A reinvigorated era of bacterial secondary metabolite discovery

Current Opinion in Chemical Biology

Volumn 24, Issue , 2015, Pages 104-111

  Sidebottom, Ashley M ^a   Carlson, Erin E ^a,b  

^a INDIANA UNIVERSITY   (United States)

^b University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BACTERIAL METABOLISM; CHROMATOGRAPHY; DATA PROCESSING; ELECTROSPRAY MASS SPECTROMETRY; GENE CLUSTER; MASS SPECTROMETRY; METABOLITE; METABOLOMICS; NONHUMAN; REVIEW; BACTERIUM; CHEMISTRY; GENETICS; GENOMICS; METABOLISM; PROCEDURES;

BACTERIA (MICROORGANISMS);

BIOLOGICAL PRODUCT;

BACTERIA; BIOLOGICAL PRODUCTS; GENOMICS; MASS SPECTROMETRY; METABOLOMICS;

EID: 84913555115     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.10.014     Document Type: Review

References (61)

1. Fleming A.G. Responsibilities and opportunities of the private practitioner in preventive medicine. Can Med Assoc J 1929, 20:11-13.
2. Bentley S.D., Chater K.F., Cerdeño-Tárraga A-M., Challis G.L., Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., et al. Complete genome sequence of the model actinomycete Steptomyces coelicolor A3(2). Nature 2002, 417:141-147.
3. Udwary D.W., Zeigler L., Asolkar R.N., Singan V., Lapidus A., Fenical W., Jensen P.R., Moore B.S. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A 2007, 104:10376-10381.
4. Stewart E.J. Growing unculturable bacteria. J Bacteriol 2012, 194:4151-4160.
5. Winter J.M., Behnken S., Hertwek C. Genomics-inspired discovery of natural products. Curr Opin Chem Biol 2011, 15:22-31.
6. Ongley S.E., Bian X., Neilan B., Müller R. Recent advances in the heterologous expression of microbial natural product biosynthetic pathways. Nat Prod Rep 2013, 30:1121-1138.
7. Cortina N.S., Krug D., Plaza A., Revermann O., Müller R. Myxoprincomide: a natural product from Myxococcus xanthus discovered by comprehensive analysis of the secondary metabolome. Angew Chem Int Ed 2012, 51:811-816.
8. Kuppusami S., Clokie M.R.J., Panayi T., Ellis A.M., Monks P.S. Metabolite profiling of Clostridium difficile ribotypes using small molecular weight volatile organic compounds. Metabolomics 2014, 10.1007/s11306-014-0692-4.
9. Craney A., Ozimok C., Pimentel-Elardo S.M., Capretta A., Nodwell J.R. Chemical perturbation of secondary metabolism demonstrates important links to primary metabolism. Chem Biol 2012, 19:1020-1027.
10. Wohlleben W., Mast Y., Muth G., Röttgen M., Stegmann E., Weber T. Synthetic biology of secondary metabolite biosynthesis in actinomycetes: engineering precursor supply as a way to optimize antibiotic production. FEBS Lett 2012, 586:2171-2176.
11. Helfrich E.J.N., Reiter S., Piel J. Recent advances in genome-based polyketide discovery. Curr Opin Biotechnol 2014, 29:107-115.
12. Kersten R.D., Lane A.L., Nett M., Richter T.K.S., Duggan B.M., Dorrestein P.C., Moore B.S. Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica. Chem Bio Chem 2013, 14:955-962.
13. Kersten R.D., Yang L.Y., Xu Y., Cimermancic P., Nam S-J., Fenical W., Fischbach M.A., Moore B.S., Dorrestein P.C. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 2011, 7:794-802.
14. Franke J., Ishida K., Hertweck C. Genomics-driven discovery of burkholderic acid, a noncanonical, cryptic polyketide from human pathogenic Burkholderia species. Angew Chem Int Ed 2012, 51:11611-11615.
15. Gomez-Escribano J.P., Song L., Fox D.J., Yeo V., Bibb M.J., Challis G.L. Structure and biosynthesis of the unusual polyketide alkaloid coelimycin P1, a metabolic product of the cpk gene cluster of Streptomyces coelicolor M145. Chem Sci 2012, 3:2716-2720.
16. Eustáquio A.S., Nam S.-J., Penn K., Lechner A., Wilson M.C., Fenical W., Jensen P.R., Moore B.S. The discovery of salinosporamide K from the marine bacterium "Salinispora pacifica" by genome mining gives insight into pathway evolution. Chem Bio Chem 2011, 12:61-64.
17. McIntosh J.A., Donia M.S., Schmidt E.W. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Nat Prod Rep 2009, 26:537-559.
18. Challis G.L. Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology 2008, 154:1555-1569.
