Show legend Show as text

Structure type: oligomer
Compound class: O-glycoprotein
Contained glycoepitopes: IEDB_130701,IEDB_136104,IEDB_143632,IEDB_144983,IEDB_152206,IEDB_983930,SB_136,SB_196,SB_44,SB_67,SB_72

• Article ID: 2730
  Herrmann GF, Wang P, Shen GJ, Garcia-Junceda E, Khan SH, Matta KL, Wong CH "Large scale production of recombinant a-1,2-mannosyltransferase from E. coli for the study of acceptor specificity and use of the recombinant whole cells in synthesis" - Journal of Organic Chemistry 59 (1994) 6356-6362
  
  Publication DOI: 10.1021/jo00100a043
  Journal NLM ID: 2985193R
  Publisher: Columbus, OH: American Chemical Society
  
   
  
  Escherichia coli
  CSDB ID 141631 (all data & tools)

Show legend Show as text

Structure type: cyclic polymer repeating unit ; 1388.7577 [M+H]+
C₆₆H₁₀₅N₁₁O₂₁
Trivial name: desmamides A
Compound class: lipoglycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_150900

• Article ID: 6224
  Freitas S, Castelo-Branco R, Wenzel-Storjohann A, Vasconcelos VM, Tasdemir D, Leão PN "Structure and Biosynthesis of Desmamides A-C, Lipoglycopeptides from the Endophytic Cyanobacterium Desmonostoc muscorum LEGE 12446" - Journal of Natural Products 85(7) (2022) 1704-1714
  

  Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixation. Here, we report the discovery of two new lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The desmamides are decapeptides featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate incubation experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis.

  structure, NMR spectroscopy, mass spectrometry, cyanobacteria, marine, lipoglycopeptides, Desmonostoc muscorum

  NCBI PubMed ID: 35793792
  Publication DOI: 10.1021/acs.jnatprod.2c00162
  Journal NLM ID: 7906882
  Publisher: American Society of Pharmacognosy
  Correspondence: P.N. Leão
  Institutions: Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal, Department of Biology, Faculty of Sciences, University of Porto Rua do Campo Alegre, Porto, Portugal, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, FTIR, HPLC, extraction, optical rotation measurement, bioinformatic analysis, HR-ESI-MS, antibacterial assay, cell viability assay, flash chromatography, genome sequencing, Marfey’s method, LC-HR-ESI-MS
  
   
  
  Desmonostoc muscorum LEGE 12446
  CSDB ID 8455 (all data & tools)

Show legend Show as text

Structure type: cyclic polymer repeating unit ; 1430.7666 [M+H]+
C₆₈H₁₀₈N₁₁O₂₂
Trivial name: desmamides B
Compound class: lipoglycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_150900

• Article ID: 6224
  Freitas S, Castelo-Branco R, Wenzel-Storjohann A, Vasconcelos VM, Tasdemir D, Leão PN "Structure and Biosynthesis of Desmamides A-C, Lipoglycopeptides from the Endophytic Cyanobacterium Desmonostoc muscorum LEGE 12446" - Journal of Natural Products 85(7) (2022) 1704-1714
  

  Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixation. Here, we report the discovery of two new lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The desmamides are decapeptides featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate incubation experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis.

  structure, NMR spectroscopy, mass spectrometry, cyanobacteria, marine, lipoglycopeptides, Desmonostoc muscorum

  NCBI PubMed ID: 35793792
  Publication DOI: 10.1021/acs.jnatprod.2c00162
  Journal NLM ID: 7906882
  Publisher: American Society of Pharmacognosy
  Correspondence: P.N. Leão
  Institutions: Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal, Department of Biology, Faculty of Sciences, University of Porto Rua do Campo Alegre, Porto, Portugal, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, FTIR, HPLC, extraction, optical rotation measurement, bioinformatic analysis, HR-ESI-MS, antibacterial assay, cell viability assay, flash chromatography, genome sequencing, Marfey’s method, LC-HR-ESI-MS
  
   
  
