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Volumn 15, Issue 1, 2014, Pages

Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species

Author keywords

Genome sequence; Nocardia asteroides; Nocardia brasiliensis; Nocardia cyriacigeorgica; Nocardia farcinica; Nocardia otitidiscaviarum; Nonribosomal peptide synthetase; Type I polyketide synthase

Indexed keywords

NONRIBOSOMAL PEPTIDE SYNTHETASE; POLYKETIDE SYNTHASE; TYPE I POLYKETIDE SYNTHASE; UNCLASSIFIED DRUG;

EID: 84900303120     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-323     Document Type: Article
Times cited : (41)

References (54)
  • 1
    • 0028265313 scopus 로고
    • Nocardia species: host-parasite relationships
    • 358319, 8055469
    • Beaman BL, Beaman L. Nocardia species: host-parasite relationships. Clin Microbiol Rev 1994, 7(2):213-264. 358319, 8055469.
    • (1994) Clin Microbiol Rev , vol.7 , Issue.2 , pp. 213-264
    • Beaman, B.L.1    Beaman, L.2
  • 2
    • 3242886579 scopus 로고    scopus 로고
    • Nocardial infections in Japan from 1992 to 2001, including the first report of infection by Nocardia transvalensis
    • Kageyama A, Yazawa K, Ishikawa J, Hotta K, Nishimura K, Mikami Y. Nocardial infections in Japan from 1992 to 2001, including the first report of infection by Nocardia transvalensis. Eur J Epidemiol 2004, 19(4):383-389.
    • (2004) Eur J Epidemiol , vol.19 , Issue.4 , pp. 383-389
    • Kageyama, A.1    Yazawa, K.2    Ishikawa, J.3    Hotta, K.4    Nishimura, K.5    Mikami, Y.6
  • 3
    • 33646231490 scopus 로고    scopus 로고
    • Clinical and Laboratory Features of the Nocardia spp. Based on Current Molecular Taxonomy
    • 10.1128/CMR.19.2.259-282.2006, 1471991, 16614249
    • Brown-Elliott BA, Brown JM, Conville PS, Wallace RJ. Clinical and Laboratory Features of the Nocardia spp. Based on Current Molecular Taxonomy. Clin Microbiol Rev 2006, 19(2):259-282. 10.1128/CMR.19.2.259-282.2006, 1471991, 16614249.
    • (2006) Clin Microbiol Rev , vol.19 , Issue.2 , pp. 259-282
    • Brown-Elliott, B.A.1    Brown, J.M.2    Conville, P.S.3    Wallace, R.J.4
  • 4
    • 84900345745 scopus 로고    scopus 로고
    • Japan: Chiba University, Medical Mycology Research Center
    • Medical Mycology Research Center Japan: Chiba University, http://www.pf.chiba-u.ac.jp/eng/index.html, Medical Mycology Research Center.
  • 5
    • 84900317148 scopus 로고    scopus 로고
    • NBRC culture collection
    • NBRC culture collection http://www.nbrc.nite.go.jp/e/index.html, NBRC culture collection.
  • 6
    • 84900309830 scopus 로고    scopus 로고
    • American Type Culture Collection
    • American Type Culture Collection, http://www.atcc.org/.
  • 7
    • 84900333847 scopus 로고    scopus 로고
    • Leibniz Institute DSMZ-German Collection of Microorganisms and cell culture
    • Leibniz Institute DSMZ-German Collection of Microorganisms and cell culture https://www.dsmz.de/, Leibniz Institute DSMZ-German Collection of Microorganisms and cell culture.
  • 12
    • 84900303901 scopus 로고    scopus 로고
    • Japan: Chiba University, IFM culture collections of MMRC
    • IFM culture collections of MMRC Japan: Chiba University, http://www.pf.chiba-u.ac.jp/eng/bioresoures/index.html, IFM culture collections of MMRC.
  • 14
    • 84900301157 scopus 로고    scopus 로고
    • DNA Data Bank of Japan
    • DNA Data Bank of Japan http://www.ddbj.nig.ac.jp/index-e.html, DNA Data Bank of Japan.
