1887

Abstract

Strain DSM 7029, isolated from a soil sample in Greece, can produce antitumour glidobactins, and has been found, as a heterologous host, to produce useful nonribosomal peptide synthetase–polyketide synthase hybrid molecules known as epothilones. This strain was originally named ‘’ of the family and the order . However, phylogenetic analysis of the 16S rRNA gene sequence of strain DSM 7029 indicated that it was clustered with members of . Significant growth occurred at 25–42 °C, pH 5.0–10.0 and in the presence of 0–0.2 % (w/v) NaCl. The predominant ubiquinone was Q-8. The major fatty acids were Cω7/Cω6, C and Cω7. The G+C content of genomic DNA was 67.51 mol%. The strain was clearly distinguishable from other neighbouring members and genera and , using phylogenetic analysis, fatty acid composition data and a range of physiological and biochemical characteristics and genome analysis. Therefore, strain DSM 7029 represents a novel species of the genus , for which the name sp. nov. is proposed.

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2019-09-01
2024-04-23
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References

  1. Konishi M, Tomita K, Oka M, Numata K. inventors; Bristol-Myers Company, New York, assignee. Peptide antibiotics. United States patent 4. 692 1987 pp. 510
  2. Oka M, Yaginuma K, Numata K, Konishi M, Oki T et al. Glidobactins A, B and C, new antitumor antibiotics. II. Structure elucidation. J Antibiot 1988; 41:1338–1350 [View Article][PubMed]
    [Google Scholar]
  3. Oka M, Ohkuma H, Kamei H, Konishi M, Oki T et al. Glidobactins D, E, F, G and H; minor components of the antitumor antibiotic glidobactin. J Antibiot 1988; 41:1906–1909 [View Article][PubMed]
    [Google Scholar]
  4. Oka M, Nishiyama Y, Ohta S, Kamei H, Konishi M et al. Glidobactins A, B and C, new antitumor antibiotics. I. Production, isolation, chemical properties and biological activity. J Antibiot 1988; 41:1331–1337 [View Article][PubMed]
    [Google Scholar]
  5. Numata K, Oka M, Nakakita Y, Murakami T, Miyaki T et al. Enzymatic formation of glidobactamine: a peptide nucleus of glidobactins A, B and C, new lipopeptide antitumor antibiotics. J Antibiot 1988; 41:1351–1357 [View Article][PubMed]
    [Google Scholar]
  6. Numata K, Murakami T, Oka M, Yamamoto H, Hatori M et al. Enhanced production of the minor components of glidobactins in Polyangium brachysporum . J Antibiot 1988; 41:1358–1365 [View Article][PubMed]
    [Google Scholar]
  7. Schellenberg B, Bigler L, Dudler R. Identification of genes involved in the biosynthesis of the cytotoxic compound glidobactin from a soil bacterium. Environ Microbiol 2007; 9:1640–1650 [View Article][PubMed]
    [Google Scholar]
  8. Tang B, Yu Y, Zhang Y, Zhao G, Ding X. Complete genome sequence of the glidobactin producing strain [Polyangium] brachysporum DSM 7029. J Biotechnol 2015; 210:83–84 [View Article][PubMed]
    [Google Scholar]
  9. Elbanna K, Lütke-Eversloh T, Van Trappen S, Mergaert J, Swings J et al. Schlegelella thermodepolymerans gen. nov., sp. nov., a novel thermophilic bacterium that degrades poly(3-hydroxybutyrate-co-3-mercaptopropionate). Int J Syst Evol Microbiol 2003; 53:1165–1168 [View Article][PubMed]
    [Google Scholar]
  10. Chou YJ, Sheu SY, Sheu DS, Wang JT, Chen WM. Schlegelella aquatica sp. nov., a novel thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2006; 56:2793–2797 [View Article][PubMed]
    [Google Scholar]
  11. Dong L, Ming H, Liu L, Zhou EM, Yin YR et al. Zhizhongheella caldifontis gen. nov., sp. nov., a novel member of the family Comamonadaceae . Antonie Van Leeuwenhoek 2014; 105:755–761 [View Article][PubMed]
    [Google Scholar]
  12. Takeda M, Kamagata Y, Ghiorse WC, Hanada S, Koizumi J. Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile. Int J Syst Evol Microbiol 2002; 52:895–900 [View Article][PubMed]
