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Investigation of secondary metabolism in the industrial butanol hyper-producer Clostridium saccharoperbutylacetonicum N1-4

  • Natural Products - Original Paper
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Journal of Industrial Microbiology & Biotechnology

Abstract

Clostridium saccharoperbutylacetonicum N1-4 (Csa) is a historically significant anaerobic bacterium which can perform saccharolytic fermentations to produce acetone, butanol, and ethanol (ABE). Recent genomic analyses have highlighted this organism’s potential to produce polyketide and nonribosomal peptide secondary metabolites, but little is known regarding the identity and function of these metabolites. This study provides a detailed bioinformatic analysis of seven biosynthetic gene clusters (BGCs) present in the Csa genome that are predicted to produce polyketides/nonribosomal peptides. An RNA-seq-based untargeted transcriptomic approach revealed that five of seven BGCs were expressed during ABE fermentation. Additional characterization of a highly expressed nonribosomal peptide synthetase gene led to the discovery of its associated metabolite and its biosynthetic pathway. Transcriptomic analysis suggested an association of this nonribosomal peptide synthetase gene with butanol tolerance, which was supported by butanol challenge assays.

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References

  1. Alsaker KV, Paredes C, Papoutsakis ET (2010) Metabolite stress and tolerance in the production of biofuels and chemicals: Gene-expression-based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum. Biotechnol Bioeng 105:1131–1147. https://doi.org/10.1002/bit.22628

    Article  CAS  PubMed  Google Scholar 

  2. Al-Shorgani NKN, Kalil MS, Yusoff WMW (2012) Biobutanol production from rice bran and de-oiled rice bran by Clostridium saccharoperbutylacetonicum N1–4. Bioprocess Biosyst Eng 35:817–826. https://doi.org/10.1007/s00449-011-0664-2

    Article  CAS  PubMed  Google Scholar 

  3. Anders S, Pyl PT, Huber W (2015) HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169. https://doi.org/10.1093/bioinformatics/btu638

    Article  CAS  PubMed  Google Scholar 

  4. Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics. Available online at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed 24 Feb 2020

  5. Avci A, Kiliç NK, Dönmez G, Dönmez S (2014) Evaluation of hydrogen production by Clostridium strains on beet molasses. Environ Technol (United Kingdom) 35:278–285. https://doi.org/10.1080/09593330.2013.826251

    Article  CAS  Google Scholar 

  6. Baba S, Tashiro Y, Shinto H, Sonomoto K (2012) Development of high-speed and highly efficient butanol production systems from butyric acid with high density of living cells of Clostridium saccharoperbutylacetonicum. J Biotechnol 157:605–612. https://doi.org/10.1016/j.jbiotec.2011.06.004

    Article  CAS  PubMed  Google Scholar 

  7. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. https://doi.org/10.1093/nar/gkz310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Dada O, Yusoff WMW, Kalil MS (2013) Biohydrogen production from ricebran using Clostridium saccharoperbutylacetonicum N1–4. Int J Hydrogen Energy 38:15063–15073. https://doi.org/10.1016/j.ijhydene.2013.07.048

    Article  CAS  Google Scholar 

  9. del Cerro C, Felpeto-Santero C, Rojas A, Tortajada M, Ramón D, García JL (2013) Genome sequence of the butanol hyperproducer Clostridium saccharoperbutylacetonicum N1–4. Genome Announc 1:e0007013. https://doi.org/10.1128/genomeA.00071-13

    Article  PubMed  Google Scholar 

  10. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343–345. https://doi.org/10.1038/nmeth.1318

    Article  CAS  PubMed  Google Scholar 

  11. Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G (2014) Interactive XCMS online: Simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem 86:6931–6939. https://doi.org/10.1021/ac500734c

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Green EM (2011) Fermentative production of butanol-the industrial perspective. Curr Opin Biotechnol 22:337–343. https://doi.org/10.1016/j.copbio.2011.02.004

    Article  CAS  PubMed  Google Scholar 

  13. Green EM, Boynton ZL, Harris LM, Rudolph FB, Papoutsakis ET, Bennett GN (1996) Genetic manipulation of acid formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824. Microbiology 142:2079–2086. https://doi.org/10.1099/13500872-142-8-2079

    Article  CAS  PubMed  Google Scholar 

  14. Guo CJ, Chang FY, Wyche TP, Backus KM, Acker TM, Funabashi M, Taketani M, Donia MS, Nayfach S, Pollard KS, Craik CS, Cravatt BF, Clardy J, Voigt CA, Fischbach MA (2017) Discovery of reactive microbiota-derived metabolites that inhibit host proteases. Cell 168:517–526.e18. https://doi.org/10.1016/j.cell.2016.12.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Guo M, Song W, Buhain J (2015) Bioenergy and biofuels: History, status, and perspective. Renew Sustain Energy Rev 42:712–725. https://doi.org/10.1016/j.rser.2014.10.013

