Antonie van Leeuwenhoek

, Volume 108, Issue 5, pp 1075–1090 | Cite as

Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation

  • C. A. Contador
  • V. Rodríguez
  • B. A. Andrews
  • J. A. AsenjoEmail author
Original Paper


The first manually curated genome-scale metabolic model for Salinispora tropica strain CNB-440 was constructed. The reconstruction enables characterization of the metabolic capabilities for understanding and modeling the cellular physiology of this actinobacterium. The iCC908 model was based on physiological and biochemical information of primary and specialised metabolism pathways. The reconstructed stoichiometric matrix consists of 1169 biochemical conversions, 204 transport reactions and 1317 metabolites. A total of 908 structural open reading frames (ORFs) were included in the reconstructed network. The number of gene functions included in the reconstructed network corresponds to 20 % of all characterized ORFs in the S. tropica genome. The genome-scale metabolic model was used to study strain-specific capabilities in defined minimal media. iCC908 was used to analyze growth capabilities in 41 different minimal growth-supporting environments. These nutrient sources were evaluated experimentally to assess the accuracy of in silico growth simulations. The model predicted no auxotrophies for essential amino acids, which was corroborated experimentally. The strain is able to use 21 different carbon sources, 8 nitrogen sources and 4 sulfur sources from the nutrient sources tested. Experimental observation suggests that the cells may be able to store sulfur. False predictions provided opportunities to gain new insights into the physiology of this species, and to gap fill the missing knowledge. The incorporation of modifications led to increased accuracy in predicting the outcome of growth/no growth experiments from 76 to 93 %. iCC908 can thus be used to define the metabolic capabilities of S. tropica and guide and enhance the production of specialised metabolites.


Salinispora tropica Metabolic capabilities Strain adaptation Genome-scale metabolic reconstruction 



We thank Dr. M. Goodfellow for helpful advice regarding biomass composition of S. tropica CNB-440. This work was supported by the Conicyt Basal Centre Grant for the CeBiB (FB0001) to C.A.C. and V.R. and the PharmaSea European Union project to C.A.C.

Conflict of interest

The authors have declared no conflict of interest.

Supplementary material

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Supplementary material 1 (XLSX 407 kb)
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Supplementary material 2 (PDF 156 kb)
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Supplementary material 3 (XLSX 71 kb)
10482_2015_561_MOESM4_ESM.pdf (75 kb)
Supplementary material 4 (PDF 74 kb)


