Gene sequence based clustering assists in dereplication of Pseudoalteromonas luteoviolacea strains with identical inhibitory activity and antibiotic production

Marine Drugs

Volumn 10, Issue 8, 2012, Pages 1729-1740

  Vynne, Nikolaj G ^a   Mansson, Maria ^a   Gram, Lone ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Biodiscovery; Indolmycin; Pentabromopseudilin; Pseudoalteromonas luteoviolacea; Violacein

Indexed keywords

ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT; BACTERIAL RNA; INDOLMYCIN; NATURAL PRODUCT; RNA 16S; UNCLASSIFIED DRUG; VIOLACEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CLASSIFICATION; CONTROLLED STUDY; DRUG ACTIVITY; DRUG DETERMINATION; DRUG RESEARCH; DRUG SYNTHESIS; GENE CLUSTER; GENE SEQUENCE; GENOTYPE; GYRB GENE; LISTONELLA ANGUILLARUM; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PSEUDOALTEROMONAS; PSEUDOALTEROMONAS LUTEOVIOLACEA; RECA GENE; REPRODUCIBILITY; RNA SEQUENCE; STAPHYLOCOCCUS AUREUS; STRAIN DIFFERENCE;

LISTONELLA ANGUILLARUM; PSEUDOALTEROMONAS LUTEOVIOLACEA; STAPHYLOCOCCUS AUREUS;

EID: 84865987010     PISSN: None     EISSN: 16603397     Source Type: Journal    
DOI: 10.3390/md10081729     Document Type: Article

References (53)

