메뉴 건너뛰기




Volumn 109, Issue 7, 2012, Pages 1798-1807

Genome-scale metabolic representation of Amycolatopsis balhimycina

Author keywords

Amycolatopsis balhimycina; Balhimycin; Genome annotation; Metabolic reconstruction; Modeling

Indexed keywords

AMYCOLATOPSIS BALHIMYCINA; BALHIMYCIN; BASE PAIRS; BIOSYNTHETIC PATHWAY; CONTIGS; EVOLUTIONARY PROGRAMMING ALGORITHMS; EXPERIMENTAL DATA; FLUX BALANCE ANALYSIS; FUNCTIONAL ANNOTATION; GENOME ANNOTATION; GENOME SEQUENCES; GENOME SEQUENCING; GENOME-SCALE METABOLIC MODELS; GLYCOPEPTIDE ANTIBIOTICS; GLYCOPEPTIDES; IN-SILICO; KEY REACTIONS; METABOLIC MODELS; METABOLIC REACTIONS; METABOLIC RECONSTRUCTION; METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS; OPEN READING FRAME; PHENOTYPIC BEHAVIOR; PROTEIN-ENCODING GENES; RATIONAL DESIGN; SOCIETAL PROBLEMS;

EID: 84861195660     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.24436     Document Type: Article
Times cited : (20)

