Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052

Microbiology (United Kingdom)

Volumn 159, Issue PART 12, 2013, Pages 2558-2570

  Sandoval Espinola, Walter J ^a   Makwana, Satya T ^a   Chinn, Mari S ^b   Thon, Michael R ^c   Andrea Azcarate Peril M ^d   Bruno Bárcena, José M ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b North Carolina State University   (United States)

^c UNIVERSITY OF SALAMANCA   (Spain)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; BUTANOL; DNA 16S; FRUCTOSE; GLUCOSE; PROTEIN SERINE THREONINE KINASE; SOLUTE BINDING PROTEIN; SUCROSE; TRANSFER RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BATCH FERMENTATION; CLOSTRIDIUM BEIJERINCKII; COMPARATIVE STUDY; CONTROLLED STUDY; CULTURE MEDIUM; GENE FUNCTION; GENE INSERTION SEQUENCE; GENE MUTATION; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HYDROLYSIS; INDEL MUTATION; MISSENSE MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PHENOTYPE; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPOROGENESIS;

BUTANOLS; CARBON; CLOSTRIDIUM BEIJERINCKII; CULTURE MEDIA; DNA, BACTERIAL; FRUCTOSE; GENOME, BACTERIAL; GLUCOSE; GROWTH INHIBITORS; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SOLVENTS;

EID: 84888867372     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.069534-0     Document Type: Article

References (65)

