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Vershinin Z, Zaretsky M, Eichler J. N-glycosylation in Archaea - Expanding the process, components and roles of a universal post-translational modification. BBA ADVANCES 2024; 6:100120. [PMID: 39296579 PMCID: PMC11407970 DOI: 10.1016/j.bbadva.2024.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 09/21/2024] Open
Abstract
While performed by all three domains of life, N-glycosylation in Archaea is less well described than are the parallel eukaryal and bacterial processes. Still, what is known of the archaeal version of this universal post-translational modification reveals numerous seemingly domain-specific traits. Specifically, the biosynthesis of archaeal N-linked glycans relies on distinct pathway steps and components, rare sugars and sugar modifications, as well as unique lipid carriers upon which N-linked glycans are assembled. At the same time, Archaea possess the apparently unique ability to simultaneously modify their glycoproteins with very different N-linked glycans. In addition to these biochemical aspects of archaeal N-glycosylation, such post-translational modification has been found to serve a wide range of roles possibly unique to Archaea, including allowing these microorganisms to not only cope with the harsh physical conditions of the niches they can inhabit but also providing the ability to adapt to transient changes in such environments.
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Affiliation(s)
- Zlata Vershinin
- Dept. of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Marianna Zaretsky
- Dept. of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Jerry Eichler
- Dept. of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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Notaro A, Zaretsky M, Molinaro A, De Castro C, Eichler J. N-glycosylation in Archaea: Unusual sugars and unique modifications. Carbohydr Res 2023; 534:108963. [PMID: 37890267 DOI: 10.1016/j.carres.2023.108963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Archaea are microorganisms that comprise a distinct branch of the universal tree of life and which are best known as extremophiles, residing in a variety of environments characterized by harsh physical conditions. One seemingly universal trait of Archaea is the ability to perform N-glycosylation. At the same time, archaeal N-linked glycans present variety in terms of both composition and architecture not seen in the parallel eukaryal or bacterial processes. In this mini-review, many of the unique and unusual sugars found in archaeal N-linked glycans as identified by nuclear magnetic resonance spectroscopy are described.
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Affiliation(s)
- Anna Notaro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy
| | - Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel.
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Ding J, Zhao L, Wang L, Zhao W, Zhai Z, Leng L, Wang Y, He C, Zhang Y, Zhang H, Li H, Meng H. Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota. Genet Sel Evol 2016; 48:93. [PMID: 27894254 PMCID: PMC5127100 DOI: 10.1186/s12711-016-0270-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 11/10/2016] [Indexed: 11/21/2022] Open
Abstract
Background The gastrointestinal tract is populated by a complex and vast microbial network, with a composition that reflects the relationships of the symbiosis, co-metabolism, and co-evolution of these microorganisms with their host. The mechanism that underlies such interactions between the genetics of the host and gut microbiota remains elusive. Results To understand how genetic variation of the host shapes the gut microbiota and interacts with it to affect the metabolic phenotype of the host, we compared the abundance of microbial taxa and their functional performance between two lines of chickens (fat and lean) that had undergone long-term divergent selection for abdominal fat pad weight, which resulted in a 4.5-fold increase in the fat line compared to the lean line. Our analysis revealed that the proportions of Fusobacteria and Proteobacteria differed significantly between the two lines (8 vs. 18% and 33 vs. 24%, respectively) at the phylum level. Eight bacterial genera and 11 species were also substantially influenced by the host genotype. Differences between the two lines in the frequency of host alleles at loci that influence accumulation of abdominal fat were associated with differences in the abundance and composition of the gut microbiota. Moreover, microbial genome functional analysis showed that the gut microbiota was involved in pathways that are associated with fat metabolism such as lipid and glycan biosynthesis, as well as amino acid and energy metabolism. Interestingly, citrate cycle and peroxisome proliferator activated receptor (PPAR) signaling pathways that play important roles in lipid storage and metabolism were more prevalent in the fat line than in the lean line. Conclusions Our study demonstrates that long-term divergent selection not only alters the composition of the gut microbiota, but also influences its functional performance by enriching its relative abundance in microbial taxa. These results support the hypothesis that the host and gut microbiota interact at the genetic level and that these interactions result in their co-evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0270-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinmei Ding
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, People's Republic of China
| | - Lele Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, People's Republic of China.,Shanghai Animal Disease Control Center, Shanghai, 201103, People's Republic of China
| | - Lifeng Wang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, 010018, People's Republic of China
| | - Wenjing Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, People's Republic of China
| | - Zhengxiao Zhai
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, People's Republic of China
| | - Li Leng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Yuxiang Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chuan He
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, People's Republic of China
| | - Yan Zhang
- Shanghai Personal Biotechnology Limited Company, Shanghai, 200231, People's Republic of China
| | - Heping Zhang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Key Laboratory of Dairy Biotechnology and Engineering, Hohhot, 010018, People's Republic of China
| | - Hui Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - He Meng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, People's Republic of China.
