Show legend Show as text

Structure type: oligomer
Compound class: EPS
Contained glycoepitopes: IEDB_115017

• Article ID: 4556
  Kondo K, Umezu T, Shimura S, Narizuka R, Koizumi JI, Mashima T, Katahira M, Takeda M "Structure of perosamine-containing polysaccharide, a component of the sheath of Thiothrix fructosivorans" - International Journal of Biological Macromolecules 59 (2013) 59-66
  

  A sheath-forming and sulfur-oxidizing bacterium, Thiothrix fructosivorans, was heterotrophically cultured. The sheath, which is an extracellular microtube, was prepared by selectively removing the cells using lysozyme, sodium dodecyl sulfate, and sodium hydroxide. Solid-state 13C-nuclear magnetic resonance (NMR) spectrum revealed that the sheath is assembled from a glycan possessing acetyl and methyl groups. When the sheath was deacetylated, the original microtube structure was lost and the sheath became soluble under acidic conditions, revealing the importance of acetyl groups in maintaining the sheath structure. Equimolar d-glucose, d-glucosamine, and l-fucose were detected in the acid hydrolysate of the sheath by gas liquid chromatography. In addition to these sugars, β-GlcN-(1→4)-Glc and unidentified sugar were detected by analyzing the hydrolysate using high-performance liquid chromatography analysis. 1H and 13C NMR spectroscopy was used to identify a disaccharide composed of 4-deoxy-4-aminorhamnose (perosamine, Rha4N) and fucose. N-Acetyl-perosamine prepared from the disaccharide was polarimetric and exhibited a d-configuration. The previously unidentified disaccharide was found to be α-D-Rhap4N-(1→3)-d-Fuc. According to 1H and 13C NMR analyses, the deacetylated sheath-forming polysaccharide was found to h have a main chain of [→4)-β-D-GlcpN-(1→4)-β-D-Glcp-(1→]n, to which disaccharide side chains of α-D-Rhap4N-(1→3)-α-L-Fucp-(1→ were attached at position 3 of Glc.

  polysaccharide, structural analysis, perosamine, Sheath, Thiothrix fructosivorans

  NCBI PubMed ID: 23587998
  Publication DOI: 10.1016/j.ijbiomac.2013.04.013
  Journal NLM ID: 7909578
  Publisher: Butterworth-Heinemann
  Correspondence: M. Takeda
  Institutions: Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
  Methods: 13C NMR, 1H NMR, NMR-2D, partial acid hydrolysis, sugar analysis, acid hydrolysis, GLC, de-N-acetylation, NMR-1D, HPLC, N-acetylation
  
   
  
  Thiothrix fructosivorans (ATCC 49749)
  CSDB ID 29619 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: amicetin
Compound class: glycoside
Contained glycoepitopes: IEDB_115017

• Article ID: 5369
  Zhang H, Li S, Xiao J, Zhang G, Zhu Y, Niu S, Ju J, Zhang C "Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation" - Applied and Environmental Microbiology 78(7) (2012) 2393-2401
  

  Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.

  biosynthesis, amicetin, Streptomyces vinaceusdrappus NRRL 2363, gene cloning

  NCBI PubMed ID: 22267658
  Publication DOI: 10.1128/AEM.07185-11
  Journal NLM ID: 7605801
  Publisher: American Society for Microbiology
  Correspondence: czhang2006@gmail.com
  Institutions: CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
  Methods: DNA sequencing, DNA techniques, TLC, HPLC, UV, extraction, column chromatography, cell growth, HPLC-MS, centrifugation
  
   
  
  Streptomyces lividans TK64::pCSG3104, Streptomyces vinaceusdrappus NRRL 2363, Streptomyces vinaceusdrappus AM1001 (Δorf(-1) mutant), Streptomyces vinaceusdrappus AM1011 (Δorf1 mutant)
  CSDB ID 45982 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: plicacetin
Compound class: glycoside
Contained glycoepitopes: IEDB_115017

• Article ID: 5369
  Zhang H, Li S, Xiao J, Zhang G, Zhu Y, Niu S, Ju J, Zhang C "Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation" - Applied and Environmental Microbiology 78(7) (2012) 2393-2401
  

  Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.

  biosynthesis, amicetin, Streptomyces vinaceusdrappus NRRL 2363, gene cloning

  NCBI PubMed ID: 22267658
  Publication DOI: 10.1128/AEM.07185-11
  Journal NLM ID: 7605801
  Publisher: American Society for Microbiology
  Correspondence: czhang2006@gmail.com
  Institutions: CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
  Methods: DNA sequencing, DNA techniques, TLC, HPLC, UV, extraction, column chromatography, cell growth, HPLC-MS, centrifugation
  