1. Annous, B. A. & Blaschek, H. P. (1991). Isolation and characterization of Clostridium acetobutylicum mutants with enhanced amylolytic activity. Appl Environ Microbiol 57, 2544-2548.
2. Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q. & other authors (2009). BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6, 677-681.
3. Chojecki, A. & Blaschek, H. P. (1986). Effect of carbohydrate source on alpha-amylase and glucoamylase formation by Clostridium acetobutylicum SA-1. J Ind Microbiol 1, 63-67.
4. Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H. & Farrow, J. A. E. (1994). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44, 812-826.
5. Dai, Z., Dong, H., Zhu, Y., Zhang, Y., Li, Y. & Ma, Y. (2012). Introducing a single secondary alcohol dehydrogenase into butanoltolerant Clostridium acetobutylicum Rh8 switches ABE fermentation to high level IBE fermentation. Biotechnol Biofuels 5, 44.
6. Ezeji, T., Qureshi, N. & Blaschek, H. P. (2007a). Butanol production from agricultural residues: impact of degradation products on Clostridium beijerinckii growth and butanol fermentation. Biotechnol Bioeng 97, 1460-1469.
7. Ezeji, T. C., Qureshi, N. & Blaschek, H. P. (2007b). Production of acetone butanol (AB) from liquefied corn starch, a commercial substrate, using Clostridium beijerinckii coupled with product recovery by gas stripping. J Ind Microbiol Biotechnol 34, 771-777.
8. Ezeji, T., Milne, C., Price, N. D. & Blaschek, H. P. (2010). Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms. Appl Microbiol Biotechnol 85, 1697-1712.
9. Formanek, J., Mackie, R. & Blaschek, H. P. (1997). Enhanced butanol production by Clostridium beijerinckii BA101 grown in semidefined P2 medium containing 6 percent maltodextrin or glucose. Appl Environ Microbiol 63, 2306-2310.
10. Garrett, R. A., Vestergaard, G. & Shah, S. A. (2011). Archaeal CRISPR-based immune systems: exchangeable functional modules. Trends Microbiol 19, 549-556.
11. Gottschal, J. C. & Morris, J. G. (1981). Non-production of acetone and butanol by Clostridium acetobutylicum during glucose and ammonium limitation in continuous culture. Biotechnol Lett 3, 525-530.
12. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. & Eddy, S. R. (2003). Rfam: an RNA family database. Nucleic Acids Res 31, 439-441.
13. Grissa, I., Vergnaud, G. & Pourcel, C. (2007a). CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35 (Web Server), W52-W57.
14. Grissa, I., Vergnaud, G. & Pourcel, C. (2007b). The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8, 172.
15. Grissa, I., Vergnaud, G. & Pourcel, C. (2008). CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 36 (Web Server), W145-W148.
16. Hamada, M., Wijaya, E., Frith, M. C. & Asai, K. (2011). Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinformatics 27, 3085-3092.
17. Harris, L. M., Desai, R. P., Welker, N. E. & Papoutsakis, E. T. (2000). Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition? Biotechnol Bioeng 67, 1-11.
18. Heluane, H., Evans, M. R., Dagher, S. F. & Bruno-Bárcena, J. M. (2011). Meta-analysis and functional validation of nutritional requirements of solventogenic clostridia growing under butanol stress conditions and coutilization of D-glucose and D-xylose. Appl Environ Microbiol 77, 4473-4485.
19. Jain, M. K., Beacom, D. & Datta, R. (1993). Mutant strain of C. acetobutylicum and process for making butanol. US Patent US 5192673A.
20. Jang, Y. S., Lee, J., Malaviya, A., Seung, Y., Cho, J. H. & Lee, S. Y. (2012a). Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering. Biotechnol J 7, 186-198.
21. Jang, Y. S., Lee, J. Y., Lee, J., Park, J. H., Im, J. A., Eom, M. H., Lee, J., Lee, S. H., Song, H. & other authors (2012b). Enhanced butanol production obtained by reinforcing the direct butanol-forming route in Clostridium acetobutylicum. MBio 3, e00314-12.
22. Jia, K., Zhang, Y. & Li, Y. (2012). Identification and characterization of two functionally unknown genes involved in butanol tolerance of Clostridium acetobutylicum. PLoS ONE 7, e38815.
23. Johnson, J. L., Toth, J., Santiwatanakul, S. & Chen, J. S. (1997). Cultures of "Clostridium acetobutylicum" from various collections comprise Clostridium acetobutylicum, Clostridium beijerinckii, and two other distinct types based on DNA-DNA reassociation. Int J Syst Bacteriol 47, 420-424.
24. Kashket, E. R. & Cao, Z. Y. (1993). Isolation of a degeneration resistant mutant of Clostridium acetobutylicum NCIMB 8052. Appl Environ Microbiol 59, 4198-4202.