  Desmonostoc muscorum LEGE 12446
  CSDB ID 20935 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_130701,IEDB_135813,IEDB_137340,IEDB_137485,IEDB_140116,IEDB_141793,IEDB_141807,IEDB_141828,IEDB_144983,IEDB_149158,IEDB_150900,IEDB_151079,IEDB_151531,IEDB_152206,IEDB_153220,IEDB_164174,IEDB_429156,IEDB_857734,IEDB_983930,SB_197,SB_198,SB_44,SB_67,SB_72,SB_73,SB_77

• Article ID: 6724
  Altmann F, Schweiszer S, Weber C "Kinetic comparison of peptide: N-glycosidases F and A reveals several differences in substrate specificity" - Glycoconjugate Journal 12 (1995) 84-93
  

  The initial velocities of hydrolysis of nineteen glycopeptides by peptide: N-glycosidase F and A were determined. Substrates were prepared from bovine fetuin, hen ovalbumin, pineapple stem bromelain, bovine fibrin and taka-amylase. From these glycopeptides, several variants with regard to peptide and carbohydrate structure were prepared and derivatized with dabsyl chloride, dansyl chloride or activated resorufin. Tyrosine containing glycopeptides were also used without an additional chromophore. Enzymatic hydrolysis of glycopeptides was quantified by narrow bore, reversed phase HPLC with turnaround cycle times of down to 6 min, but usually 15 min. KM values ranging from 30 to 64 μM and from 4 to 36 μM were found for N-glycosidase F and A, respectively. Relative velocities of hydrolysis of the different substrates by each enzyme varied considerably. Little, if any, similarity of the performance of N-glycosidase F and A with the different substrates was observed. The minimal carbohydrate structure released by peptide: N-glycosidase F was a di-N-acetylchitobiose. N-glycosidase A could release even a single N-acetylglucosamine, albeit 3000 times slower than a di-N-acetylchitobiose or larger glycans. In general the structure of the intact glycan had little effect on activity, and with both enzymes the rate of hydrolysis appeared to be primarily governed by peptide structure and length. However, N-glycosidase F did not release glycans α-1,3-fucosylated at the asparagine linked N-acetylglucosamine irrespective of the presence of xylose in the substrate.

  NCBI PubMed ID: 7540902
  Journal NLM ID: 8603310
  Publisher: Kluwer Academic Publishers
  Institutions: Institut für Chemie, Univesität fur Bodenkultur Wien, Austria
  
   
  
  Aspergillus oryzae
  CSDB ID 129098 (all data & tools)

Show legend Show as text

Structure type: monomer ; 1435.8620 [M+H]+
C₆₉H₁₁₈N₁₂O₂₀
Trivial name: dictyonamide B
Compound class: glycopeptide

• Article ID: 8333
  Komatsu K, Shigemori H, Kobayashi J "Dictyonamides A and B, new peptides from marine-derived fungus" - Journal of Organic Chemistry 66(18) (2001) 6189-6192
  

  A new anthracycline derived pentacyclic metabolite, seragakinone A, was isolated from the mycelium of a fungus (K063), which was separated from an Okinawan marine red alga. Further investigation on extracts of the mycelium of the same fungus resulted in the isolation of two new peptides, dictyonamides A (1) and B (2). Dictyonamide A (1) showed inhibitory activity against cyclin-dependent kinase 4 with IC50 value of 16.5 μg/mL, while compound 2 did not show such activity (IC50 > 50 μg/mL)

  peptides, marine-derived fungus, dictyonamides, Ceratodictyon spongiosum

  NCBI PubMed ID: 11529752
  Publication DOI: 10.1021/jo0156767
  Journal NLM ID: 2985193R
  Publisher: Columbus, OH: American Chemical Society
  Correspondence: jkobay@pharm.hokudai.ac.jp
  Institutions: Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
  Methods: 13C NMR, 1H NMR, NMR-2D, IR, FAB-MS, acid hydrolysis, GC, amino acid analysis, FAB-MS/MS, HPLC, UV, extraction, optical rotation measurement, cell growth, derivatization, evaporation, HR-FAB-MS
  
   
  
  (fungi) sp. K063
  CSDB ID 48025 (all data & tools)

Show legend Show as text

Structure type: monomer
Trivial name: dictyonamide B
Compound class: glycopeptide, glycoside