   
  
  Streptomyces lividans TK64::pCSG3104
  CSDB ID 45983 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: norplicacetin
Compound class: glycoside
Contained glycoepitopes: IEDB_115017

• Article ID: 5369
  Zhang H, Li S, Xiao J, Zhang G, Zhu Y, Niu S, Ju J, Zhang C "Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation" - Applied and Environmental Microbiology 78(7) (2012) 2393-2401
  

  Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.

  biosynthesis, amicetin, Streptomyces vinaceusdrappus NRRL 2363, gene cloning

  NCBI PubMed ID: 22267658
  Publication DOI: 10.1128/AEM.07185-11
  Journal NLM ID: 7605801
  Publisher: American Society for Microbiology
  Correspondence: czhang2006@gmail.com
  Institutions: CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
  Methods: DNA sequencing, DNA techniques, TLC, HPLC, UV, extraction, column chromatography, cell growth, HPLC-MS, centrifugation
  
   
  
  Streptomyces lividans TK64::pCSG3104
  CSDB ID 45984 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: sheath-forming polysaccharide (SFP)
Contained glycoepitopes: IEDB_115017

• Article ID: 5455
  Kawasaki Y, Kondo K, Narizuka R, Endo T, Katahira M, Kawamura I, Sato M, Takeda M "Presence of N-L-lactyl-D-perosamine residue in the sheath-forming polysaccharide of Thiothrix fructosivorans" - International Journal of Biological Macromolecules 82 (2016) 772-779
  

  Thiothrix fructosivorans forms a microtube (sheath) that encloses a line of cells. This sheath is an assemblage of [→4)-GlcN-(1→4)-Glc-(1→]n with side chains of Rha4N-(1→3)-Fuc(1→ at position 3 of Glc. The sheath-forming polysaccharide (SFP) may have some substitutions but this is not yet confirmed. To investigate the possible substitutions, the sheath was prepared by mild treatments. Solid-state NMR analysis suggested the presence of N-substitution. The sheath was hydrolyzed with concentrated HCl at 0 degrees C, followed by derivatization with 4-aminobenzoic acid ethyl ester (ABEE). The presence of N-lactyl-Rha4N-Fuc-ABEE was suggested by NMR spectroscopy. Lactic acid was determined to be the l-isomer by chiral HPLC analysis. To estimate the N-lactylation degree, the sheath was N-acetylated. N-Acetyl-Rha4N-Fuc-ABEE and N-lactyl-Rha4N-Fuc-ABEE were then collectively recovered, and their abundance ratio was determined to be 1:4 by NMR analysis. When hydrolysis was performed at 40 degrees C, GlcNAc-ABEE was obtained. For estimation of the N-acetylation degree, the sheath was N-acetylated with deuterated acetic anhydride and then N-acetyl-GlcN-ABEE was prepared. The content of deuterated N-acetyl-GlcN-ABEE was determined to be 50% based on the relative intensity of the acetyl proton signal in the 1D-(1)H NMR spectrum. It was concluded that Rha4N is mostly N-l-lactylated and GlcN is substoichiometrically N-acetylated.

  polysaccharide, perosamine, Sheath, Thiothrix fructosivorans, N-Lactylation

  NCBI PubMed ID: 26464130
  Publication DOI: 10.1016/j.ijbiomac.2015.10.028
  Journal NLM ID: 7909578
  Publisher: Butterworth-Heinemann
  Correspondence: mtake@ynu.ac.jp
  Institutions: Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan, Institute of Advanced Energy, Kyoto University, Gokasho, Uji 611-0011, Japan, Graduate School of Energy Science, Kyoto University, Gokasho, Uji 611-0011, Japan, CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki 214-8571, Japan
  Methods: 13C NMR, 1H NMR, NMR-2D, GC, HPLC, microscopy, N-acetylation, RP-HPLC, N-lactylation, reductive amination
  
   
  
  Thiothrix fructosivorans I (ATCC 49749)
  CSDB ID 1042 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: sheath polysaccharide
Contained glycoepitopes: IEDB_115017,IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 5507
  Takeda M, Kondo K, Yamada M, Sumikawa M, Koizumi J, Mashima T, Katahira M "Presence of alternating glucosaminoglucan in the sheath of Thiothrix nivea" - International Journal of Biological Macromolecules 50(1) (2012) 236-244
  