    Article  CAS  Google Scholar 

  16. Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J (2012) How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? BMC Genomics 13:734. https://doi.org/10.1186/1471-2164-13-734

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hayashi S, Aono R, Hanai T, Mori H, Kobayashi T, Honda H (2003) Analysis of organic solvent tolerance in Escherichia coli using gene expression profiles from DNA microarrays. J Biosci Bioeng 95:379–383. https://doi.org/10.1263/jbb.95.379

    Article  CAS  PubMed  Google Scholar 

  18. Herman NA, Kim SJ, Li JS, Cai W, Koshino H, Zhang W (2017) The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation. Nat Commun 8:1514. https://doi.org/10.1038/s41467-017-01809-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Herman NA, Li J, Bedi R, Turchi B, Liu X, Miller MJ, Zhang W (2017) Development of a high-efficiency transformation method and implementation of rational metabolic engineering for the industrial butanol hyperproducer clostridium saccharoperbutylacetonicum strain N1–4. Appl Environ Microbiol 83:e02942–e3016. https://doi.org/10.1128/AEM.02942-16

    Article  CAS  PubMed  Google Scholar 

  20. Hertweck C (2009) The biosynthetic logic of polyketide diversity. Angew Chemie - Int Ed 48:4688–4716. https://doi.org/10.1002/anie.200806121

    Article  CAS  Google Scholar 

  21. Jones DT, Woods DR (1986) Acetone-butanol fermentation revisited. Microbiol Rev 50:484–524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Keis S, Shaheen R, Jones DT (2001) Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov. Int J Syst Evol Microbiol 51:2095–2103. https://doi.org/10.1099/00207713-51-6-2095

    Article  CAS  PubMed  Google Scholar 

  23. Kiyoshi K, Furukawa M, Seyama T, Kadokura T, Nakazato A, Nakayama S (2015) Butanol production from alkali-pretreated rice straw by co-culture of Clostridium thermocellum and Clostridium saccharoperbutylacetonicum. Bioresour Technol 186:325–328. https://doi.org/10.1016/j.biortech.2015.03.061

    Article  CAS  PubMed  Google Scholar 

  24. Kobayashi G, Eto K, Tashiro Y, Okubo K, Sonomoto K, Ishizaki A (2005) Utilization of excess sludge by acetone-butanol-ethanol fermentation employing Clostridium saccharoperbutylacetonicum N1–4 (ATCC 13564). J Biosci Bioeng 99:517–519. https://doi.org/10.1263/jbb.99.517

    Article  CAS  PubMed  Google Scholar 

  25. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Li JS, Barber CC, Zhang W (2019) Natural products from anaerobes. J Ind Microbiol Biotechnol 46:375–383. https://doi.org/10.1007/s10295-018-2086-5

    Article  CAS  PubMed  Google Scholar 

  27. Li Q, Chen J, Minton NP, Zhang Y, Wen Z, Liu J, Yang H, Zeng Z, Ren X, Yang J, Gu Y, Jiang W, Jiang Y, Yang S (2016) CRISPR-based genome editing and expression control systems in Clostridium acetobutylicum and Clostridium beijerinckii. Biotechnol J 11:961–972. https://doi.org/10.1002/biot.201600053

    Article  CAS  PubMed  Google Scholar 

  28. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Medema MH, Fischbach MA (2015) Computational approaches to natural product discovery. Nat Chem Biol 11:639–648. https://doi.org/10.1038/nchembio.1884

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Medema MH, Takano E, Breitling R (2013) Detecting sequence homology at the gene cluster level with multigeneblast. Mol Biol Evol 30:1218–1223. https://doi.org/10.1093/molbev/mst025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Moon HG, Jang YS, Cho C, Lee J, Binkley R, Lee SY (2016) One hundred years of clostridial butanol fermentation. FEMS Microbiol Lett. https://doi.org/10.1093/femsle/fnw001

    Article  PubMed  Google Scholar 

  32. Motoyoshi H (1960) Process for producing butanol by fermentation. US patent 2,945,786 A. Available online at: https://patentimages.storage.googleapis.com/49/26/b4/90db109ee4d8c4/US2945786.pdf. Accessed 24 Feb 2020

