Habitat-specific type I polyketide synthases in soils and street sediments

  • Patrick Hill
  • Jörn Piel
  • Stéphane Aris-Brosou
  • Václav Krištůfek
  • Christopher N. Boddy
  • Lubbert Dijkhuizen
Environmental Microbiology

Abstract

Actinomycetes produce many pharmaceutically useful compounds through type I polyketide biosynthetic pathways. Soil has traditionally been an important source for these actinomycete-derived pharmaceuticals. As the rate of antibiotic discovery has decreased and the incidence of antibiotic resistance has increased, researchers have looked for alternatives to soil for bioprospecting. Street sediment, where actinomycetes make up a larger fraction of the bacterial population than in soil, is one such alternative environment. To determine if these differences in actinomycetal community structure are reflected in type I polyketide synthases (PKSI) distribution, environmental DNA from soils and street sediments was characterized by sequencing amplicons of PKSI-specific PCR primers. Amplicons covered two domains: the last 80 amino acids of the ketosynthase (KS) domain and the first 240 amino acids of the acyltransferase (AT) domain. One hundred and ninety clones from ten contrasting soils from six regions and nine street sediments from six cities were sequenced. Twenty-five clones from two earthworm-affected samples were also sequenced. UniFrac lineage-specific analysis identified two clades that clustered with actinomycetal GenBank matches that were street sediment-specific, one similar to the PKSI segment of the mycobactin siderophore involved in mycobacterial virulence. A clade of soil-specific sequences clustered with GenBank matches from the ambruticin and jerangolid pathways of Sorangium cellulosum. All three of these clades were found in sites >700 km apart. Street sediments are enriched in actinomycetal PKSIs. Non-actinomycetal PKSI pathways may be more chemically diverse than actinomycetal PKSIs. Common soil and street sediment PKIs are globally distributed.

Keywords

Natural product discovery Polyketides Urban microbiology Bioprospecting Mycobactin 

Supplementary material

10295_2013_1362_MOESM1_ESM.pdf (412 kb)
Supplementary material 1 (PDF 411 kb) Fig. S1:A8-1 Cophylogeny
10295_2013_1362_MOESM2_ESM.pdf (403 kb)
Supplementary material 2 (PDF 403 kb) Fig. S2:A8-3 Cophylogeny
10295_2013_1362_MOESM3_ESM.pdf (397 kb)
Supplementary material 3 (PDF 397 kb) Fig. S3: A6 Cophylogeny
10295_2013_1362_MOESM4_ESM.pdf (402 kb)
Supplementary material 4 (PDF 402 kb) Fig. S4: A5 Cophylogeny
10295_2013_1362_MOESM5_ESM.pdf (398 kb)
Supplementary material 5 (PDF 397 kb) Fig. S5: Mbt CophylogenyFor all Cophylogenies, sequences in blue are from soil, in red from street sediments and in orange from earthworm-affected environments.
10295_2013_1362_MOESM6_ESM.xls (104 kb)
Supplementary material 6 (XLS 103 kb) Table S1: an Excel file with a description of environmental sequences
10295_2013_1362_MOESM7_ESM.xls (226 kb)
Supplementary material 7 (XLS 226 kb) Table S2: an Excel file with BLASTP matches of environmental sequences
10295_2013_1362_MOESM8_ESM.xls (48 kb)
Supplementary material 8 (XLS 48 kb) Table S3: an Excel file with a description of 99 comparable sequences from GenBank
10295_2013_1362_MOESM9_ESM.xlsx (11 kb)
Supplementary material 9 (XLSX 11 kb) Table S4: an Excel file comparing sequences from cosmopolitan nodes and known PKSI pathways