References (58)
  • 2
    • 79952109977 scopus 로고    scopus 로고
    • Intra- and extra-cellular flux distributions of TCA and glyoxalate cycle and vancomycin production of Amycolatopsis orieantalis grown in different glycerol concentration
    • Ayar-Kayali H, Tarhan L. 2010. Intra- and extra-cellular flux distributions of TCA and glyoxalate cycle and vancomycin production of Amycolatopsis orieantalis grown in different glycerol concentration. Prikl Biokhim Mikrobiol 46: 519- 526.
    • (2010) Prikl Biokhim Mikrobiol , vol.46 , pp. 519-526
    • Ayar-Kayali, H.1    Tarhan, L.2
  • 3
    • 0032900737 scopus 로고    scopus 로고
    • CRITICA: coding region identification tool invoking comparative analysis
    • Badger JH, Olsen GJ. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 16: 512- 524.
    • (1999) Mol Biol Evol , vol.16 , pp. 512-524
    • Badger, J.H.1    Olsen, G.J.2
  • 4
    • 0035149952 scopus 로고    scopus 로고
    • Genetic methods and strategies for secondary metabolite yield improvement in actinomycetes
    • Baltz RH. 2000. Genetic methods and strategies for secondary metabolite yield improvement in actinomycetes. Antonie van Leeuwenhoek 79: 251- 259.
    • (2000) Antonie van Leeuwenhoek , vol.79 , pp. 251-259
    • Baltz, R.H.1
  • 6
    • 20444397992 scopus 로고    scopus 로고
    • Genome-scale analysis of Streptomyces coelicolor A3 (2) metabolism
    • Borodina I, Krabben P, Nielsen J. 2005. Genome-scale analysis of Streptomyces coelicolor A3 (2) metabolism. Genome Res 15: 820- 829.
    • (2005) Genome Res , vol.15 , pp. 820-829
    • Borodina, I.1    Krabben, P.2    Nielsen, J.3
  • 8
    • 69249083586 scopus 로고    scopus 로고
    • Waves of resistance: Staphylococcus aureus in the antibiotic era
    • Chamber HF, Deleo FR. 2009. Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat Rev Microbiol 7: 629- 641.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 629-641
    • Chamber, H.F.1    Deleo, F.R.2
  • 9
    • 0037417230 scopus 로고    scopus 로고
    • Infection with vancomycin resistant Staphylococcus aureus containing the vanA resistance gene
    • Chang S, Sievert DM, Hageman JC. 2003. Infection with vancomycin resistant Staphylococcus aureus containing the vanA resistance gene. N Engl J Med 348: 1342- 1347.
    • (2003) N Engl J Med , vol.348 , pp. 1342-1347
    • Chang, S.1    Sievert, D.M.2    Hageman, J.C.3
  • 10
    • 0035910072 scopus 로고    scopus 로고
    • Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine
    • Chen H, Tseng CC, Hubbard BK, Walsh CT. 2001. Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3, 5-dihydroxyphenylglycine. PNAS 98: 14901- 14906.
    • (2001) PNAS , vol.98 , pp. 14901-14906
    • Chen, H.1    Tseng, C.C.2    Hubbard, B.K.3    Walsh, C.T.4
  • 14
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing B, Green P. 1998a. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186- 194.
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 15
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing B, Hillier L, Wendl MC, Green P. 1998b. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175- 185.
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 19
    • 10844238213 scopus 로고    scopus 로고
    • Object-oriented software for quadratic programming
    • Gertz EM, Wright SJ. 2003. Object-oriented software for quadratic programming. ACM Trans Math Software 29: 58- 81.
    • (2003) ACM Trans Math Software , vol.29 , pp. 58-81
    • Gertz, E.M.1    Wright, S.J.2
  • 20
    • 0031955116 scopus 로고    scopus 로고
    • Consed: a graphical tool for sequence finishing
    • Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res 8: 195- 202.
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 21
    • 0036087169 scopus 로고    scopus 로고
    • SUPERFAMILY: HMMs representing all proteins of known structure SCOP sequence searches, alignments and genome assignments
    • Gough J, Chothia C. 2002. SUPERFAMILY: HMMs representing all proteins of known structure SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res 30: 268- 272.
    • (2002) Nucleic Acids Res , vol.30 , pp. 268-272
    • Gough, J.1    Chothia, C.2
  • 22
    • 84861194330 scopus 로고    scopus 로고
    • Antibiotic production and primary metabolism in the actinomycetes Nonomuraea sp ATCC 39727. Ph.D. Thesis. BioCentrum, Technical University of Denmark, Denmark.
    • Gunnarsson N. 2004a. Antibiotic production and primary metabolism in the actinomycetes Nonomuraea sp ATCC 39727. Ph.D. Thesis. BioCentrum, Technical University of Denmark, Denmark.
    • (2004)
    • Gunnarsson, N.1
  • 23
    • 2442671961 scopus 로고    scopus 로고
    • Identification of the Entner-Doudoroff pathway in an antibiotic-producing actinomycete species
    • Gunnarsson N, Mortensen UH, Sosio M, Nielsen J. 2004b. Identification of the Entner-Doudoroff pathway in an antibiotic-producing actinomycete species. Mol Microbiol 52: 895- 902.
    • (2004) Mol Microbiol , vol.52 , pp. 895-902
    • Gunnarsson, N.1    Mortensen, U.H.2    Sosio, M.3    Nielsen, J.4
  • 28
    • 0037805576 scopus 로고    scopus 로고
    • The KEGG database
    • Kanehisa M. 2002. The KEGG database. Novartis Found Symp 247: 91- 9101.
    • (2002) Novartis Found Symp , vol.247 , pp. 91-9101
    • Kanehisa, M.1
  • 31
    • 0030998236 scopus 로고    scopus 로고
    • Glycopeptide resistance in multiple antibiotic-resistant Gram-positive bacteria: a current challenge for novel semi-synthetic glycopeptide derivatives
    • Malabarba A, Nicas T, Ciabatti R. 1997. Glycopeptide resistance in multiple antibiotic-resistant Gram-positive bacteria: a current challenge for novel semi-synthetic glycopeptide derivatives. Eur J Med Chem 32: 459- 478.
    • (1997) Eur J Med Chem , vol.32 , pp. 459-478
    • Malabarba, A.1    Nicas, T.2    Ciabatti, R.3
  • 34
    • 84861201491 scopus 로고
    • Physiological Engineering Aspects of Penicillium chrysogenum. Ph.D. thesis. Polyteknisk Forlag, Technical University of Denmark, Denmark.
    • Nielsen J. 1995. Physiological Engineering Aspects of Penicillium chrysogenum. Ph.D. thesis. Polyteknisk Forlag, Technical University of Denmark, Denmark.
    • (1995)
    • Nielsen, J.1
  • 36
    • 0028349583 scopus 로고