  1. Ahmed L, Jensen PR, Freel KC, Brown R, Jones AL, Kim BY, Goodfellow M (2013) Salinispora pacifica sp. nov., an actinomycete from marine sediments. Antonie Van Leeuwenhoek 103:1069–1078. doi: 10.1007/s10482-013-9886-4 CrossRefPubMedGoogle Scholar
  2. Alam MT, Merlo ME, Consortium TS, Hodgson DA, Wellington EMH, Takano E, Breitling R (2010) Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genom 11:202. doi: 10.1186/1471-2164-11-202 CrossRefGoogle Scholar
  3. Alam MT, Medema MH, Takano E, Breitling R (2011) Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism. FEBS Lett 585:2389–2394. doi: 10.1016/j.febslet.2011.06.014 CrossRefPubMedGoogle Scholar
  4. Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2:727–738. doi: 10.1038/nprot.2007.99 CrossRefPubMedGoogle Scholar
  5. Beer LL, Moore BS (2007) Biosynthetic convergence of salinosporamides A and B in the marine actinomycete Salinispora tropica. Org Lett 9:845–848. doi: 10.1021/ol063102o CrossRefPubMedGoogle Scholar
  6. Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 15:820–829. doi: 10.1101/gr.3364705 PubMedCentralCrossRefPubMedGoogle Scholar
  7. Campodonico MA, Andrews BA, Asenjo JA, Palsson BØ, Feist AM (2014) Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng 25:140–158. doi: 10.1016/j.ymben.2014.07.009 CrossRefPubMedGoogle Scholar
  8. Chaudhary AK, Dhakal D, Sohng JK (2013) An insight into the “-Omics” based engineering of streptomycetes for secondary metabolite overproduction. Biomed Res Int. doi: 10.1155/2013/968518 PubMedCentralPubMedGoogle Scholar
  9. Contador CA, Shene C, Yoshikuni Y, Olivera A, Buschmann A, Andrews BA, Asenjo JA (2015) Analyzing redox balance in a synthetic yeast platform to improve utilization of brown macroalgae as feedstock. Metab Eng Commun 2:76–84. doi: 10.1016/j.meteno.2015.06.004 CrossRefGoogle Scholar
  10. Covert MW, Knight EM, Reed JL, Herrgård MJ, Palsson BØ (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429:92–96. doi: 10.1038/nature02456 CrossRefPubMedGoogle Scholar
  11. Cragg GM, Grothaus PG, Newman DJ (2009) Impact of natural products on developing new anti-cancer agents. Chem Rev 109:3012–3043. doi: 10.1021/cr900019j CrossRefPubMedGoogle Scholar
  12. Dahl C, Prange A (2006) Microbiology monographs(1). In: Shively JM (ed) Inclusions in prokaryotes. Springer, Heidelberg. doi: 10.1007/7171_002 Google Scholar
  13. Dineshkumar K, Aparna V, Madhuri KZ, Hopper W (2014) Biological activity of sporolides A and B from Salinispora tropica: in silico target prediction using ligand-based pharmacophore mapping and in vitro activity validation on HIV-1 reverse transcriptase. Chem Biol Drug Design 83:350–361. doi: 10.1111/cbdd.12252 CrossRefGoogle Scholar
  14. Edwards J, Ibarra R, Palsson BØ (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125–130. doi: 10.1038/84379 CrossRefPubMedGoogle Scholar
  15. Enquist-Newman M, Faust AME, Bravo DD et al (2014) Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature 505:239–243. doi: 10.1038/nature12771 CrossRefPubMedGoogle Scholar
  16. Eustáquio AS, McGlinchey RP, Liu Y et al (2009) Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-l-methionine. Proc Natl Acad Sci USA 106:12295–12300. doi: 10.1073/pnas.0901237106 PubMedCentralCrossRefPubMedGoogle Scholar
  17. Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ (2009) Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7:129–143. doi: 10.1038/nrmicro1949 PubMedCentralCrossRefPubMedGoogle Scholar
  18. Feist AM, Zielinski DC, Orth JD, Schellenberger J, Markus J, Palsson BØ (2010) Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 12:173–186. doi: 10.1016/j.ymben.2009.10.003 PubMedCentralCrossRefPubMedGoogle Scholar
  19. Feling RH, Buchanan GO, Mincer TJ, Kauffman CA, Jensen PR, Fenical W (2003) Salinosporamide A: A highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora. Angew Chem Int Ed 42:355–357. doi: 10.1002/anie.200390115 CrossRefGoogle Scholar
  20. Fenical W, Jensen PR (2006) Developing a new resource for drug discovery: marine actinomycete bacteria. Nat Chem Biol 2:666–673. doi: 10.1038/nchembio841 CrossRefPubMedGoogle Scholar