References

  1. 1.
    Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinforma 21:2104–2105CrossRefGoogle Scholar
  2. 2.
    Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55:539–552PubMedCrossRefGoogle Scholar
  3. 3.
    Ayuso–Sacido A, Genilloud O (2005) New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb Ecol 49:24–49Google Scholar
  4. 4.
    Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552PubMedCrossRefGoogle Scholar
  5. 5.
    Chavadi SS, Stirrett KL, Edupuganti UR, Vergnolle O, Sadhanandan G, Marchiano E, Martin C, Qiu WG, Soll CE, Quadri LE (2011) Mutational and phylogenetic analyses of the mycobacterial mbt gene cluster. J Bacteriol 193:5905–5913PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Connon S A, Lester ED, Shafaat HS, Obenhuber DC, Ponce A (2007) Bacterial diversity in hyperarid Atacama Desert soils. J Geophys Res 112: G04S17, doi: 10.1029/2006JG000311
  7. 7.
    Dong XY, Wang LH, Sun MJ, Zong Y, Jiao YL, Jiao BH (2008) Screening, identifying and function analysis of polyketide synthase I domains from soil and seawater of Yangshan Harbor. Microbiology 35:1359–1366Google Scholar
  8. 8.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Faizal I, Lestari R, Kurnia F, Latif A, Hadianto D, Kusumawati N, Rachmawati I, Marwoto B, Purbowasito W (2008) Polymorphism analysis of polyketide synthase gene from Actinomycetes genome DNA of Taman Nasional Gunung Halimun soil by using metagenome method. J Biotechnology Res Tropical Reg 1: biotechindonesia.org/journal/jbr/jbr-2008-00-01/jrb-1-08-2.pdfGoogle Scholar
  10. 10.
    Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DA, Caporaso JG (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. PNAS 109:21390–21395PubMedCrossRefGoogle Scholar
  11. 11.
    Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and non-ribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 106:3468–3496PubMedCrossRefGoogle Scholar
  12. 12.
    Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perrière G, Simonet P, Nalin R (2004) Phylogenetic analysis of polyketide I domains from soil metagenomic libraries allows selection of promising clones. Appl Environ Microbiol 70:5522–5527PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321PubMedCrossRefGoogle Scholar
  14. 14.
    Hall N (2013) After the gold rush. Genome Biol 14:115–117PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Haydock SF, Aparicio JF, Molnár I, Schwecke T, Khaw LE, König A, Marsden AFA, Galloway IS, Staunton J, Leadlay PF (1995) Divergent sequence motifs correlated with the substrate specificity of (methlyl) malonyl-CoA: acyl carrier protein during transcyclase domains in modular polyketide synthases. FEBS Lett 374:246–248PubMedCrossRefGoogle Scholar
  16. 16.
    Hill P, Krištůfek V, Dijkhuizen L, Boddy C, Kroetsch D, van Elsas D (2011) Land use intensity controls actinobacterial community structure. Microb Ecol 61:286–302PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Jenke-Kodama H, Sandmann A, Műller R, Dittmann E (2005) Evolutionary implications of bacterial polyketide synthases. Mol Biol Evol 22:2027–2039PubMedCrossRefGoogle Scholar
  18. 18.
    Jensen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728CrossRefGoogle Scholar
  19. 19.
    Johnson MJ, Lee KY, Scow KM (2003) DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma 114:279–303CrossRefGoogle Scholar
  20. 20.
    Julien B, Tian ZQ, Reid R, Reeves CD (2006) Analysis of the ambruticin and jerangolid gene clusters of sorangium cellulosum reveals unusual mechanisms of polyketide biosynthesis. Chem Biol 13:1277–1286PubMedCrossRefGoogle Scholar
  21. 21.
    Lam KS (2007) New aspects of natural products in drug discovery. Trends Microbiol 15:279–289PubMedCrossRefGoogle Scholar
  22. 22.
    Lee FYF, Borzilleri R, Fairchild CR, Kamath A, Smykla R, Kramer R, Vite G (2008) Preclinical discovery of ixabepilone, a highly active antineoplastic agent. Cancer Chemother Pharmacol 63:157–166PubMedCrossRefGoogle Scholar
  23. 23.
    Lozupone C, Hamady M, Knight R (2006) UniFrac: an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371PubMedCentralPubMedCrossRefGoogle Scholar
  24. 24.
