamydomonas reinhardtii and the model land plant, Arabidopsis thaliana, to establish their evolutionary context. Our approach allowed the identification of cell wall proteins and proteins modified with N-glycans that are identical to those of embryophytes, which suggests that the P. margaritaceum secretome is more closely related to those of land plants than to those of chlorophytes. The results of this study support the hypothesis that many of the proteins associated with plant cell wall modification as well as other extracellular processes evolved prior to the colonization of terrestrial habitats.
Collapse
Affiliation(s)
- Eliel Ruiz-May
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic, Carretera Antigua a Coatepec 351, Congregación el Haya, CP 91070 Xalapa, Veracruz, Mexico.
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - David S Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, NY 12866, USA.
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
35
|
Fujinami D, Taguchi Y, Kohda D. Asn-linked oligosaccharide chain of a crenarchaeon, Pyrobaculum calidifontis, is reminiscent of the eukaryotic high-mannose-type glycan. Glycobiology 2017; 27:701-712. [PMID: 28510654 DOI: 10.1093/glycob/cwx044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/18/2017] [Accepted: 05/13/2017] [Indexed: 12/19/2022] Open
Abstract
Pyrobaculum calidifontis is a hyperthermophilic archaeon that belongs to the phylum Crenarchaeota. In contrast to the phylum Euryarchaeota, only the N-glycan structure of the genus Sulfolobus is known in Crenarchaeota. Here, we enriched glycoproteins from cultured P. calidifontis cells, by ConA lectin chromatography. The MASCOT search identified proteins with at least one potential N-glycosylation site. The tandem mass spectrometry (MS/MS) analysis of 12 small tryptic glycopeptides confirmed the canonical N-glycosylation consensus in P. calidifontis. We determined the N-linked oligosaccharide structure produced by an in vitro enzymatic oligosaccharyl transfer reaction. Pyrobaculum calidifontis cells were cultured in rich medium supplemented with 13C-glucose, for the metabolic labeling of N-oligosaccharide donors. An incubation with a synthetic peptide substrate produced glycopeptides with isotopically labeled oligosaccharide moieties. The MS and nuclear magnetic resonance analyses revealed that the P. calidifontisN-glycan has a biantennary, high-mannose-type structure consisting of up to 11 monosaccharide residues. The base portion of the P. calidifontisN-glycan strongly resembles the eukaryotic core structure, α-Man-(1-3)-(α-Man-(1-6)-)β-Man-(1-4)-β-GlcNAc-(1-4)-β-GlcNAc-Asn. Structural differences exist in the anomeric configuration between Man and GlcNAc, and the chitobiose structure is chemically modified: one GlcNAc residue is oxidized to glucoronate, and the GlcNAc residues are both modified with an additional acetamido group at the C-3 position. As a result, the core structure of the P. calidifontisN-glycan is α-Man-(1-3)-(α-Man-(1-6)-)α-Man-(1-4)-β-GlcANAc3NAc-(1-4)-β-GlcNAc3NAc-Asn, in which the unique features of the P. calidifontisN-glycan are underlined. In spite of these differences, the structure of the P. calidifontisN-glycan is the most similar to the eukaryotic counterparts, among all archaeal N-glycans reported to date.
Collapse
Affiliation(s)
- Daisuke Fujinami
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuya Taguchi
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.,Research Center for Advanced Immunology, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.,Research Center for Live-Protein Dynamics, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
36
|
Biomimetic Principles to Develop Blood Compatible Surfaces. Int J Artif Organs 2017; 40:22-30. [DOI: 10.5301/ijao.5000559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2017] [Indexed: 12/11/2022]
Abstract
Functionalized biomaterial surface patterns capable of resisting nonspecific adsorption while retaining their bioactivity are crucial in the advancement of biomedical technologies, but currently available biomaterials intended for use in whole blood frequently suffer from nonspecific adsorption of proteins and cells, leading to a loss of activity over time. In this review, we address two concepts for the design and modification of blood compatible biomaterial surfaces, zwitterionic modification and surface functionalization with glycans – both of which are inspired by the membrane structure of mammalian cells – and discuss their potential for biomedical applications.
