Antisense-RNA-mediated gene downregulation in clostridium pasteurianum

Fermentation

Volumn 1, Issue 1, 2015, Pages 113-126

  Pyne, Michael E ^a,c   Moo Young, Murray ^a   Chung, Duane A ^a,b   Perry Chou, C ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b Algaeneers Inc   (Canada)

^c Dept of Electrical and Computer Engineering   (Canada)

Author keywords

Antisense RNA; Biofuels; Clostridium; Gene knockdown; Gene reporter; Genetic engineering; Glycerol; Metabolic engineering

Indexed keywords

EID: 84987921975     PISSN: None     EISSN: 23115637     Source Type: Journal    
DOI: 10.3390/fermentation1010113     Document Type: Article

References (49)

1. Ahn, J.H.; Sang, B.I.; Urn, Y. Butanol production from thin stillage using Clostridium pasteurianum. Bioresour. Technol. 2011, 102, 4934–4937.
2. Ensen, T.O.; Kvist, T.; Mikkelsen, M.J.; Christensen, P.V.; Westermann, P. Fermentation of crude glycerol from biodiesel production by Clostridium pasteurianum. J. Ind. Microbiol. Biotechnol. 2012, 39, 709–717.
3. Taconi, K.A.; Venkataramanan, K.P.; Johnson, D.T. Growth and solvent production by Clostridium pasteurianum ATCC (R) 6013 (Tm) utilizing biodiesel-derived crude glycerol as the sole carbon source. Environ. Prog. Sustain. Energy 2009, 28, 100–110.
4. Biebl, H. Fermentation of glycerol by Clostridium pasteurianum—Batch and continuous culture studies. J. Ind. Microbiol. Biotechnol. 2001, 27, 18–26.
5. Lee, S.Y.; Park, J.H.; Jang, S.H.; Nielsen, L.K.; Kim, J.; Jung, K.S. Fermentative butanol production by Clostridia. Biotechnol. Bioeng. 2008, 101, 209–228.
6. Pfromm, P.H.; Amanor-Boadu, V.; Nelson, R.; Vadlani, P.; Madl, R. Bio-butanol vs. bio-ethanol: A technical and economic assessment for corn and switchgrass fermented by yeast or Clostridium acetobutylicum. Biomass Bioenergy 2010, 34, 515–524.
7. Swana, J.; Yang, Y.; Behnam, M.; Thompson, R. An analysis of net energy production and feedstock availability for biobutanol and bioethanol. Bioresour. Technol. 2011, 102, 2112–2117.
8. Johnson, D.T.; Taconi, K.A. The glycerin glut: Options for the value-added conversion of crude glycerol resulting from biodiesel production. Environ. Prog. 2007, 26, 338–348.
9. Yazdani, S.S.; Gonzalez, R. Anaerobic fermentation of glycerol: A path to economic viability for the biofuels industry. Curr. Opin. Biotechnol. 2007, 18, 213–219.
10. Van Haandel, A.C.; Catunda, P.F.C. Profitability increase of alcohol distilleries by the rational use of byproducts. Water Sci. Technol. 1994, 29, 117–124.
11. Johnston, M.; Holloway, T. A global comparison of national biodiesel production potentials. Environ. Sci. Technol. 2007, 41, 7967–7973.
12. Pyne, M.E.; Moo-Young, M.; Chung, D.A.; Chou, C.P. Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum. Biotechnol. Biofuels 2013, 6, 50.
13. Pyne, M.E.; Moo-Young, M.; Chung, D.A.; Chou, C.P. Expansion of the genetic toolkit for metabolic engineering of Clostridium pasteurianum: Chromosomal gene disruption of the endogenous cpaai restriction enzyme. Biotechnol. Biofuels 2014, 7, 163.
14. Kolek, J.; Sedlář, K.; Provazník, I.; Patáková, P. Draft genome sequence of Clostridium pasteurianum NRRL B-598, a potential butanol or hydrogen producer. Genome Announc. 2014, 2, doi:10.1128/genomeA.00192-14.