    Luo K, Du G-P, Zhao Z-X, Xie BY, Li D-J (2010) Phylogenetic analysis of type I polyketide synthase and non-ribosomal peptide synthase genes from Mila Mountain in Tibet plateau. J Hunan Agric Uni (Nat Sci) 36:506–511Google Scholar
  25. 25.
    Neilson JW, Quade J, Ortiz M, Nelson WM, Legatzki A, Tian F, LaComb M, Betancourt JL, Wing RA, Soderlund CA, Maier RM (2012) Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles 16:553–566PubMedCrossRefGoogle Scholar
  26. 26.
    Okoro CK, Brown R, Jones AL, Andrews BA, Asenjo JA, Goodfellow M, Bull AT (2009) Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile. Antonie Leeuwenhoek 95:121–133PubMedCrossRefGoogle Scholar
  27. 27.
    Pang MF, Tan G-YA, Abdullah N, Lee C-W, Ng C-C (2008) Phylogenetic analysis of type I and type II polyketide synthase from tropical forest soil. Biotechnology 7:660–668CrossRefGoogle Scholar
  28. 28.
    Paradis A (2006) Analysis of phylogenetics and evolution. Springer, Berlin Heidelberg New YorkGoogle Scholar
  29. 29.
    Parsley LC, Linneman J, Goode AM, Becklund K, George I, Goodman RM, Lopanik NB, Liles MR (2011) Polyketide synthase pathways identified from a metagenomic library are derived from soil Acidobacteria. FEMS Microbiol Ecol 78:176–187PubMedCrossRefGoogle Scholar
  30. 30.
    Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40:D290–D301PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Rateb ME, Houssen WE, Arnold M, Abdelrahman MH, Deng H, Harrison WTA, Okoro CK, Asenjo JA, Andrews BA, Ferguson G, Bull A, Goodfellow M, Ebel R, Jaspars M (2011) Chaxamycins A-D, bioactive ansamycins from a hyper-arid desert Streptomyces sp. J Nat Prod 74:1491–1499PubMedCrossRefGoogle Scholar
  32. 32.
    Reddy BV, Kallifidas D, Kim JH, Charlop-Powers Z, Feng Z, Brady SF (2012) Natural product biosynthetic gene diversity in geographically distinct soil micro biomes. Appl Environ Microb 78:3744–3752CrossRefGoogle Scholar
  33. 33.
    Reeves CD, Murli S, Ashley GW, Piagentini M, Hutchinson CR, McDaniel R (2001) Alteration of the substrate specificity of a modular polyketide synthase acyltransferase domain through site-specific mutations. Biochemistry 40:15464–15470PubMedCrossRefGoogle Scholar
  34. 34.
    Robinson DF, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53:131–147CrossRefGoogle Scholar
  35. 35.
    Saul-Tcherkas V, Steinberger Y (2011) Soil microbial diversity in the vicinity of a Negev Desert shrub–Reaumuria negevensis. Microb Ecol 61:64–81PubMedCrossRefGoogle Scholar
  36. 36.
    Smith S, Tsai S-C (2007) The type I fatty acid and polyketide synthases: a tale of two megasynthases. Nat Prod Rep 24:1041–1072PubMedCentralPubMedCrossRefGoogle Scholar
  37. 37.
    Tamura K, Peterson D, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCrossRefGoogle Scholar
  38. 38.
    Watve MG, Tickoo R, Jog MM, Bhole BD (2001) How many antibiotics are produced by the genus Streptomyces? Arch Microbiol 176:386–390PubMedCrossRefGoogle Scholar
  39. 39.
    Yadav G, Gokhale RS, Mohanty D (2003) Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J Mol Biol 328:335–363PubMedCrossRefGoogle Scholar
  40. 40.
    Zhao B, Gao Z, Shao Y, Yan J, Hu Y, Yu J, Liu Q, Chen F (2012) Diversity analysis of type I ketosynthase in rhizosphere soil of cucumber. J Basic Microbiol 52:224–231PubMedCrossRefGoogle Scholar
  41. 41.
    Zhao J, Yang N, Zeng R (2008) Phylogenetic analysis of type I polyketide synthase and non-ribosomal peptide synthetase genes in Antarctic sediment. Extremophiles 12:97–105PubMedCrossRefGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2013

Authors and Affiliations

  • Patrick Hill
    • 1
  • Jörn Piel
    • 2
  • Stéphane Aris-Brosou
    • 1
  • Václav Krištůfek
    • 3
  • Christopher N. Boddy
    • 1
    • 5
  • Lubbert Dijkhuizen
    • 6
  1. 1.Department of BiologyUniversity of OttawaOttawaCanada
  2. 2.Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZurichZurichSwitzerland
  3. 3.Biology Centre AS CR, v. v. i.-Institute of Soil BiologyČeské BudějoviceCzech Republic
  4. 4.Department of Microbial Ecology, Centre for Evolutionary and Ecological StudiesUniversity of GroningenGroningenThe Netherlands
  5. 5.Department of ChemistryUniversity of OttawaOttawaCanada
  6. 6.Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands

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