Collapse
|
37
|
Evolution of protein N-glycosylation process in Golgi apparatus which shapes diversity of protein N-glycan structures in plants, animals and fungi. Sci Rep 2017; 7:40301. [PMID: 28074929 PMCID: PMC5225481 DOI: 10.1038/srep40301] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/01/2016] [Indexed: 01/21/2023] Open
Abstract
Protein N-glycosylation (PNG) is crucial for protein folding and enzymatic activities, and has remarkable diversity among eukaryotic species. Little is known of how unique PNG mechanisms arose and evolved in eukaryotes. Here we demonstrate a picture of onset and evolution of PNG components in Golgi apparatus that shaped diversity of eukaryotic protein N-glycan structures, with an emphasis on roles that domain emergence and combination played on PNG evolution. 23 domains were identified from 24 known PNG genes, most of which could be classified into a single clan, indicating a single evolutionary source for the majority of the genes. From 153 species, 4491 sequences containing the domains were retrieved, based on which we analyzed distribution of domains among eukaryotic species. Two domains in GnTV are restricted to specific eukaryotic domains, while 10 domains distribute not only in species where certain unique PNG reactions occur and thus genes harboring these domains are supoosed to be present, but in other ehkaryotic lineages. Notably, two domains harbored by β-1,3 galactosyltransferase, an essential enzyme in forming plant-specific Lea structure, were present in separated genes in fungi and animals, suggesting its emergence as a result of domain shuffling.
Collapse
|
38
|
Abstract
Simple and complex carbohydrates (glycans) have long been known to play major metabolic, structural and physical roles in biological systems. Targeted microbial binding to host glycans has also been studied for decades. But such biological roles can only explain some of the remarkable complexity and organismal diversity of glycans in nature. Reviewing the subject about two decades ago, one could find very few clear-cut instances of glycan-recognition-specific biological roles of glycans that were of intrinsic value to the organism expressing them. In striking contrast there is now a profusion of examples, such that this updated review cannot be comprehensive. Instead, a historical overview is presented, broad principles outlined and a few examples cited, representing diverse types of roles, mediated by various glycan classes, in different evolutionary lineages. What remains unchanged is the fact that while all theories regarding biological roles of glycans are supported by compelling evidence, exceptions to each can be found. In retrospect, this is not surprising. Complex and diverse glycans appear to be ubiquitous to all cells in nature, and essential to all life forms. Thus, >3 billion years of evolution consistently generated organisms that use these molecules for many key biological roles, even while sometimes coopting them for minor functions. In this respect, glycans are no different from other major macromolecular building blocks of life (nucleic acids, proteins and lipids), simply more rapidly evolving and complex. It is time for the diverse functional roles of glycans to be fully incorporated into the mainstream of biological sciences.
Collapse
Affiliation(s)
- Ajit Varki
- Departments of Medicine and Cellular & Molecular Medicine, Glycobiology Research and Training Center, University of California at San Diego, La Jolla, CA 92093-0687, USA
| |
Collapse
|
39
|
Lombard J. Early evolution of polyisoprenol biosynthesis and the origin of cell walls. PeerJ 2016; 4:e2626. [PMID: 27812422 PMCID: PMC5088576 DOI: 10.7717/peerj.2626] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/27/2016] [Indexed: 11/30/2022] Open
Abstract
After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes). Here, we provide the first systematic phylogenomic report on the polyisoprenol biosynthesis pathways in the three domains of life. This study shows that, whereas the last steps of the polyisoprenol biosynthesis are unique to the respective domain of life of which they are characteristic, the enzymes required for basic unsaturated polyisoprenol synthesis can be traced back to the respective last common ancestor of each of the three domains of life. As a result, regardless of the topology of the tree of life that may be considered, the most parsimonious hypothesis is that these enzymes were inherited in modern lineages from the cenancestor. This observation supports the presence of an enzymatic mechanism to synthesize unsaturated polyisoprenols in the cenancestor and, since these molecules are notorious lipid carriers in glycosylation pathways involved in the synthesis of a wide diversity of prokaryotic cell walls, it provides the first indirect evidence of the existence of a hypothetical unknown cell wall synthesis mechanism in the cenancestor.
Collapse
Affiliation(s)
- Jonathan Lombard
- Biosciences, University of Exeter, Exeter, United Kingdom; National Evolutionary Synthesis Center, Durham, NC, United States of America
| |
Collapse
|