15. Pyne, M.E.; Utturkar, S.; Brown, S.D.; Moo-Young, M.; Chung, D.A.; Chou, C.P. Improved draft genome sequence of Clostridium pasteurianum strain ATCC 6013 (DSM 525) using a hybrid next-generation sequencing approach. Genome Announc. 2014, 2, e00790-14.
16. Rappert, S.; Song, L.; Sabra, W.; Wang, W.; Zeng, A.P. Draft genome sequence of type strain Clostridium pasteurianum DSM 525 (ATCC 6013), a promising producer of chemicals and fuels. Genome Announc. 2013, 1, doi:10.1128/genomeA.00232-12.
17. Poehlein, A.; Grosse-Honebrink, A.; Zhang, Y.; Minton, N.P.; Daniel, R. Complete genome sequence of the nitrogen-fixing and solvent-producing Clostridium pasteurianum DSM 525. Genome Announc. 2015, 3, doi:10.1128/genomeA.01591-14.
18. Rotta, C.; Poehlein, A.; Schwarz, K.; Mcclure, P.; Daniel, R.; Minton, N.P. Closed genome sequence of Clostridium pasteurianum ATCC 6013. Genome Announc. 2015, 3, doi:10.1128/genomeA.01596-14.
19. Pyne, M.E.; Liu, X.; Moo-Young, M.; Chung, D.A.; Chou, C.P. Genomic-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum. unpublished work, 2015.
20. Pyne, M.E.; Bruder, M.; Moo-Young, M.; Chung, D.A.; Chou, C.P. Technical guide for genetic advancement of underdeveloped and intractable Clostridium. Biotechnol. Adv. 2014, 32, 623–641.
21. Papoutsakis, E.T. Engineering solventogenic Clostridia. Curr. Opin. Biotechnol. 2008, 19, 420–429.
22. Song, C.W.; Lee, J.; Lee, S.Y. Genome engineering and gene expression control for bacterial strain development. Biotechnol. J. 2015, 10, 56–68.
23. Cooksley, C.M.; Zhang, Y.; Wang, H.Z.; Redl, S.; Winzer, K.; Minton, N.P. Targeted mutagenesis of the Clostridium acetobutylicum acetone-butanol-ethanol fermentation pathway. Metab. Eng. 2012, 14, 630–641.
24. Desai, R.P.; Papoutsakis, E.T. Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl. Environ. Microbiol. 1999, 65, 936–945.
25. Tummala, S.B.; Welker, N.E.; Papoutsakis, E.T. Design of antisense rna constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J. Bacteriol. 2003, 185, 1923–1934.
26. Gheshlaghi, R.; Scharer, J.M.; Moo-Young, M.; Chou, C.P. Metabolic pathways of Clostridia for producing butanol. Biotechnol. Adv. 2009, 27, 764–781.
27. Dabrock, B.; Bahl, H.; Gottschalk, G. Parameters affecting solvent production by Clostridium pasteurianum. Appl. Environ. Microbiol. 1992, 58, 1233–1239.
28. Simons, R.; Kleckner, N. Biological regulation by antisense RNA in prokaryotes. Annu. Rev. Genet. 1988, 22, 567–600.
29. Wagner, E.G.H.; Simons, R.W. Antisense RNA control in bacteria, phages, and plasmids. Annu. Rev. Microbiol. 1994, 48, 713–742.
30. Tummala, S.B.; Junne, S.G.; Papoutsakis, E.T. Antisense RNA downregulation of coenzyme a transferase combined with alcohol-aldehyde dehydrogenase overexpression leads to predominantly alcohologenic Clostridium acetobutylicum fermentations. J. Bacteriol. 2003, 185, 3644–3653.
31. Perret, S.; Maamar, H.; Belaich, J.P.; Tardif, C. Use of antisense rna to modify the composition of cellulosomes produced by Clostridium cellulolyticum. Mol. Microbiol. 2004, 51, 599–607.
32. Nakayama, S.I.; Kosaka, T.; Hirakawa, H.; Matsuura, K.; Yoshino, S.; Furukawa, K. Metabolic engineering for solvent productivity by downregulation of the hydrogenase gene cluster Hupcba in Clostridium saccharoperbutylacetonicum Strain N1-4. Appl. Microbiol. Biotechnol. 2008, 78, 483–493.