19. Mohimani H., Kersten R.D., Liu W-T., Wang M., Purvine S.O., Wu S., Brewer H.M., Pasa-Tolic L., Bandeira N., Moore B.S., et al. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol 2014, 9:1545-1551.
20. Just-Baringo X., Albericio F., Álvarez M. Thiopeptide antibiotics: retrospective and recent advances. Mar Drugs 2014, 12:317-351.
21. Kenney G.E., Rosenzweig A.C. Genome mining for methanobactins. BMC Biol 2014, 11:1-17.
22. Blin K., Medema M.H., Kazempour D., Fischbach M.A., Breitling R., Takano E., Weber T. antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 2013, 41:W204-W212.
23. Weber T., Rausch C., Lopez P., Hoof I., Gaykova V., Huson D.H., Wohlleben W. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J Biotechnol 2009, 140:13-17.
24. Li M.H.T., Ung P.M.U., Zajkowski J., Garneau-Tsodikova S., Sherman D.H. Automated genome mining for natural products. BMC Bioinformatics 2009, 10:1-10.
25. Röttig M., Medema M.H., Blin K., Weber T., Rausch C., Kohlbacher O. NRPSpredictor2 - a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res 2011, 39:W362-W367.
26. Anand S., Prasad M.V.R., Yadav G., Kumar N., Shehara J., Ansari M.Z., Mohanty D. SBSPKS: structure based sequence analysis of polyketide synthases. Nucleic Acid Res 2010, 3:W487-W496.
27. Dunn W.B., Erban A., Weber R.J.M., Creek D.J., Brown M., Breitling R., Hankemeier T., Goodacre R., Neumann S., Kopka J., et al. Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics 2013, 9:44-66.
28. Hou Y., Braun D.R., Michel C.R., Klassen J.L., Adnani N., Wyche T.P., Bugni T.S. Microbial strain prioritization using metabolomics tools for the discovery of natural products. Anal Chem 2012, 84:4277-4283.
29. Lewis K. Platforms for antibiotic discovery. Nat Rev Drug Discov 2013, 12:371-387.
30. Bose U., Hewavitharana A.K., Vidgen M.E., Ng Y.K., Shaw P.N., Fuerst J.A., Hodson M. Discovering the recondite secondary metabolome spectrum of Salinospora species: a study of inter-species diversity. PLoS ONE 2014, 9:e91488.
31. Lu W., Clasquin M.F., Melamud E., Amador-Noguez D., Caudy A.A., Rabinowitz J.D. Metabolic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal Chem 2010, 82:3212-3221.
32. Siddiquee S., Cheong B.E., Taslima K., Kausar H., Hasan M.M. Separation and identification of volatile compounds from liquid cultures of Trichoderma harzianum by GC-MS using three different capillary columns. J Chromatogr Sci 2012, 50:358-367.
33. Haglund P.S., Löfstrand K., Siek K., Asplund L. Powerful GC-TOF-MS techniques for screening, identification and quantification of halogenated natural products. Mass Spectrom (Tokyo) 2013, 2. 10.5702/massspectrometry.S0018.
34. Elshafie H.S., Bufo S.A., Racioppi R., Cemele I. Biochemical characterization of volatile secondary metabolites produced by Burkholderia gladioli pv. agaricicola. Int J Drug Disc 2013, 5:181-184.
35. David F., Dunkle M., Tienpont B., Mitsui K., Ochiai N., Sasamoto K., Higashi N., Sandra P. Gas chromatography with soft ionization mass spectrometry for the characterization of natural products. Spectroscopy 2013, 14-21.
36. Peterson A.C., Hauschild J.P., Quarmby S.T., Krumwiede D., Lange O., Lemke R.A.S., Grosse-Coosmann F., Horning S., Donohue T.J., Westphall M.S., et al. Development of a GC/quadrupole-orbitrap mass spectrometer, Part I: Design and characterization. Anal Chem 2014, 86:10036-10043.
37. Sidebottom A.M., Johnson A.R., Karty J.A., Trader D.J., Carlson E.E. Integrated metabolomics approach facilitates discovery of an unpredicted natural product suite from Streptomyces coelicolor M145. ACS Chem Biol 2013, 8:2009-2016.
38. Shi X., Wang S., Yang Q., Lu X., Xu G. Comprehensive two-dimensional chromatography for analyzing complex samples: recent new advances. Anal Methods 2014, 6:7112-7123.
39. Sheldon M.T., Mistrik R., Croley T.R. Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J Am Soc Mass Spectrom 2009, 20:370-376.
40. Halouska S., Zhang B., Gaupp R., Lei S., Snell E., Fenton R.J., Barletta R.G., Somerville G.A., Powers R. Revisiting protocols for the NMR analysis of bacterial metabolomes. J Integr Omics 2013, 3:120-137.