  A sheath-forming sulfa oxidizer, Thiothrix nivea, was mixotrophically cultured in a medium supplemented with acetic acid and sodium disulfide. Its sheath, a microtube-like extracellular supermolecule, was prepared by selectively removing the cells with lysozyme, sodium dodecyl sulfate, and sodium hydroxide. The sheath was not visibly affected by hydrazine treatment, suggesting that it is not a proteinous supermolecule. From the acid hydrolysate of the sheath, glucose and glucosamine were detected in an approximate molar ratio of 1:1. Three other saccharic compounds were detected and recovered by HPLC as fluorescent derivatives prepared by reaction with 4-aminobenzoic acid ethyl ester. Nuclear magnetic resonance (NMR) analysis suggested that one of the derivatives was derived from an unidentified deoxypentose. NMR analysis for the other 2 derivatives showed that they were derived from β-1,4-linked disaccharides and tetrasaccharides, which were composed of glucose and glucosamine. The sheath was readily broken down by weak HCl treatment, releasing an unidentified deoxypentose and polymer. Chemical analysis showed the presence of β-1,4-linked D-Glcp and D-GlcNp in the polymer. NMR analysis revealed that the polymer had a repeating unit of →4)-D-Glcp-(β1→4)-D-GlcNp-(β1→. The solid-state 1D-(13)C NMR spectrum of the polymer in N-acetylated form supported this result. The molecular weight of the polymer was estimated to be 8.2x10(4) by size exclusion chromatography. Based on these results, the sheath of T. nivea is hypothesized to be assembled from alternately β-1,4-linked glucosaminoglucan grafted with unidentified deoxypentose.

  structural analysis, Sheath, Thiothrix nivea, glucosaminoglucan

  NCBI PubMed ID: 22085752
  Publication DOI: 10.1016/j.ijbiomac.2011.10.024
  Journal NLM ID: 7909578
  Publisher: Butterworth-Heinemann
  Correspondence: mtake@ynu.ac.jp
  Institutions: Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Hodogaya, Yokohama, Japan
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, sugar analysis, chemical analysis, GLC, STD NMR, N-acetylation, RP-HPLC, enzymatic treatments, SEM, fluorescent labeling, SPM
  
   
  
  Thiothrix nivea ATCC 35
  CSDB ID 2327 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: sheath polysaccharide
Contained glycoepitopes: IEDB_115017,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 5507
  Takeda M, Kondo K, Yamada M, Sumikawa M, Koizumi J, Mashima T, Katahira M "Presence of alternating glucosaminoglucan in the sheath of Thiothrix nivea" - International Journal of Biological Macromolecules 50(1) (2012) 236-244
  

  A sheath-forming sulfa oxidizer, Thiothrix nivea, was mixotrophically cultured in a medium supplemented with acetic acid and sodium disulfide. Its sheath, a microtube-like extracellular supermolecule, was prepared by selectively removing the cells with lysozyme, sodium dodecyl sulfate, and sodium hydroxide. The sheath was not visibly affected by hydrazine treatment, suggesting that it is not a proteinous supermolecule. From the acid hydrolysate of the sheath, glucose and glucosamine were detected in an approximate molar ratio of 1:1. Three other saccharic compounds were detected and recovered by HPLC as fluorescent derivatives prepared by reaction with 4-aminobenzoic acid ethyl ester. Nuclear magnetic resonance (NMR) analysis suggested that one of the derivatives was derived from an unidentified deoxypentose. NMR analysis for the other 2 derivatives showed that they were derived from β-1,4-linked disaccharides and tetrasaccharides, which were composed of glucose and glucosamine. The sheath was readily broken down by weak HCl treatment, releasing an unidentified deoxypentose and polymer. Chemical analysis showed the presence of β-1,4-linked D-Glcp and D-GlcNp in the polymer. NMR analysis revealed that the polymer had a repeating unit of →4)-D-Glcp-(β1→4)-D-GlcNp-(β1→. The solid-state 1D-(13)C NMR spectrum of the polymer in N-acetylated form supported this result. The molecular weight of the polymer was estimated to be 8.2x10(4) by size exclusion chromatography. Based on these results, the sheath of T. nivea is hypothesized to be assembled from alternately β-1,4-linked glucosaminoglucan grafted with unidentified deoxypentose.

  structural analysis, Sheath, Thiothrix nivea, glucosaminoglucan

  NCBI PubMed ID: 22085752
  Publication DOI: 10.1016/j.ijbiomac.2011.10.024
  Journal NLM ID: 7909578
  Publisher: Butterworth-Heinemann
  Correspondence: mtake@ynu.ac.jp
  Institutions: Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Hodogaya, Yokohama, Japan
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, sugar analysis, chemical analysis, GLC, STD NMR, N-acetylation, RP-HPLC, enzymatic treatments, SEM, fluorescent labeling, SPM
  
   
  
  Thiothrix nivea ATCC 35
  CSDB ID 2328 (all data & tools)