1. Newman, D.J. Natural products as leads to potential drugs: An old process or the new hope for drug discovery? J. Med. Chem. 2008, 51, 2589-2599. (Pubitemid 351620778)
2. Clardy, J.; Fischbach, M.A.; Walsh, C.T. New antibiotics from bacterial natural products. Nat. Biotechnol. 2006, 24, 1541-1550. (Pubitemid 44967478)
3. Molinari, G. Natural Products in Drug Discovery: Present Status and Perspectives. In Pharmaceutical Biotechnology; Guzmán, C.A., Feuerstein, G.Z., Eds.; Springer: New York, NY, USA, 2009; pp. 13-27.
4. Baker, D.D.; Chu, M.; Oza, U. The value of natural products to future pharmaceutical discovery. Nat. Prod. Rep. 2007, 24, 1225-1244. (Pubitemid 350151353)
5. Fenical, W. Chemical studies of marine bacteria - developing a new resource. Chem. Rev. 1993, 93, 1673-1683.
6. Long, R.A.; Azam, F. Antagonistic interactions among marine pelagic bacteria. Appl. Environ. Microb. 2001, 67, 4975-4983. (Pubitemid 33701259)
7. Gulder, T.A.M.; Moore, B.S. Chasing the treasures of the sea - bacterial marine natural products. Curr. Opin. Microbiol. 2009, 12, 252-260.
8. Taori, K.; Paul, V.J.; Luesch, H. Structure and activity of largazole, a potent antiproliferative agent from the Floridian marine cyanobacterium Symploca sp. J. Am. Chem. Soc. 2008, 130, 1806-1807. (Pubitemid 351238618)
9. Nicolaou, K.C.; Harrison, S.T. Total Synthesis of Abyssomicin C and atrop-Abyssomicin C. Angew. Chem. Int. Ed. 2006, 45, 3256-3260. (Pubitemid 44098984)
10. Brinkhoff, T.; Bach, G.; Heidorn, T.; Liang, L.; Schlingloff, A.; Simon, M. Antibiotic production by a Roseobacter clade-affiliated species from the German Wadden Sea and its antagonistic effects on indigenous isolates. Appl. Environ. Microb. 2004, 70, 2560-2565. (Pubitemid 38500568)
11. Hjelm, M.; Bergh, Ø.; Riaza, A.; Nielsen, J.; Melchiorsen, J.; Jensen, S.; Duncan, H.; Ahrens, P.; Birkbeck, H.; Gram, L. Selection and identification of autochthonous potential probiotic bacteria from turbot larvae (Scophthalmus maximus) rearing units. Syst. Appl. Microbiol. 2004, 27, 360-371. (Pubitemid 38724496)
12. Bowman, J.P. Bioactive compound synthetic capacity and ecological significance of marine bacterial genus Pseudoalteromonas. Mar. Drugs 2007, 5, 220-241.
13. Vynne, N.G.; Månsson, M.; Nielsen, K.F.; Gram, L. Bioactivity, chemical profiling and 16S rRNA based phylogeny of Pseudoalteromonas strains collected on a global research cruise. Mar. Biotechnol. 2011, 13, 1062-1073.
14. Wietz, M.; Gram, L.; Jørgensen, B.; Schramm, A. Latitudinal patterns in the abundance of major marine bacterioplankton groups. Aquat. Microb. Ecol. 2010, 61, 179-189.
15. Mikhailov, V.V.; Romanenko, L.A.; Ivanova, E.P. The genus Alteromonas and related Proteobacteria. In The Prokaryotes, 3rd ed.; Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H., Stackebrandt, E., Eds.; Springer: New York, NY, USA, 2002; pp. 597-645.
16. Corley, D.G.; Durley, R.C. Strategies for Database Dereplication of Natural Products. J. Nat. Prod. 1994, 57, 1484-1490.
17. Sashidhara, K.V.; Rosaiah, J.N. Various dereplication strategies using LC-MS for rapid natural product lead identification and drug discovery. Nat. Prod. Commun. 2007, 2, 193-202.
18. Hook, D.J.; Pack, E.J.; Yacobucci, J.J.; Guss, J. Approaches to automating the dereplication of bioactive natural products - the key step in high throughput screening of bioactive materials from natural sources. J. Biomol. Screen. 1997, 2, 145-152. (Pubitemid 127690003)
19. Nielsen, K.F.; Månsson, M.; Rank, C.; Frisvad, J.C.; Larsen, T.O. Dereplication of microbial natural products by LC-DAD-TOFMS. J. Nat. Prod. 2011, 74, 2338-2348.
20. Larsen, T.O.; Smedsgaard, J.; Nielsen, K.F.; Hansen, M.E.; Frisvad, J.C. Phenotypic taxonomy and metabolite profiling in microbial drug discovery. Nat. Prod. Rep. 2005, 22, 672-695. (Pubitemid 43000329)
21. Smedsgaard, J.; Nielsen, J. Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics. J. Exp. Bot. 2005, 56, 273-286. (Pubitemid 40191444)
22. Knight, V.; Sanglier, J.J.; DiTullio, D.; Braccili, S.; Bonner, P.; Waters, J.; Hughes, D.; Zhang, L. Diversifying microbial natural products for drug discovery. Appl. Microbiol. Biotechnol. 2003, 62, 446-458. (Pubitemid 37372436)
23. Porsby, C.H.; Nielsen, K.F.; Gram, L. Phaeobacter and Ruegeria species of the Roseobacter clade colonize separate niches in a Danish turbot (Scophthalmus maximus)-rearing farm and antagonize Vibrio anguillarum under different growth conditions. Appl. Environ. Microb. 2008, 74, 7356-7364. (Pubitemid 352773609)
24. Jensen, P.R.; Williams, P.G.; Oh, D.C.; Zeigler, L.; Fenical, W. Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl. Environ. Microb. 2007, 73, 1146-1152.
25. Goodfellow, M.; Fiedler, H.P. A guide to successful bioprospecting: Informed by actinobacterial systematics. Antonie Van Leeuwenhoek 2010, 98, 119-142.