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Kalam Azad MA, Wang F, Kim HR. Identification of a novel sugar compound from Korean pine seeds. Food Sci Biotechnol 2015. [DOI: 10.1007/s10068-015-0265-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Lodowska J, Wolny D, Węglarz L. The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) as a characteristic component of bacterial endotoxin — a review of its biosynthesis, function, and placement in the lipopolysaccharide core. Can J Microbiol 2013; 59:645-55. [DOI: 10.1139/cjm-2013-0490] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) is a characteristic component of bacterial lipopolysaccharide (LPS, endotoxin). It connects the carbohydrate part of LPS with C6 of glucosamine or 2,3-diaminoglucose of lipid A by acid-labile α-ketosidic linkage. The number of Kdo units present in LPS, the way they are connected, and the occurrence of other substituents (P, PEtn, PPEtn, Gal, or β-l-Ara4N) account for structural diversity of the inner core region of endotoxin. In a majority of cases, Kdo is crucial to the viability and growth of bacterial cells. In this paper, the biosynthesis of Kdo and the mechanism of its incorporation into the LPS structure, as well as the location of this unique component in the endotoxin core structures, have been described.
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Affiliation(s)
- Jolanta Lodowska
- Department of Biochemistry, Faculty of Pharmacy, Medical University of Silesia, Narcyzow 1 Street, 41-200 Sosnowiec, Poland
| | - Daniel Wolny
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Silesia, Narcyzow 1 St., 41-200 Sosnowiec, Poland
| | - Ludmiła Węglarz
- Department of Biochemistry, Faculty of Pharmacy, Medical University of Silesia, Narcyzow 1 Street, 41-200 Sosnowiec, Poland
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Vinogradov E, Deschatelets L, Lamoureux M, Patel GB, Tremblay TL, Robotham A, Goneau MF, Cummings-Lorbetskie C, Watson DC, Brisson JR, Kelly JF, Gilbert M. Cell surface glycoproteins from Thermoplasma acidophilum are modified with an N-linked glycan containing 6-C-sulfofucose. Glycobiology 2012; 22:1256-67. [PMID: 22692048 DOI: 10.1093/glycob/cws094] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Thermoplasma acidophilum is a thermoacidophilic archaeon that grows optimally at pH 2 and 59°C. This extremophile is remarkable by the absence of a cell wall or an S-layer. Treating the cells with Triton X-100 at pH 3 allowed the extraction of all of the cell surface glycoproteins while keeping cells intact. The extracted glycoproteins were partially purified by cation-exchange chromatography, and we identified five glycoproteins by N-terminal sequencing and mass spectrometry of in-gel tryptic digests. These glycoproteins are positive for periodic acid-Schiff staining, have a high content of Asn including a large number in the Asn-X-Ser/Thr sequon and have apparent masses that are 34-48% larger than the masses deduced from their amino acid sequences. The pooled glycoproteins were digested with proteinase K and the purified glycopeptides were analyzed by NMR. Structural determination showed that the carbohydrate part was represented by two structures in nearly equal amounts, differing by the presence of one terminal mannose residue. The larger glycan chain consists of eight residues: six hexoses, one heptose and one sugar with an unusual residue mass of 226 Da which was identified as 6-deoxy-6-C-sulfo-D-galactose (6-C-sulfo-D-fucose). Mass spectrometry analyses of the peptides obtained by trypsin and chymotrypsin digestion confirmed the principal structures to be those determined by NMR and identified 14 glycopeptides derived from the main glycoprotein, Ta0280, all containing the Asn-X-Ser/Thr sequons. Thermoplasma acidophilum appears to have a "general" protein N-glycosylation system that targets a number of cell surface proteins.
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Affiliation(s)
- Evgeny Vinogradov
- Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario, Canada K1A 0R6
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Ruiz-Matute AI, Hernández-Hernández O, Rodríguez-Sánchez S, Sanz ML, Martínez-Castro I. Derivatization of carbohydrates for GC and GC-MS analyses. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 879:1226-40. [PMID: 21186143 DOI: 10.1016/j.jchromb.2010.11.013] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 09/29/2010] [Accepted: 11/08/2010] [Indexed: 11/26/2022]
Abstract
GC and GC-MS are excellent techniques for the analysis of carbohydrates; nevertheless the preparation of adequate derivatives is necessary. The different functional groups that can be found and the diversity of samples require specific methods. This review aims to collect the most important methodologies currently used, either published as new procedures or as new applications, for the analysis of carbohydrates. A high diversity of compounds with diverse functionalities has been selected: neutral carbohydrates (saccharides and polyalcohols), sugar acids, amino and iminosugars, polysaccharides, glycosides, glycoconjugates, anhydrosugars, difructose anhydrides and products resulting of Maillard reaction (osuloses, Amadori compounds). Chiral analysis has also been considered, describing the use of diastereomers and derivatives to be eluted on chiral stationary phases.