  • 15
    • 84900302712 scopus 로고    scopus 로고
    • Microbial Genome Annotation Pipeline
    • Microbial Genome Annotation Pipeline http://www.migap.org/index.php/en/aboutpipeline, Microbial Genome Annotation Pipeline.
  • 17
    • 84869234479 scopus 로고    scopus 로고
    • Genome-wide survey of polyketide synthase and nonribosomal peptide synthetase gene clusters in Streptomyces turgidiscabies NBRC 16081
    • 10.2323/jgam.58.363, 23149681
    • Komaki H, Ichikawa N, Oguchi A, Hanamaki T, Fujita N. Genome-wide survey of polyketide synthase and nonribosomal peptide synthetase gene clusters in Streptomyces turgidiscabies NBRC 16081. J Gen Appl Microbiol 2012, 58(5):363-372. 10.2323/jgam.58.363, 23149681.
    • (2012) J Gen Appl Microbiol , vol.58 , Issue.5 , pp. 363-372
    • Komaki, H.1    Ichikawa, N.2    Oguchi, A.3    Hanamaki, T.4    Fujita, N.5
  • 18
    • 84900305489 scopus 로고    scopus 로고
    • InterPro domain database
    • InterPro domain database http://www.ebi.ac.uk/interpro/, InterPro domain database.
  • 19
    • 42449105845 scopus 로고    scopus 로고
    • In silico characterization of proteins: UniProt, InterPro and Integr8
    • 10.1007/s12033-007-9003-x, 18219596
    • Mulder NJ, Kersey P, Pruess M, Apweiler R. In silico characterization of proteins: UniProt, InterPro and Integr8. Mol Biotechnol 2008, 38(2):165-177. 10.1007/s12033-007-9003-x, 18219596.
    • (2008) Mol Biotechnol , vol.38 , Issue.2 , pp. 165-177
    • Mulder, N.J.1    Kersey, P.2    Pruess, M.3    Apweiler, R.4
  • 20
    • 84900312145 scopus 로고    scopus 로고
    • PKS/NRPS analysis Web-site
    • PKS/NRPS analysis Web-site http://nrps.igs.umaryland.edu/nrps, PKS/NRPS analysis Web-site.
  • 21
    • 84900327251 scopus 로고    scopus 로고
    • KEGG MOTIF Search
    • KEGG MOTIF Search http://www.genome.jp/tools/motif/, KEGG MOTIF Search.
  • 22
    • 84900305656 scopus 로고    scopus 로고
    • Antibiotics and Secondary Metabolite Analysis Shell (antiSMASH)
    • Antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) http://www.secondarymetabolites.org/, Antibiotics and Secondary Metabolite Analysis Shell (antiSMASH).
  • 23
    • 79959920872 scopus 로고    scopus 로고
    • AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
    • Web Server issue, 3125804, 21672958
    • Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011, 39(Web Server issue):W339-W346. 3125804, 21672958.
    • (2011) Nucleic Acids Res , vol.39
    • Medema, M.H.1    Blin, K.2    Cimermancic, P.3    de Jager, V.4    Zakrzewski, P.5    Fischbach, M.A.6    Weber, T.7    Takano, E.8    Breitling, R.9
  • 25
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • 10.1016/S0022-2836(05)80360-2, 2231712
    • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410. 10.1016/S0022-2836(05)80360-2, 2231712.
    • (1990) J Mol Biol , vol.215 , Issue.3 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3    Myers, E.W.4    Lipman, D.J.5
  • 26
    • 84900321873 scopus 로고    scopus 로고
    • NCBI/BLAST Home
    • NCBI/BLAST Home http://blast.ncbi.nlm.nih.gov/, NCBI/BLAST Home.
  • 27
    • 70350722394 scopus 로고    scopus 로고
    • Genomic basis for natural product biosynthetic diversity in the actinomycetes
    • 10.1039/b817069j, 3063060, 19844637
    • Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 2009, 26(11):1362-1384. 10.1039/b817069j, 3063060, 19844637.