    [Google Scholar]
  13. Chen WM, Chang JS, Chiu CH, Chang SC, Chen WC et al. Caldimonas taiwanensis sp. nov., a amylase producing bacterium isolated from a hot spring. Syst Appl Microbiol 2005; 28:415–420 [View Article][PubMed]
    [Google Scholar]
  14. Imker HJ, Krahn D, Clerc J, Kaiser M, Walsh CT. N-acylation during glidobactin biosynthesis by the tridomain nonribosomal peptide synthetase module GlbF. Chem Biol 2010; 17:1077–1083 [View Article][PubMed]
    [Google Scholar]
  15. Bian X, Huang F, Wang H, Klefisch T, Müller R et al. Heterologous production of glidobactins/luminmycins in Escherichia coli Nissle containing the glidobactin biosynthetic gene cluster from Burkholderia DSM7029. Chembiochem 2014; 15:2221–2224 [View Article][PubMed]
    [Google Scholar]
  16. Bian X, Tang B, Yu Y, Tu Q, Gross F et al. Heterologous Production and Yield Improvement of Epothilones in Burkholderiales Strain DSM 7029. ACS Chem Biol 2017; 12:1805–1812 [View Article][PubMed]
    [Google Scholar]
  17. Philipp G, Murray RGE, Wood W, Krieg N. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  18. Fu XZ, Tan D, Aibaidula G, Wu Q, Chen JC et al. Development of Halomonas TD01 as a host for open production of chemicals. Metab Eng 2014; 23:78–91 [View Article][PubMed]
    [Google Scholar]
  19. Yu TT, Zhou EM, Yin YR, Yao JC, Ming H et al. Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophilus Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov. Antonie Van Leeuwenhoek 2013; 104:369–376 [View Article][PubMed]
    [Google Scholar]
  20. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  21. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
    [Google Scholar]
  22. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  23. Gomila M, Pinhassi J, Falsen E, Moore ER, Lalucat J. Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae . Int J Syst Evol Microbiol 2010; 60:809–814 [View Article][PubMed]
    [Google Scholar]
  24. Xie CH, Yokota A. Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively. Int J Syst Evol Microbiol 2005; 55:2419–2425 [View Article][PubMed]
    [Google Scholar]
  25. Gomila M, Bowien B, Falsen E, Moore ER, Lalucat J. Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water. Int J Syst Evol Microbiol 2007; 57:2629–2635 [View Article][PubMed]
    [Google Scholar]
  26. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
    [Google Scholar]
  27. Lang E, Reichenbach H. Designation of type strains for seven species of the order Myxococcales and proposal for neotype strains of Cystobacter ferrugineus, Cystobacter minus and Polyangium fumosum . Int J Syst Evol Microbiol 2013; 63:4354–4360 [View Article][PubMed]
    [Google Scholar]
  28. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  29. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  30. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  31. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article][PubMed]
    [Google Scholar]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  33. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  34. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article][PubMed]
    [Google Scholar]
  35. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. Isme J 2017; 11:2399–2406 [View Article][PubMed]
    [Google Scholar]
  36. Zhi XY, Jiang Z, Yang LL, Huang Y. The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach. Mol Phylogenet Evol 2017; 107:246–255 [View Article][PubMed]
    [Google Scholar]
  37. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
    [Google Scholar]
  38. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. Chemical Methods in Bacterial Systematics 1985267–285
    [Google Scholar]
  39. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  40. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
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