  33. Nakayama S, Kiyoshi K, Kadokura T, Nakazato A (2011) Butanol production from crystalline cellulose by Cocultured Clostridium thermocellum and Clostridium saccharoperbutylacetonicum N1–4. Appl Environ Microbiol 77:6470–6475. https://doi.org/10.1128/AEM.00706-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Navarro-Muñoz J, Selem-Mojica N, Mullowney M, Kautsar S, Tryon J, Parkinson E, De Los SE, Yeong M, Cruz-Morales P, Abubucker S, Roeters A, Lokhorst W, Fernàndez-Guerra A, Cappelini LTD, Thomson R, Metcalf W, Kelleher N, Barona-Gomez F, Medema MH (2019) A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data. Nat Chem Biol 16:60–68. https://doi.org/10.1038/s41589-019-0400-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Noguchi T, Tashiro Y, Yoshida T, Zheng J, Sakai K, Sonomoto K (2013) Efficient butanol production without carbon catabolite repression from mixed sugars with Clostridium saccharoperbutylacetonicum N1–4. J Biosci Bioeng 116:716–721. https://doi.org/10.1016/j.jbiosc.2013.05.030

    Article  CAS  PubMed  Google Scholar 

  36. Oshiro M, Hanada K, Tashiro Y, Sonomoto K (2010) Efficient conversion of lactic acid to butanol with pH-stat continuous lactic acid and glucose feeding method by Clostridium saccharoperbutylacetonicum. Appl Microbiol Biotechnol 87:1177–1185. https://doi.org/10.1007/s00253-010-2673-5

    Article  CAS  PubMed  Google Scholar 

  37. Patakova P, Linhova M, Rychtera M, Paulova L, Melzoch K (2013) Novel and neglected issues of acetone-butanol-ethanol (ABE) fermentation by clostridia: Clostridium metabolic diversity, tools for process mapping and continuous fermentation systems. Biotechnol Adv 31:58–67. https://doi.org/10.1016/j.biotechadv.2012.01.010

    Article  CAS  PubMed  Google Scholar 

  38. Pfeifer BA, Admiraal SJ, Gramajo H, Cane DE, Khosla C (2001) Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 291:1790–1792. https://doi.org/10.1126/science.1058092

    Article  CAS  PubMed  Google Scholar 

  39. Pidot S, Ishida K, Cyrulies M, Hertweck C (2014) Discovery of clostrubin, an exceptional polyphenolic polyketide antibiotic from a strictly anaerobic bacterium. Angew Chemie - Int Ed 53:7856–7859. https://doi.org/10.1002/anie.201402632

    Article  CAS  Google Scholar 

  40. Poehlein A, Krabben P, Dürre P, Daniel R (2014) Complete genome sequence of the solvent producer Clostridium saccharoperbutylacetonicum strain DSM 14923. Genome Announc 2:e01056–e1114. https://doi.org/10.1128/genomeA.01056-14

    Article  PubMed  PubMed Central  Google Scholar 

  41. Raaijmakers JM, Mazzola M (2012) Diversity and Natural Functions of Antibiotics Produced by Beneficial and Plant Pathogenic Bacteria. Annu Rev Phytopathol 50:403–424. https://doi.org/10.1146/annurev-phyto-081211-172908

    Article  CAS  PubMed  Google Scholar 

  42. Richter H, Qureshi N, Heger S, Dien B, Cotta MA, Angenent LT (2012) Prolonged conversion of n-butyrate to n-butanol with Clostridium saccharoperbutylacetonicum in a two-stage continuous culture with in-situ product removal. Biotechnol Bioeng 109:913–921. https://doi.org/10.1002/bit.24380

    Article  CAS  PubMed  Google Scholar 

  43. Rocha DJP, Santos CS, Pacheco LGC (2015) Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis. Antonie van Leeuwenhoek, Int J Gen Mol Microbiol 108:685–693. https://doi.org/10.1007/s10482-015-0524-1

    Article  CAS  Google Scholar 

  44. Sauer M (2016) Industrial production of acetone and butanol by fermentation-100 years later. FEMS Microbiol Lett. https://doi.org/10.1093/femsle/fnw134

    Article  PubMed  PubMed Central  Google Scholar 

  45. Schneider BA, Balskus EP (2018) Discovery of small molecule protease inhibitors by investigating a widespread human gut bacterial biosynthetic pathway. Tetrahedron 74:3215–3230. https://doi.org/10.1016/j.tet.2018.03.043

    Article  CAS  Google Scholar 

  46. Shabuer G, Ishida K, Pidot SJ, Roth M, Dahse HM, Hertweck C (2015) Plant pathogenic anaerobic bacteria use aromatic polyketides to access aerobic territory. Science 350:670–674. https://doi.org/10.1126/science.aac9990

    Article  CAS  PubMed  Google Scholar 

  47. Shimizu K, Hayashi S, Kako T, Suzuki M, Tsukagoshi N, Doukyu N, Kobayashi T, Honda H (2005) Discovery of glpC, an organic solvent tolerance-related gene in Escherichia coli, using gene expression profiles from DNA microarrays. Appl Environ Microbiol 71:1093–1096. https://doi.org/10.1128/AEM.71.2.1093-1096.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Shukor H, Al-Shorgani NKN, Abdeshahian P, Hamid AA, Anuar N, Rahman NA, Kalil MS (2014) Production of butanol by Clostridium saccharoperbutylacetonicum N1–4 from palm kernel cake in acetone-butanol-ethanol fermentation using an empirical model. Bioresour Technol 170:565–573. https://doi.org/10.1016/j.biortech.2014.07.055