  21. Goodfellow M, Kampfer P, Busse H-J, Trujillo ME, Suzuki K, Ludwig W, Whitman W (eds.) (2012) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn. Springer, BerlinGoogle Scholar
  22. Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28:977–982. doi: 10.1038/nbt.1672 CrossRefPubMedGoogle Scholar
  23. Hirsch AM, Valdés M (2010) Micromonospora: an important microbe for biomedicine and potentially for biocontrol and biofuels. Soil Biol Biochem 42:536–542. doi: 10.1016/j.soilbio.2009.11.023 CrossRefGoogle Scholar
  24. Jensen PR, Dwight R, Fenical W (1991) Distribution of actinomycetes in near-shore tropical marine sediments. Appl Environ Microbiol 57:1102–1108PubMedCentralPubMedGoogle Scholar
  25. Kawamoto I (1992) Microbiological characteristics of genus Micromonospora. Actinomycetol 6:91–104. doi: 10.3209/saj.6_91 CrossRefGoogle Scholar
  26. Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY (2011) Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Opin Biotechnol 23:1–7. doi: 10.1016/j.copbio.2011.10.007 CrossRefGoogle Scholar
  27. Kjeldsen KR, Nielsen J (2009) In silico genome-scale reconstruction and validation of the corynebacterium glutamicum metabolic network. Biotechnol Bioeng 102:583–597. doi: 10.1002/bit.22067 CrossRefPubMedGoogle Scholar
  28. Kostromins A, Stalidzans E (2012) Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism. BioSystems 109:233–239. doi: 10.1016/j.biosystems.2012.03.002 CrossRefPubMedGoogle Scholar
  29. Kroppenstedt RM, Mayilraj S, Wink JM, Kallow W, Schumann P, Secondini C, Stackebrandt E (2005) Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov. Syst Appl Microbiol 28:328–339. doi: 10.1016/j.syapm.2004.12.011 CrossRefPubMedGoogle Scholar
  30. Lam KS (2007) New aspects of natural products in drug discovery. Trends Microbiol 15:279–289. doi: 10.1016/j.tim.2007.04.001 CrossRefPubMedGoogle Scholar
  31. Lechner A, Eustáquio AS, Gulder TAM, Hafner M, Moore BS (2011) Selective overproduction of the proteasome inhibitor salinosporamide A via precursor pathway regulation. Chem Biol 18:1527–1536. doi: 10.1016/j.chembiol.2011.10.014 PubMedCentralCrossRefPubMedGoogle Scholar
  32. Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, GermanyGoogle Scholar
  33. Licona-Cassani C, Marcellin E, Quek LE, Jacob S, Nielsen LK (2012) Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production. Antonie Van Leeuwenhoek 102:493–502. doi: 10.1007/s10482-012-9783-2 CrossRefPubMedGoogle Scholar
  34. Macleod RA (1965) The question of the existence of specific marine bacteria. Bacteriol Rev 29:9–24PubMedCentralPubMedGoogle Scholar
  35. Maki JS (2013) Bacterial intracellular sulfur globules: structure and function. J Mol Microbiol Biotechnol 23:270–280. doi: 10.1159/000351335 CrossRefPubMedGoogle Scholar
  36. Maldonado LA, Fenical W, Jensen PR, Kauffman CA, Mincer TJ, Ward AC, Bull AT, Goodfellow M (2005) Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae. Int J Syst Evol Microbiol 55:1759–1766. doi: 10.1099/ijs.0.63625-0 CrossRefPubMedGoogle Scholar
  37. McGlinchey RP, Nett M, Eustáquio AS, Asolkar RN, Fenical W, Moore BS (2008a) Engineered biosynthesis of antiprotealide and other unnatural salinosporamide proteasome inhibitors. J Am Chem Soc 9:1–14. doi: 10.1021/ja8029398 Google Scholar
  38. McGlinchey RP, Nett M, Moore BS (2008b) Unraveling the biosynthesis of the sporolide cyclohexenone building block. J Am Chem Soc 130:2406–2407. doi: 10.1021/ja710488m CrossRefPubMedGoogle Scholar
  39. Medema MH, Alam MT, Heijne WHM, van den Berg MA, Müller U, Trefzer A, Bovenberg RAL, Breitling R, Takano E (2011) Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus. Microb Biotechnol 4:300–305. doi: 10.1111/j.1751-7915.2010.00226.x PubMedCentralCrossRefPubMedGoogle Scholar
  40. Mincer TJ, Jensen PR, Kauffman CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Society 68:5005–5011. doi: 10.1128/AEM.68.10.5005 Google Scholar
  41. Monk J, Nogales J, Palsson BØ (2014) Optimizing genome-scale network reconstructions. Nat Biotechnol 32:447–452. doi: 10.1038/nbt.2870 CrossRefPubMedGoogle Scholar