41. Robinette S.L., Brüschweiler R., Schroeder F.C., Edison A.S. NMR in metabolomics and natural products research: two sides of the same coin. Accounts Chem Res 2012, 45:288-297.
42. Porzel A., Farag M.A., Mülbradt J., Wessjohann L.A. Metabolite profiling and fingerprinting of Hypericum species: a comparison of MS and NMR metabolomics. Metabolomics 2014, 10:574-588.
43. Forseth R.R., Fox E.M., Chung D., Howlett B.J., Keller N.P., Schroeder F.C. Identification of cryptic products of the gliotoxin gene cluster using NMR-based comparative metabolomics and a model for gliotoxin biosynthesis. J Am Chem Soc 2011, 133:9678-9681.
44. Smith C.A., Want E.J., O'Maille G., Abagyan R., Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification. Anal Chem 2006, 78:779-787.
45. Pluskal T., Castillo S., Villar-Briones A., Oreŝiĉ M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 2010, 11:395.
46. Patti G., Tautenhahn R., Siuzdak G. Meta-analysis of untargeted metabolomic data from multiple profiling experiments. Nat Protoc 2012, 7:508-516.
47. Kanehisa M., Goto S., Sato Y., Kawashima M., Furumichi M., Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014, 42:D199-D205.
48. Horai H., Arita M., Kanaya S., Nihei Y., Ikeda T., Suwa K., Ojima Y., Tanaka K., Tanaka S., Aoshima K., et al. MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 2010, 45:703-714.
49. Smith C.A., O'Maille G., Want E.J., Qin C., Trauger S.A., Brandon T.R., Custodio D.E., Abagyan R., Siuzdak G. METLIN a metabolite mass spectral database. Ther Drug Monit 2005, 27:747-751.
50. Lucas X., Senger C., Erxleben A., Grüning B.A., Döring K., Mosch J., Flemming S., Günther S. Streptome DB: a resource for natural compounds isolated from Streptomyces species. Nucleic Acids Res 2013, 41:D1130-D1136.
51. Keller L., Surette M.G. Communication in bacteria: an ecological and evolutionary perspective. Nat Rev Microbiol 2006, 4:249-258.
52. Rumbaugh K.P., Trivedi U., Watters C., Burton-Chellew M.N., Diggie S.P., West S.A. Kin selection, quorum sensing and virulence in pathogenic bacteria. Proc R Soc B 2012, 279:3584-3588.
53. Verma S.C., Miyashiro T. Quorum sensing in the squid-Vibrio symbiosis. Int J Mol Sci 2013, 14:16386-16401.
54. González A., Bellenberg S., Mamani S., Ruiz L., Echeverría A., Soulère L., Doutheau A., Demergasso C., Sand W., Queneau Y., et al. AHL signaling molecules with a large acyl chain enhance biofilm formation ion sulfur and metal sulfoxides by the bioleaching bacterium Acidithiobacillus ferrooxidans. Appl Microbiol Biotechnol 2013, 97:3729-3737.
55. Watrous J., Roach P., Alexandrov T., Heath B.S., Yang J.Y., Kersten R.D., van der Voort M., Pogliano K., Gross H., Raaijmakers J.M., et al. Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A 2012, 109:10150-10151.
56. Yang J.Y., Phelan V.V., Simkovsky R., Watrous J.D., Trial R.M., Fleming T.C., Wenter R., Moore B.S., Golden S.S., Pogliano K., et al. Primer on agar-based microbial imaging mass spectrometry. J Bacteriol 2012, 194:6023-6028.
57. Vartoukian S.R., Palmer R.M., Wade W.G. Strategies for culture of 'unculturable' bacteria. FEMS Microbiol Lett 2010, 309:1-7.
58. Andersson D.I., Hughes D. Microbiological effects of sublethal levels of antibiotics. Nat Rev Microbiol 2014, 12:465-478.
59. Nalca Y., Jänsch L., Bredenbruch F., Geffers R., Buer J., Häussler S. Quorum-sensing antagonistic activities of azithromycin in Pseudomonas aeruginosa PAO1: a global approach. Antimicrob Agents Chem 2006, 50:1680-1688.
60. Ji G., Beavis R., Novick R.P. Bacterial interference caused by autoinducing peptide variants. Science 1997, 276:2027-2030.
61. Li D., Renzoni A., Estoppey T., Bisognano C., Francois P., Kelley W.L., Lew D.P., Schrenzel J., Vaudaux P. Induction of fibronectin adhesins in quinolone-resistant Staphylococcus aureus by subinhibitory levels of ciprofloxacin or by sigma B transcription factor activity is mediated by two separate pathways. Antimicrob Agents Chem 2005, 49:916-924.