    • (2009) Nat Prod Rep , vol.26 , Issue.11 , pp. 1362-1384
    • Nett, M.1    Ikeda, H.2    Moore, B.S.3
  • 28
    • 14544294545 scopus 로고    scopus 로고
    • Bioactive microbial metabolites
    • 10.1038/ja.2005.1, 15813176
    • Berdy J. Bioactive microbial metabolites. J Antibiot (Tokyo) 2005, 58(1):1-26. 10.1038/ja.2005.1, 15813176.
    • (2005) J Antibiot (Tokyo) , vol.58 , Issue.1 , pp. 1-26
    • Berdy, J.1
  • 29
    • 84865683314 scopus 로고    scopus 로고
    • Thoughts and facts about antibiotics: where we are now and where we are heading
    • 10.1038/ja.2012.27, 22511224
    • Berdy J. Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot (Tokyo) 2012, 65(8):385-395. 10.1038/ja.2012.27, 22511224.
    • (2012) J Antibiot (Tokyo) , vol.65 , Issue.8 , pp. 385-395
    • Berdy, J.1
  • 30
    • 0001075443 scopus 로고
    • Über eine neue pathogene Cladothrixund eine durch sie hervorgerufene Pseudotuberculosis (Cladothrichica)
    • Eppinger H. Über eine neue pathogene Cladothrixund eine durch sie hervorgerufene Pseudotuberculosis (Cladothrichica). Beitrage zur pathologischen Anatomie 1891, 9:287-328.
    • (1891) Beitrage zur pathologischen Anatomie , vol.9 , pp. 287-328
    • Eppinger, H.1
  • 33
    • 2642541132 scopus 로고
    • A Comparison of Nocardia asteroides and Nocardia brasiliensis
    • Gordon RE, Mihm JM. A Comparison of Nocardia asteroides and Nocardia brasiliensis. J Gen Microbial 1959, 20:129-135.
    • (1959) J Gen Microbial , vol.20 , pp. 129-135
    • Gordon, R.E.1    Mihm, J.M.2
  • 34
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
    • 10.1093/molbev/msr121, 3203626, 21546353
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 35
    • 24744433982 scopus 로고    scopus 로고
    • Evolutionary implications of bacterial polyketide synthases
    • 10.1093/molbev/msi193, 15958783
    • Jenke-Kodama H, Sandmann A, Müller R, Dittmann E. Evolutionary implications of bacterial polyketide synthases. Mol Biol Evol 2005, 22(10):2027-2039. 10.1093/molbev/msi193, 15958783.
    • (2005) Mol Biol Evol , vol.22 , Issue.10 , pp. 2027-2039
    • Jenke-Kodama, H.1    Sandmann, A.2    Müller, R.3    Dittmann, E.4
  • 36
    • 0347719360 scopus 로고    scopus 로고
    • A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms
    • 10.1073/pnas.0305439101, 314182, 14695899
    • Portevin D, De Sousa-D'Auria C, Houssin C, Grimaldi C, Chami M, Daffé M, Guilhot C. A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms. Proc Natl Acad Sci U S A 2004, 101(1):314-31937. 10.1073/pnas.0305439101, 314182, 14695899.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , Issue.1 , pp. 314-31937
    • Portevin, D.1    De Sousa-D'Auria, C.2    Houssin, C.3    Grimaldi, C.4    Chami, M.5    Daffé, M.6    Guilhot, C.7
  • 37
    • 56249145109 scopus 로고    scopus 로고
    • Epsilon-poly-L-lysine dispersity is controlled by a highly unusual nonribosomal peptide synthetase
    • 10.1038/nchembio.125, 18997795
    • Yamanaka K, Murayama C, Takagi H, Hamano Y. Epsilon-poly-L-lysine dispersity is controlled by a highly unusual nonribosomal peptide synthetase. Nat Chem Biol 2008, 4(12):766-772. 10.1038/nchembio.125, 18997795.