• Article ID: 6181
  Hussain H, Mamadalieva NZ, Ali I, Elizbit, Green IR, Wang D, Zou L, Simal-Gandara J, Cao H, Xiao J "Fungal glycosides: Structure and biological function" - Trends in Food Science and Technology 110 (2021) 611-651
  

  Background: Natural products acquire vast and intriguing structural diversity and have been recognized as a tremendously diverse source of new lead compounds. Numerous bioactive secondary metabolites are present in the form of glycosylated molecules in which the sugar parts are normally associated with the interaction along with molecular recognition of the cellular target. Scope and approach: The presence of sugar entities are crucial as well as in some cases necessary, for therapeutic effects. Establishing novel and potent glycosylated secondary metabolites has formed a main goal in the natural product field from fungi and bacteria. These compounds possess a diverse range of sugar units. Key findings and conclusions: Fungi is considered one of the important sources for approved drugs with a diverse range of mode of action. The sugar part in numerous pharmacologically active natural products enhances bioavailability, biological potential, reduce toxicity, and improve stability. The vast majority of glyocosides showed antimicrobial effects, cytotoxic, antiviral and antiinflammatory effects. Notably, numerous fungal glycosides presented in this review illustrate significant antimicrobial effects towards various microorganisms especially against plant pathogens. The antimicrobial effects of these fungal glycosides indicate that these metabolites could be employed as natural preservatives in food in order to abolish or control the growth of pathogenic and spoilage microorganisms.

  glycoside, antimicrobial, fungi, food preservative, secondary metabolites

  Publication DOI: 10.1016/j.tifs.2021.02.029
  Journal NLM ID: 9426004
  Publisher: Cambridge, UK: Elsevier Trends Journals
  Correspondence: Hussain H ; Hussain H ; Xiao J ; Xiao J
  Institutions: Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany, Institute of the Chemistry of Plant Substances of the Academy Sciences of Uzbekistan, Tashkent, Uzbekistan, School of Pharmaceutical Sciences and Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China, Department Materials Engineering, National University of Sciences and Technology (NUST) H12, Islamabad, Pakistan, Department of Chemistry and Polymer Science, University of Stellenbosch, Matieland, South Africa, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo - Ourense Campus, Ourense, Spain
  
   
  
  (fungi) sp. K063
  CSDB ID 51556 (all data & tools)
• Article ID: 8335
  Bugni TS, Ireland CM "Marine-derived fungi: a chemically and biologically diverse group of microorganisms" - Natural Product Reports 21(1) (2004) 143-163
  

  A diverse array of secondary metabolites have been isolated and characterized from marine-derived fungi. The structures and biological activities of these metabolites are presented. Additionally, some basic principles of mycology are covered. Overall, 273 structures are presented and the review contains 162 references

  biological activity, cytotoxicity, metabolites, marine-derived fungi

  NCBI PubMed ID: 15039840
  Publication DOI: 10.1039/b301926h
  Journal NLM ID: 8502408
  Publisher: London: Royal Society of Chemistry
  Correspondence: cireland@pharm.utah.edu
  Institutions: Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA
  
   
  
  (fungi) sp. K063
  CSDB ID 48028 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycopeptide
Contained glycoepitopes: IEDB_114085,IEDB_114701,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_148491,IEDB_150900,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_167188,IEDB_174332,IEDB_174333,IEDB_983930,SB_198,SB_44,SB_67,SB_72,SB_86

• Article ID: 6724
  Altmann F, Schweiszer S, Weber C "Kinetic comparison of peptide: N-glycosidases F and A reveals several differences in substrate specificity" - Glycoconjugate Journal 12 (1995) 84-93
  