    Article  CAS  PubMed  Google Scholar 

  49. Skinnider MA, Merwin NJ, Johnston CW, Magarvey NA (2017) PRISM 3: Expanded prediction of natural product chemical structures from microbial genomes. Nucleic Acids Res 45:W49–W54. https://doi.org/10.1093/nar/gkx320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, Von Mering C (2015) STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447–D452. https://doi.org/10.1093/nar/gku1003

    Article  CAS  PubMed  Google Scholar 

  51. Tashiro Y, Takeda K, Kobayashi G, Sonomoto K, Ishizaki A, Yoshino S (2004) High butanol production by Clostridium saccharoperbutylacetonicum N1–4 in fed-batch culture with pH-stat continuous butyric acid and glucose feeding method. J Biosci Bioeng 98:263–268. https://doi.org/10.1263/jbb.98.263

    Article  CAS  PubMed  Google Scholar 

  52. Thang VH, Kanda K, Kobayashi G (2010) Production of Acetone-Butanol-Ethanol (ABE) in direct fermentation of cassava by Clostridium saccharoperbutylacetonicum N1–4. Appl Biochem Biotechnol 161:157–170. https://doi.org/10.1007/s12010-009-8770-1

    Article  CAS  PubMed  Google Scholar 

  53. Tomas CA, Beamish J, Papoutsakis ET (2004) Transcriptional Analysis of Butanol Stress and Tolerance in Clostridium acetobutylicum. J Bacteriol 186:2006–2018. https://doi.org/10.1128/JB.186.7.2006-2018.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET (2012) Clostridia: The importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol 23:364–381

    Article  CAS  PubMed  Google Scholar 

  55. Walsh CT (2016) Insights into the chemical logic and enzymatic machinery of NRPS assembly lines. Nat Prod Rep 33:127–135. https://doi.org/10.1039/c5np00035a

    Article  CAS  PubMed  Google Scholar 

  56. Wei H, Fu Y, Magnusson L, Baker JO, Maness PC, Xu Q, Yang S, Bowersox A, Bogorad I, Wang W, Tucker MP, Himmel ME, Ding SY (2014) Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-seq. Front Microbiol 5:142. https://doi.org/10.3389/fmicb.2014.00142

    Article  PubMed  PubMed Central  Google Scholar 

  57. Xu T, Li Y, Shi Z, Hemme CL, Li Y, Zhu Y, Van Nostrand JD, He Z, Zhou J (2015) Efficient genome editing in clostridium cellulolyticum via CRISPR-Cas9 nickase. Appl Environ Microbiol 81:4423–4431. https://doi.org/10.1128/AEM.00873-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Yao D, Dong S, Wang P, Chen T, Wang J, Yue ZB, Wang Y (2017) Robustness of Clostridium saccharoperbutylacetonicum for acetone-butanol-ethanol production: Effects of lignocellulosic sugars and inhibitors. Fuel 208:549–557. https://doi.org/10.1016/j.fuel.2017.07.004

    Article  CAS  Google Scholar 

  59. Zhang J, Wang P, Wang X, Feng J, Sandhu HS, Wang Y (2018) Enhancement of sucrose metabolism in Clostridium saccharoperbutylacetonicum N1–4 through metabolic engineering for improved acetone–butanol–ethanol (ABE) fermentation. Bioresour Technol 270:430–438. https://doi.org/10.1016/j.biortech.2018.09.059

    Article  CAS  PubMed  Google Scholar 

  60. Zhang W, Bolla ML, Kahne D, Walsh CT (2010) A three enzyme pathway for 2-amino-3-hydroxycyclopent-2-enone formation and incorporation in natural product biosynthesis. J Am Chem Soc 132:6402–6411. https://doi.org/10.1021/ja1002845

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank J. Pelton (UC Berkeley) for helping with NMR spectroscopic analysis, the University of California-Berkeley QB3 Functional Genomics Laboratory and Vincent J. Coates Genomic Sequencing Laboratory for performing the RNA-Seq library preparation and sequencing. This work was financially supported by the Energy Biosciences Institute, Alfred P. Sloan Foundation, and the National Institutes of Health (DP2AT009148).

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Li, J.S., Barber, C.C., Herman, N.A. et al. Investigation of secondary metabolism in the industrial butanol hyper-producer Clostridium saccharoperbutylacetonicum N1-4. J Ind Microbiol Biotechnol 47, 319–328 (2020). https://doi.org/10.1007/s10295-020-02266-8

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