    • (2008) Nat Chem Biol , vol.4 , Issue.12 , pp. 766-772
    • Yamanaka, K.1    Murayama, C.2    Takagi, H.3    Hamano, Y.4
  • 38
    • 33746208944 scopus 로고    scopus 로고
    • HC-toxin
    • Walton JD. HC-toxin. Phytochem 2006, 67(14):1406-1413.
    • (2006) Phytochem , vol.67 , Issue.14 , pp. 1406-1413
    • Walton, J.D.1
  • 39
    • 78650871561 scopus 로고    scopus 로고
    • Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica
    • 10.1128/JB.00897-10, 3019813, 21097631
    • Hoshino Y, Chiba K, Ishino K, Fukai T, Igarashi Y, Yazawa K, Mikami Y, Ishikawa J. Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica. J Bacteriol 2011, 193(2):441-448. 10.1128/JB.00897-10, 3019813, 21097631.
    • (2011) J Bacteriol , vol.193 , Issue.2 , pp. 441-448
    • Hoshino, Y.1    Chiba, K.2    Ishino, K.3    Fukai, T.4    Igarashi, Y.5    Yazawa, K.6    Mikami, Y.7    Ishikawa, J.8
  • 40
    • 0026657817 scopus 로고
    • Molecular cloning and sequencing of the gene for mycocerosic acid synthase, a novel fatty acid elongating multifunctional enzyme, from Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guerin
    • Mathur M, Kolattukudy PE. Molecular cloning and sequencing of the gene for mycocerosic acid synthase, a novel fatty acid elongating multifunctional enzyme, from Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guerin. J Biol Chem 1992, 267(27):19388-19395.
    • (1992) J Biol Chem , vol.267 , Issue.27 , pp. 19388-19395
    • Mathur, M.1    Kolattukudy, P.E.2
  • 41
    • 0029061399 scopus 로고
    • The envelope of mycobacteria
    • 10.1146/annurev.bi.64.070195.000333, 7574484
    • Brennan PJ, Nikaido H. The envelope of mycobacteria. Annu Rev Biochem 1995, 64:29-63. 10.1146/annurev.bi.64.070195.000333, 7574484.
    • (1995) Annu Rev Biochem , vol.64 , pp. 29-63
    • Brennan, P.J.1    Nikaido, H.2
  • 42
    • 0037013948 scopus 로고    scopus 로고
    • Biosynthesis of polyunsaturated fatty acids by polyketide synthases
    • 10.1002/1521-3773(20020603)41:11<1866::AID-ANIE1866>3.0.CO;2-3, 19750617
    • Kaulmann U, Hertweck C. Biosynthesis of polyunsaturated fatty acids by polyketide synthases. Angew Chem Int Ed Engl 2002, 41(11):1866-1869. 10.1002/1521-3773(20020603)41:11<1866::AID-ANIE1866>3.0.CO;2-3, 19750617.
    • (2002) Angew Chem Int Ed Engl , vol.41 , Issue.11 , pp. 1866-1869
    • Kaulmann, U.1    Hertweck, C.2
  • 43
    • 43949138588 scopus 로고    scopus 로고
    • The role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis
    • 10.1021/ja801911t, 18444614
    • Jiang H, Zirkle R, Metz JG, Braun L, Richter L, Van Lanen SG, Shen B. The role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis. J Am Chem Soc 2008, 130(20):6336-6337. 10.1021/ja801911t, 18444614.
    • (2008) J Am Chem Soc , vol.130 , Issue.20 , pp. 6336-6337
    • Jiang, H.1    Zirkle, R.2    Metz, J.G.3    Braun, L.4    Richter, L.5    Van Lanen, S.G.6    Shen, B.7
  • 44
    • 0036710533 scopus 로고    scopus 로고
    • Polyunsaturated fatty acid synthesis: what will they think of next?
    • 10.1016/S0968-0004(02)02168-0, 12217522
    • Wallis JG, Watts JL, Browse J. Polyunsaturated fatty acid synthesis: what will they think of next?. Trends Biochem Sci 2002, 27(9):467. 10.1016/S0968-0004(02)02168-0, 12217522.