    • Importance of stored triacylglycerols in Streptomyces: possible carbon source for antibiotics
    • Olukoshi ER, Packter NM. 1994. Importance of stored triacylglycerols in Streptomyces: possible carbon source for antibiotics. Microbiology 140: 931- 943.
    • (1994) Microbiology , vol.140 , pp. 931-943
    • Olukoshi, E.R.1    Packter, N.M.2
  • 39
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: a comparative genomics approach
    • Osterman A, Overbeek R. 2003. Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7: 238- 251.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 40
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil KR, Rocha I, Förster J, Nielsen J. 2005. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6: 308.
    • (2005) BMC Bioinformatics , vol.6 , pp. 308
    • Patil, K.R.1    Rocha, I.2    Förster, J.3    Nielsen, J.4
  • 41
    • 0036682463 scopus 로고    scopus 로고
    • Superbug hurdles key drug barrier
    • Pearson H. 2002. Superbug hurdles key drug barrier. Nature 418: 469- 470.
    • (2002) Nature , vol.418 , pp. 469-470
    • Pearson, H.1
  • 42
    • 0345643323 scopus 로고    scopus 로고
    • Identification and analysis of the balhimycin biosynthetic gene cluster and its use for manipulating glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908
    • Pelzer S, Sübmuth R, Heckmann D, Recktenwald J, Huber P, Jung G, Wohlleben W. 1999. Identification and analysis of the balhimycin biosynthetic gene cluster and its use for manipulating glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908. Antimicrob Agents Chemother 43: 1565- 1573.
    • (1999) Antimicrob Agents Chemother , vol.43 , pp. 1565-1573
    • Pelzer, S.1    Sübmuth, R.2    Heckmann, D.3    Recktenwald, J.4    Huber, P.5    Jung, G.6    Wohlleben, W.7
  • 43
    • 84861187916 scopus 로고    scopus 로고
    • BT Antibiotic Production by Amycolatopsis balhimycina. Dissertation. BioCentrum, Technical University of Denmark, Denmark.
    • Poli E. 2005. BT Antibiotic Production by Amycolatopsis balhimycina. Dissertation. BioCentrum, Technical University of Denmark, Denmark.
    • (2005)
    • Poli, E.1
  • 44
  • 46
    • 0036230911 scopus 로고    scopus 로고
    • Nonribosomal biosynthesis of vancomycin-type antibiotics: a heptapeptide backbone and eight peptide synthetase modules
    • Recktenwald J, Shawky R, Puk O, Pfennig F, Keller U, Wohlleben W, Pelzer S. 2002. Nonribosomal biosynthesis of vancomycin-type antibiotics: a heptapeptide backbone and eight peptide synthetase modules. Microbiology 148: 1105- 1118.
    • (2002) Microbiology , vol.148 , pp. 1105-1118
    • Recktenwald, J.1    Shawky, R.2    Puk, O.3    Pfennig, F.4    Keller, U.5    Wohlleben, W.6    Pelzer, S.7
  • 47
    • 40549127097 scopus 로고    scopus 로고
    • Design and application of genome-scale reconstructed metabolic models
    • Rocha I, Förster J, Nielsen J. 2008. Design and application of genome-scale reconstructed metabolic models. Methods Mol Biol 416: 409- 431.
    • (2008) Methods Mol Biol , vol.416 , pp. 409-431
    • Rocha, I.1    Förster, J.2    Nielsen, J.3
  • 48
    • 0029804432 scopus 로고    scopus 로고
    • Growth rate control of protein and nucleic acid content in Streptomyces coelicolor A3 (2) and Escherichia coli B/r
    • Shahab N, Flett F, Oiver SG, Butler PR. 1996. Growth rate control of protein and nucleic acid content in Streptomyces coelicolor A3 (2) and Escherichia coli B/r. Microbiology 142: 1927- 1935.
    • (1996) Microbiology , vol.142 , pp. 1927-1935
    • Shahab, N.1    Flett, F.2    Oiver, S.G.3    Butler, P.R.4
  • 51
    • 1642496907 scopus 로고    scopus 로고
    • The biosynthesis of glycopeptides antibiotics-a model for complex, non-ribosomally synthesized, peptidic secondary metabolites
    • Süssmuth RD, Wohlleben W. 2004. The biosynthesis of glycopeptides antibiotics-a model for complex, non-ribosomally synthesized, peptidic secondary metabolites. Appl Microbiol Biotechnol 63: 344- 350.
    • (2004) Appl Microbiol Biotechnol , vol.63 , pp. 344-350
    • Süssmuth, R.D.1    Wohlleben, W.2
  • 52
    • 13444280436 scopus 로고    scopus 로고
    • EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
    • Tian W, Arakaki AK, Skolnick J. 2004. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Res 32: 6226- 6239.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6226-6239
    • Tian, W.1    Arakaki, A.K.2    Skolnick, J.3
  • 53
    • 75849158230 scopus 로고    scopus 로고
    • The Gene Ontology in 2010: extensions and refinements
    • The Gene Ontology consortium.
    • The Gene Ontology consortium. 2010. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38: D331- D335.
    • (2010) Nucleic Acids Res , vol.38
  • 55
    • 77955655055 scopus 로고    scopus 로고
    • Increased glycopeptide production after overexpression of shikimate pathway genes being part of the balhimycin biosynthetic gene cluster
    • Thykaer J, Nielsen J, Wohlleben W, Weber T, Gutknecht M, Lantz AE, Stegmann E. 2010. Increased glycopeptide production after overexpression of shikimate pathway genes being part of the balhimycin biosynthetic gene cluster. Metab Eng 12: 455- 461.
    • (2010) Metab Eng , vol.12 , pp. 455-461
    • Thykaer, J.1    Nielsen, J.2    Wohlleben, W.3    Weber, T.4    Gutknecht, M.5    Lantz, A.E.6    Stegmann, E.7
  • 56
    • 0242669191 scopus 로고    scopus 로고
    • Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov
    • Wink JM, Kroppenstedt RM, Ganguli BN, Nadkarni SR, Schumann P, Seibert G, Stackebrandt E. 2003. Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov. System Appl Microbiol 26: 38- 46.
    • (2003) System Appl Microbiol , vol.26 , pp. 38-46
    • Wink, J.M.1    Kroppenstedt, R.M.2    Ganguli, B.N.3    Nadkarni, S.R.4    Schumann, P.5    Seibert, G.6    Stackebrandt, E.7
  • 57
    • 64249110009 scopus 로고    scopus 로고
    • Molecular genetic approaches to analyze glycopeptide biosynthesis
    • Wohlleben W, Stegmann E, Sübmuth RD. 2009. Molecular genetic approaches to analyze glycopeptide biosynthesis. Methods Enzymol 458: 459- 486.
    • (2009) Methods Enzymol , vol.458 , pp. 459-486
    • Wohlleben, W.1    Stegmann, E.2    Sübmuth, R.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.