33. Liyanage, H.; Young, M.; Kashket, E.R. Butanol tolerance of Clostridium Beijerinckii NCIMB 8052 associated with down-regulation of GLDA by antisense RNA. J. Mol. Microbiol. Biotechnol. 2000, 2, 87–93.
34. Sillers, R.; A-Hinai, M.A.; Papoutsakis, E.T. Aldehyde-alcohol dehydrogenase and/or thiolase overexpression coupled with coa transferase downregulation lead to higher alcohol titers and selectivity in Clostridium acetobutylicum fermentations. Biotechnol. Bioeng. 2009, 102, 38–49.
35. Tummala, S.B.; Welker, N.E.; Papoutsakis, E.T. Development and characterization of a gene expression reporter system for Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 1999, 65, 3793–3799.
36. Heap, J.T.; Pennington, O.J.; Cartman, S.T.; Minton, N.P. A modular system for Clostridium shuttle plasmids. J. Microbiol. Methods 2009, 78, 79–85.
37. Bruder, M.; Moo-Young, M.; Chung, D.A.; Chou, C.P. Elimination of carbon catabolite repression in Clostridium acetobutylicum—A journey toward simultaneous use of xylose and glucose. Appl. Microbiol. Biotechnol. 2015, 99, 7579–7588.
38. Sambrook, J.; Fritsch, E.F.; Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed.; Cold Spring Harbor Press: Cold Spring Harbor, NY, USA, 1989.
39. Miller, J.H. Experiments in Molecular Genetics; Gold Spring Harbor Laboratory: Gold Spring Harbor, NY, USA, 1972.
40. Moon, C.; Lee, C.H.; Sang, B.I.; Um, Y. Optimization of medium compositions favoring butanol and 1,3-propanediol production from glycerol by Clostridium pasteurianum. Bioresour. Technol. 2011, 102, 10561–10568.
41. Graves, M.; Rabinowitz, J. In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. evidence for “extended” promoter elements in gram-positive organisms. J. Biol. Chem. 1986, 261, 11409–11415.
42. Meng, Y.; Li, J.L. Cloning, expression and characterization of a thiolase gene from Clostridium pasteurianum. Biotechnol. Lett. 2006, 28, 1227–1232.
43. Guedon, E.; Desvaux, M.; Petitdemange, H. Improvement of cellulolytic properties of Clostridium cellulolyticum by metabolic engineering. Appl. Environ. Microbiol. 2002, 68, 53–58.
44. Heap, J.T.; Pennington, O.J.; Cartman, S.T.; Carter, G.P.; Minton, N.P. The clostron: A universal gene knock-out system for the genus Clostridium. J. Microbiol. Methods 2007, 70, 452–464.
45. Rabinowitz, J. Preparation and properties of clostridial ferredoxins. Methods Enzymol. 1971, 24, 431–446.
46. Heyndrickx, M.; Devos, P.; Deley, J. Fermentation characteristics of Clostridium pasteurianum LMG 3285 grown on glucose and mannitol. J. Appl. Bacteriol. 1991, 70, 52–58.
47. Higashide, W.; Li, Y.C.; Yang, Y.F.; Liao, J.C. Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose. Appl. Environ. Microbiol. 2011, 77, 2727–2733.
48. Mermelstein, L.D.; Welker, N.E.; Bennett, G.N.; Papoutsakis, E.T. Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824. Bio-Technology 1992, 10, 190–195.
49. Kim, B.H.; Bellows, P.; Datta, R.; Zeikus, J.G. Control of carbon and electron flow in Clostridium acetobutylicum fermentations—Utilization of carbon monoxide to inhibit hydrogen production and to enhance butanol yields. Appl. Environ. Microbiol. 1984, 48, 764–770.