    • (2002) Trends Biochem Sci , vol.27 , Issue.9 , pp. 467
    • Wallis, J.G.1    Watts, J.L.2    Browse, J.3
  • 45
    • 38949118755 scopus 로고    scopus 로고
    • Significance of antioxidative functions of eicosapentaenoic and docosahexaenoic acids in marine microorganisms
    • 10.1128/AEM.02256-07, 2227742, 18065628
    • Okuyama H, Orikasa Y, Nishida T. Significance of antioxidative functions of eicosapentaenoic and docosahexaenoic acids in marine microorganisms. Appl Environ Microbiol 2008, 74(3):570-574. 10.1128/AEM.02256-07, 2227742, 18065628.
    • (2008) Appl Environ Microbiol , vol.74 , Issue.3 , pp. 570-574
    • Okuyama, H.1    Orikasa, Y.2    Nishida, T.3
  • 46
    • 33748631825 scopus 로고    scopus 로고
    • Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms
    • 10.1021/cr0503097, 16895337
    • Fischbach MA, Walsh CT. Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 2006, 106(8):3468-3496. 10.1021/cr0503097, 16895337.
    • (2006) Chem Rev , vol.106 , Issue.8 , pp. 3468-3496
    • Fischbach, M.A.1    Walsh, C.T.2
  • 47
    • 64049111007 scopus 로고    scopus 로고
    • Introduction to polyketide biosynthesis
    • Weissmam KJ. Introduction to polyketide biosynthesis. Methods Enzymol 2009, 459:3-16.
    • (2009) Methods Enzymol , vol.459 , pp. 3-16
    • Weissmam, K.J.1
  • 49
    • 0030693291 scopus 로고    scopus 로고
    • Identification and characterization of the niddamycin polyketide synthase genes from Streptomyces caelestis
    • 179704, 9393718
    • Kakavas SJ, Katz L, Stassi D. Identification and characterization of the niddamycin polyketide synthase genes from Streptomyces caelestis. J Bacteriol 1997, 179:7515-7522. 179704, 9393718.
    • (1997) J Bacteriol , vol.179 , pp. 7515-7522
    • Kakavas, S.J.1    Katz, L.2    Stassi, D.3
  • 50
    • 0030744904 scopus 로고    scopus 로고
    • Cloning of an avilamycin biosynthetic gene cluster from Streptomyces viridochromogenes Tu57
    • Gaisser S, Trefzer A, Stockert S, Kirschning A, Bechthold A. Cloning of an avilamycin biosynthetic gene cluster from Streptomyces viridochromogenes Tu57. J Bacteriol 1997, 178(20):6271-7278.
    • (1997) J Bacteriol , vol.178 , Issue.20 , pp. 6271-7278
    • Gaisser, S.1    Trefzer, A.2    Stockert, S.3    Kirschning, A.4    Bechthold, A.5
  • 51
    • 35848971002 scopus 로고    scopus 로고
    • Characterization of the maduropeptin biosynthetic gene cluster from Actinomadura madurae ATCC 39144 supporting a unifying paradigm for enediyne
    • Van Lanen SG, Oh TJ, Liu W, Wendt-Pienkowski E, Shen B. Characterization of the maduropeptin biosynthetic gene cluster from Actinomadura madurae ATCC 39144 supporting a unifying paradigm for enediyne. Biosynthesis 2007, 129(43):13082-13094.
    • (2007) Biosynthesis , vol.129 , Issue.43 , pp. 13082-13094
    • Van Lanen, S.G.1    Oh, T.J.2    Liu, W.3    Wendt-Pienkowski, E.4    Shen, B.5
  • 53
    • 84900309357 scopus 로고    scopus 로고
    • A genome database of microorganisms sequenced at NITE
    • A genome database of microorganisms sequenced at NITE http://www.bio.nite.go.jp/dogan/project/view/OPACUS, A genome database of microorganisms sequenced at NITE.


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