26. Månsson, M.; Phipps, R.K.; Gram, L.; Munro, M.H.; Larsen, T.O.; Nielsen, K.F. Explorative Solid-Phase Extraction (E-SPE) for Accelerated Microbial Natural Product Discovery. J. Nat. Prod. 2010, 73, 1126-1132.
27. Lichstein, H.C.; Vandesand, V.F. Violacein, an antibiotic pigment produced by Chromobacterium violaceum. J. Infect. Dis. 1945, 76, 47-51.
28. Marsh, W.S.; Garretson, A.L.; Wesel, E.M. PA 155 A, B, and X. Antibiotics produced by a strain of Streptomyces albus. Antibiot. Chemother. 1960, 10, 316-320.
29. Burkholder, P.R.; Pfister, R.M.; Leitz, F.H. Production of a pyrrole antibiotic by a marine bacterium. Appl. Environ. Microb. 1966, 14, 649-653.
30. Gauthier, M.J.; Flatau, G.N. Antibacterial activity of marine violet-pigmented Alteromonas with special reference to the production of brominated compounds. Can. J. Microbiol. 1976, 22, 1612-1619.
31. Matz, C.; Webb, J.S.; Schupp, P.J.; Phang, S.Y.; Penesyan, A.; Egan, S.; Steinberg, P.; Kjelleberg, S. Marine biofilm bacteria evade eukaryotic predation by targeted chemical defense. PLoS ONE 2008, 3, e2744.
32. Kanamaru, T.; Nakano, Y.; Toyoda, Y.; Miyagawa, K.I.; Tada, M.; Kaisho, T.; Nakao, M. In vitro and in vivo antibacterial activities of TAK-083, an agent for treatment of Helicobacter pylori infection. Antimicrob. Agents Chemother. 2001, 45, 2455-2459. (Pubitemid 32801895)
33. von Wittenau, M.S.; Els, H. The structure of indolmycin. J. Am. Chem. Soc. 1961, 83, 4678-4680.
34. Hurdle, J.G.; O'Neill, A.J.; Chopra, I. Anti-staphylococcal activity of indolmycin, a potential topical agent for control of staphylococcal infections. J. Antimicrob. Chemother. 2004, 54, 549-552. (Pubitemid 39177486)
35. Gomez, D.; Espinosa, E.; Bertazzo, M.; Lucas-Elio, P.; Solano, F.; Sanchez-Amat, A. The macromolecule with antimicrobial activity synthesized by Pseudoalteromonas luteoviolacea strains is an L-amino acid oxidase. Appl. Microbiol. Biotechnol. 2008, 79, 925-930.
36. Rossello-Mora, R.; Amann, R. The species concept for prokaryotes. FEMS Microbiol. Rev. 2001, 25, 39-67. (Pubitemid 32057196)
37. Coenye, T.; Gevers, D.; Peer, Y.V.; Vandamme, P.; Swings, J. Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 2005, 29, 147-167. (Pubitemid 40432465)
38. Hilario, E.; Buckley, T.R.; Young, J.M. Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atpD, carA, recA and 16S rDNA. Antonie Van Leeuwenhoek 2004, 86, 51-64. (Pubitemid 39366122)
39. Yamamoto, S.; Kasai, H.; Arnold, D.L.; Jackson, R.W.; Vivian, A.; Harayama, S. Phylogeny of the genus Pseudomonas: Intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000, 146, 2385-2394.
40. Frisvad, J.C.; Andersen, B.; Thrane, U. The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi. Mycol. Res. 2008, 112, 231-240. (Pubitemid 351313940)
41. Egan, S.; Wiener, P.; Kallifidas, D.; Wellington, E.M.H. Phylogeny of Streptomyces species and evidence for horizontal transfer of entire and partial antibiotic gene clusters. Antonie Van Leeuwenhoek 2001, 79, 127-133. (Pubitemid 32747122)
42. Ginolhac, A.; Jarrin, C.; Robe, P.; Perrière, G.; Vogel, T.M.; Simonet, P.; Nalin, R. Type I polyketide synthases may have evolved through horizontal gene transfer. J. Mol. Evol. 2005, 60, 716-725.
43. Fischbach, M.A.; Walsh, C.T.; Clardy, J. The evolution of gene collectives: How natural selection drives chemical innovation. Proc. Natl. Acad. Sci. USA 2008, 105, 4601-4608. (Pubitemid 351753784)
44. Strohl, W.R. Antimicrobials. In Microbial Diversity and Bioprospecting; Bull, A.T., Ed.; ASM Press: Washington, DC, USA, 2004; pp. 36-355.
45. Jensen, P.R. Linking species concepts to natural product discovery in the post-genomic era. J. Ind. Microbiol. Biotechnol. 2010, 37, 219-224.
46. Östling, J.; Goodman, A.E.; Kjelleberg, S. Behaviour of IncP-1 plasmids and a miniMu transposon in a marine Vibrio sp.: Isolation of starvation inducible lac operon fusions. FEMS Microbiol. Ecol. 1991, 86, 83-94.
47. Skov, M.N.; Pedersen, K.; Larsen, J.L. Comparison of pulsed-field gel electrophoresis, ribotyping, and plasmid profiling for typing of Vibrio anguillarum serovar O1. Appl. Environ. Microb. 1995, 61, 1540-1545.
48. Yamamoto, S.; Harayama, S. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl. Environ. Microb. 1995, 61, 1104-1109.
49. Pascual, J.; Macián, M.C.; Arahal, D.R.; Garay, E.; Pujalte, M.J. Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes. Int. J. Syst. Bacteriol. 2010, 60, 154-165.
50. 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.
51. Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16, 111-120. (Pubitemid 11166431)
52. Tavaré, S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 1986, 17, 57-86.
53. Clinical and Laboratory Standards Institute. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically, Approved Standard, 7th ed.; CLSI document M7-A7; Clinical and Laboratory Standards Institute: Pennsylvania, PA, USA, 2006.