  The initial velocities of hydrolysis of nineteen glycopeptides by peptide: N-glycosidase F and A were determined. Substrates were prepared from bovine fetuin, hen ovalbumin, pineapple stem bromelain, bovine fibrin and taka-amylase. From these glycopeptides, several variants with regard to peptide and carbohydrate structure were prepared and derivatized with dabsyl chloride, dansyl chloride or activated resorufin. Tyrosine containing glycopeptides were also used without an additional chromophore. Enzymatic hydrolysis of glycopeptides was quantified by narrow bore, reversed phase HPLC with turnaround cycle times of down to 6 min, but usually 15 min. KM values ranging from 30 to 64 μM and from 4 to 36 μM were found for N-glycosidase F and A, respectively. Relative velocities of hydrolysis of the different substrates by each enzyme varied considerably. Little, if any, similarity of the performance of N-glycosidase F and A with the different substrates was observed. The minimal carbohydrate structure released by peptide: N-glycosidase F was a di-N-acetylchitobiose. N-glycosidase A could release even a single N-acetylglucosamine, albeit 3000 times slower than a di-N-acetylchitobiose or larger glycans. In general the structure of the intact glycan had little effect on activity, and with both enzymes the rate of hydrolysis appeared to be primarily governed by peptide structure and length. However, N-glycosidase F did not release glycans α-1,3-fucosylated at the asparagine linked N-acetylglucosamine irrespective of the presence of xylose in the substrate.

  NCBI PubMed ID: 7540902
  Journal NLM ID: 8603310
  Publisher: Kluwer Academic Publishers
  Institutions: Institut für Chemie, Univesität fur Bodenkultur Wien, Austria
  
   
  
  Ananas comosus
  CSDB ID 129091 (all data & tools)

Show legend Show as text

Structure type: polymer biological repeating unit ; n=2
Compound class: O-glycoprotein
Contained glycoepitopes: IEDB_136017

• Article ID: 10867
  Kieliszewski MJ, O'Neill M, Leykam J, Orlando R "Tandem mass spectrometry and structural elucidation of glycopeptides from a hydroxyproline-rich plant cell wall glycoprotein indicate that contiguous hydroxyproline residues are the major sites of hydroxyproline O-arabinosylation" - Journal of Biological Chemistry 270 (1995) 2541-2549
  

  Hydroxyproline-rich glycoproteins (HRGPs) occur in the extracellular matrix of land plants and green algae. HRGPs contain from 2 to 95% of their dry weight as carbohydrate, predominantly as oligoarabinosides and/or as heteropolysaccharides which are O-linked to the hydroxyproline residues. A glycosylation code that determines the presence or absence and extent of arabinosylation at each hydroxyproline residue is likely, as each HRGP has a unique arabinosylation profile. Previously we noted a positive correlation between the contiguity of hydroxyproline residues and the extent of HRGP O-arabinosylation (Kieliszewski, M., deZacks, R., Leykam, J.F., and Lamport, D.T.A. (1992) Plant Physiol. 98, 919-926); most arabinosylated hydroxyproline residues and the longer arabinofuranoside chains occur in HRGPs where Hyp residues occur as blocks of tetrahydroxyproline, while those with little or no contiguous Hyp exhibit very little Hyp arabinosylation. In order to test this Hyp contiguity hypothesis, we have for the first time determined the arabinosylation site specifics of an HRGP, namely the proline and hydroxyproline-rich glycoprotein (PHRGP) isolated from Douglas fir (Pseudotsuga menziesii). Pronase digests of PHRGP yielded a major peptide and three glycopeptides whose structures were determined directly from the unfractionated underivatized Pronase digest by tandem mass spectrometry using collisionally induced dissociation. We corroborated the peptide and glycopeptide structures by Edman degradation, neutral sugar analyses, hydroxyproline arabinoside profiles, and further mass spectrometric analyses after purification of the major peptide and glycopeptides by a combination of hydrophilic interaction and reverse phase column chromatography. Consistent with the Hyp contiguity hypothesis, the structural analyses indicate that while the sequence Ile-Pro-Pro-Hyp is never arabinosylated and Lys-Pro-Hyp-Val-Hyp is only occasionally monoarabinosylated at Hyp-5, the peptide containing contiguous Hyp, Lys-Pro-Hyp-Hyp-Val, is always arabinosylated at Hyp-3, mainly by a triarabinoside. We also obtained precise molecular masses for both intact and anhydrous hydrogen fluoride-deglycosylated PHRGPs (73.113 and 53.834 kDa) via matrix-assisted laser desorption/ionization time of flight mass spectrometry, representing the first HRGP to be analyzed by this method.

  NCBI PubMed ID: 7852316
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Institutions: Complex Carbohydrate Research Center, University of Georgia, Athens, USA
  
   
  
  Pseudotsuga menziesii
  CSDB ID 137390 (all data & tools)