  42. Nett M, Moore BS (2009) Exploration and engineering of biosynthetic pathways in the marine actinomycete Salinispora tropica. Pure Appl Chem 81:1075–1084. doi: 10.1351/PAC-CON-08-08-08 CrossRefGoogle Scholar
  43. Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 13:603–609. doi: 10.1039/b817069j Google Scholar
  44. Oberhardt MA, Palsson BØ, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5:320. doi: 10.1038/msb.2009.77 PubMedCentralCrossRefPubMedGoogle Scholar
  45. Orth JD, Thiele I, Palsson BØ (2010) What is flux balance analysis? Nat Biotechnol 28:245–248. doi: 10.1038/nbt.1614 PubMedCentralCrossRefPubMedGoogle Scholar
  46. Penn K, Jensen PR (2012) Comparative genomics reveals evidence of marine adaptation in Salinispora species. BMC Genom 13:86. doi: 10.1186/1471-2164-13-86 CrossRefGoogle Scholar
  47. Pridham TG, Gottlieb D (1948) The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol 56:107–114PubMedCentralPubMedGoogle Scholar
  48. Schuch R, Garibian A, Saxild HH, Piggot PJ, Nygaard P (1999) Nucleosides as a carbon source in Bacillus subtilis: characterization of the drm-pupG operon. Microbiology 145:2957–2966CrossRefPubMedGoogle Scholar
  49. Stevenson IL (1967) Utilization of aromatic hydrocarbons by Arthrobacter spp. Can J Microbiol 13:205–211. doi: 10.1139/m67-027 CrossRefPubMedGoogle Scholar
  50. Tepper N, Shlomi T (2010) Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 26:536–543. doi: 10.1093/bioinformatics/btp704 CrossRefPubMedGoogle Scholar
  51. Thiele I, Palsson BØ (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5:93–121. doi: 10.1038/nprot.2009.203 PubMedCentralCrossRefPubMedGoogle Scholar
  52. Tsueng G, Lam KS (2008a) A low-sodium-salt formulation for the fermentation of salinosporamides by Salinispora tropica strain NPS21184. Appl Microbiol Biotechnol 78:821–826. doi: 10.1007/s00253-008-1357-x CrossRefPubMedGoogle Scholar
  53. Tsueng G, Lam KS (2008b) Growth of Salinispora tropica strains CNB440, CNB476, and NPS21184 in nonsaline, low-sodium media. Appl Microbiol Biotechnol 80:873–880. doi: 10.1007/s00253-008-1614-z CrossRefPubMedGoogle Scholar
  54. Tsueng G, Lam KS (2009) Effect of cobalt and vitamin B12 on the production of salinosporamides by Salinispora tropica. J Antibiot 62:213–216. doi: 10.1038/ja.2009.7 CrossRefPubMedGoogle Scholar
  55. Tsueng G, Lam KS (2010) A preliminary investigation on the growth requirement for monovalent cations, divalent cations and medium ionic strength of marine actinomycete Salinispora. Appl Microbiol Biotechnol 86:1525–1534. doi: 10.1007/s00253-009-2424-7 CrossRefPubMedGoogle Scholar
  56. Tsueng G, McArthur KA, Potts BCM, Lam KS (2007) Unique butyric acid incorporation patterns for salinosporamides A and B reveal distinct biosynthetic origins. Appl Microbiol Biotechnol 75:999–1005. doi: 10.1007/s00253-007-0899-7 CrossRefPubMedGoogle Scholar
  57. Tsueng G, Teisan S, Lam KS (2008) Defined salt formulations for the growth of Salinispora tropica strain NPS21184 and the production of salinosporamide A (NPI-0052) and related analogs. Appl Microbiol Biotechnol 78:827–832. doi: 10.1007/s00253-008-1358-9 CrossRefPubMedGoogle Scholar
  58. Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci USA 104:10376–10381. doi: 10.1073/pnas.0700962104 PubMedCentralCrossRefPubMedGoogle Scholar
  59. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813. doi: 10.1099/00221287-129-6-1743 PubMedGoogle Scholar
  60. Wong TY, Preston LA, Schiller NL (2000) ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications. Annu Rev Microbiol 54:289–340. doi: 10.1146/annurev.micro.54.1.289 CrossRefPubMedGoogle Scholar
  61. Zomorrodi AR, Maranas CD (2010) Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol 4:178. doi: 10.1186/1752-0509-4-178 PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • C. A. Contador
    • 1
  • V. Rodríguez
    • 1
  • B. A. Andrews
    • 1
  • J. A. Asenjo
    • 1
    Email author
  1. 1.Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering, CeBiBUniversity of ChileSantiagoChile

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