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Affiliation(s)
- A I Ruiz-Matute
- Instituto de Fermentaciones Industriales-CIAL (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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Wang Z, Liu X, Li J, Altman E. Structural characterization of the O-chain polysaccharide of Aeromonas caviae ATCC 15468 lipopolysaccharide. Carbohydr Res 2007; 343:483-8. [PMID: 18068695 DOI: 10.1016/j.carres.2007.11.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 11/07/2007] [Accepted: 11/12/2007] [Indexed: 11/28/2022]
Abstract
The O-chain polysaccharide produced by a mild acid degradation of Aeromonas caviae ATCC 15468 lipopolysaccharide was found to be composed of L-rhamnose, 2-acetamido-2-deoxy-D-glucose, 2-acetamido-2-deoxy-D-galactose and phosphoglycerol. Subsequent methylation and CE-ESIMS analyses and 1D/2D NMR ((1)H, (13)C and (31)P) spectroscopy showed that the O-chain polysaccharide is a high-molecular-mass acidic branched polymer of tetrasaccharide repeating units with a phosphoglycerol substituent having the following structure: [structure: see text] where Gro represents glycerol and P represents a phosphate group.
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Affiliation(s)
- Zhan Wang
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada
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Chandan V, Logan SM, Harrison BA, Vinogradov E, Aubry A, Stupak J, Li J, Altman E. Helicobacter pylori cagA and iceA genotypes status and risk of peptic ulcer in Saudi patients. Saudi Med J 2007; 85:582-90. [PMID: 17901900 DOI: 10.1139/o07-056] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To determine the prevalence of cagA+ and iceA genotypes among Helicobacter pylori (H. pylori) isolates from a group of Saudi patients with gastric complaints, and to find out any significant correlation between these strains and severe gastric clinical outcomes such as peptic ulcer and gastric cancer in Saudi population. METHODS A total of 1104 gastric biopsies from 368 patients who presented with symptoms suggestive of chronic gastritis, peptic ulcer disease, or gastric carcinoma were taken from the main hospitals in the Western region of Saudi Arabia from July 2004 to July 2005. We cultured the samples for H. pylori and a polymerase chain reaction was carried out to check for the presence or absence of cagA gene and the status of iceA genotypes. RESULTS Among the 368 suspected patients to be infected with H. pylori by means of clinical features and endoscopic findings; 103 (28%) were positive using culture technique. The relation of the presence of cagA and the development of cases to gastritis and ulcer was statistically significant (p=0.0001). Furthermore, this study revealed that 100% of ulcer cases were infected with iceA1 with a statistically significant correlation (p=0.0001), while 94.6% of gastritis and 90.9% of normal were infected with iceA2 (p=0.0001). Moreover cagA+/iceA1 combined genotypes was statistically correlated with peptic ulcer (100%) but not cagA-/iceA1 (0%; p=0.0001). CONCLUSION Certain H. pylori genotypes were more virulent than others. Multiple clinical implications based on these finding might be studied further.
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Affiliation(s)
- Vandana Chandan
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
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Wang Z, Li J, Vinogradov E, Altman E. Structural studies of the core region of Aeromonas salmonicida subsp. salmonicida lipopolysaccharide. Carbohydr Res 2005; 341:109-17. [PMID: 16297894 DOI: 10.1016/j.carres.2005.10.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 10/24/2005] [Accepted: 10/30/2005] [Indexed: 10/25/2022]
Abstract
The core oligosaccharide structure of the in vivo derived rough phenotype of Aeromonas salmonicida subsp. salmonicida was investigated by a combination of compositional, methylation, CE-MS and one- and two-dimensional NMR analyses and established as the following: [carbohydrate: see text] where R=alpha-D-Galp-(1-->4)-beta-D-GalpNAc-(1--> or alpha-D-Galp-(1--> (approx. ratio 4:3). Comparative CE-MS analysis of A. salmonicida subsp. salmonicida core oligosaccharides from strains A449, 80204-1 and an in vivo rough isolate confirmed that the structure of the core oligosaccharide was conserved among different isolates of A. salmonicida.
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Affiliation(s)
- Zhan Wang
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A 0R6
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Wang Z, Vinogradov E, Larocque S, Harrison BA, Li J, Altman E. Structural and serological characterization of the O-chain polysaccharide of Aeromonas salmonicida strains A449, 80204 and 80204-1. Carbohydr Res 2005; 340:693-700. [PMID: 15721342 DOI: 10.1016/j.carres.2005.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Revised: 01/05/2005] [Accepted: 01/06/2005] [Indexed: 11/28/2022]
Abstract
The O-chain polysaccharide (O-PS) of Aeromonas salmonicida was studied by a combination of compositional, methylation, CE-ESMS and one- and two-dimensional NMR analyses. It was found to be a branched polymer of trisaccharide-repeating units composed of L-rhamnose (Rha), D-glucose (Glc), 2-acetamido-2-deoxy-D-mannose (ManNAc) and O-acetyl group (OAc) and having the following structure: CE-ESMS analysis of A. salmonicida cells from strains A449, 80204 and 80204-1 grown under different conditions confirmed that the O-PS structure was conserved. ELISA-based serological study with native LPS-specific antisera performed on the native O-PS and its O-deacetylated and periodate-oxidized derivatives confirmed the importance of the O-PS backbone structure as an immunodominant determinant.
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Affiliation(s)
- Zhan Wang
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A 0R6
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