25. Kashket, E. R. & Cao, Z. Y. (1995). Clostridial strain degeneration. FEMS Microbiol Rev 17, 307-315.
26. Kilstrup, M., Hammer, K., Ruhdal Jensen, P. & Martinussen, J. (2005). Nucleotide metabolism and its control in lactic acid bacteria. FEMS Microbiol Rev 29, 555-590.
27. Krawitz, P., Rödelsperger, C., Jäger, M., Jostins, L., Bauer, S. & Robinson, P. N. (2010). Microindel detection in short-read sequence data. Bioinformatics 26, 722-729.
28. Kutzenok, A. & Aschner, M. (1952). Degenerative processes in a strain of Clostridium butylicum. J Bacteriol 64, 829-836.
29. Lee, J. & Blaschek, H. P. (2001). Glucose uptake in Clostridium beijerinckii NCIMB 8052 and the solvent-hyperproducing mutant BA101. Appl Environ Microbiol 67, 5025-5031.
30. Lee, S. F., Forsberg, C. W. & Gibbins, L. N. (1985a). Cellulolytic activity of Clostridium acetobutylicum. Appl Environ Microbiol 50, 220-228.
31. Lee, S. F., Forsberg, C. W. & Gibbins, L. N. (1985b). Xylanolytic activity of Clostridium acetobutylicum. Appl Environ Microbiol 50, 1068-1076.
32. Lee, J., Mitchell, W. J., Tangney, M. & Blaschek, H. P. (2005). Evidence for the presence of an alternative glucose transport system in Clostridium beijerinckii NCIMB 8052 and the solvent-hyperproducing mutant BA101. Appl Environ Microbiol 71, 3384-3387.
33. Lee, S. Y., Park, J. H., Jang, S. H., Nielsen, L. K., Kim, J. & Jung, K. S. (2008). Fermentative butanol production by clostridia. Biotechnol Bioeng 101, 209-228.
34. Li, H., Ruan, J. & Durbin, R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18, 1851-1858.
35. Lienhardt, J., Schripsema, J., Qureshi, N. & Blaschek, H. P. (2002). Butanol production by Clostridium beijerinckii BA101 in an immobilized cell biofilm reactor: increase in sugar utilization. Appl Biochem Biotechnol 98-100, 591-598.
36. Lin, Y. L. & Blaschek, H. P. (1983). Butanol production by a butanoltolerant strain of Clostridium acetobutylicum in extruded corn broth. Appl Environ Microbiol 45, 966-973.
37. Liyanage, H., Holcroft, P., Evans, V. J., Keis, S., Wilkinson, S. R., Kashket, E. R. & Young, M. (2000). A new insertion sequence, ISCb1, from Clostridium beijernickii NCIMB 8052. J Mol Microbiol Biotechnol 2, 107-113.
38. Mann, M. S., Dragovic, Z., Schirrmacher, G. & Lütke-Eversloh, T. (2012). Over-expression of stress protein-encoding genes helps Clostridium acetobutylicum to rapidly adapt to butanol stress. Biotechnol Lett 34, 1643-1649.
39. Milne, C. B., Eddy, J. A., Raju, R., Ardekani, S., Kim, P. J., Senger, R. S., Jin, Y. S., Blaschek, H. P. & Price, N. D. (2011). Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst Biol 5, 130.
40. Mitchell, W. J. (1998). Physiology of carbohydrate to solvent conversion by clostridia. Adv Microb Physiol 39, 31-130.
41. Mitchell, W. J., Shaw, J. E. & Andrews, L. (1991). Properties of the glucose phosphotransferase system of Clostridium acetobutylicum NCIB 8052. Appl Environ Microbiol 57, 2534-2539.
42. Najafpour, G. D. & Shan, C. P. (2003). Enzymatic hydrolysis of molasses. Bioresour Technol 86, 91-94.
43. Nataf, Y., Yaron, S., Stahl, F., Lamed, R., Bayer, E. A., Scheper, T. H., Sonenshein, A. L. & Shoham, Y. (2009). Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum. J Bacteriol 191, 203-209.
44. Ni, Y., Wang, Y. & Sun, Z. (2012). Butanol production from cane molasses by Clostridium saccharobutylicum DSM 13864: batch and semicontinuous fermentation. Appl Biochem Biotechnol 166, 1896-1907.
45. Ni, Y., Xia, Z., Wang, Y. & Sun, Z. (2013). Continuous butanol fermentation from inexpensive sugar-based feedstocks by Clostridium saccharobutylicum DSM 13864. Bioresour Technol 129, 680-685.
46. Nölling, J., Breton, G., Omelchenko, M. V., Makarova, K. S., Zeng, Q., Gibson, R., Lee, H. M., Dubois, J., Qiu, D. & other authors (2001). Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 183, 4823-4838.
47. Obuchowski, M. (2005). [Serine-threonine protein phosphatases from Bacillus subtilis]. Postepy Biochem 51, 95-104 (in Polish).
48. Quratulain, S., Qadeer, M. A., Chaudhry, M. Y. & Kausar, A. R. (1995). Development and characterization of butanol-resistant strain of Clostridium acetobutylicum in molasses medium. Folia Microbiol (Praha) 40, 467-471.
49. Qureshi, N. & Blaschek, H. P. (2000). Butanol production using Clostridium beijerinckii BA101 hyper-butanol producing mutant strain and recovery by pervaporation. Appl Biochem Biotechnol 84-86, 225-235.
50. Qureshi, N., Saha, B. C. & Cotta, M. A. (2007). Butanol production from wheat straw hydrolysate using Clostridium beijerinckii. Bioprocess Biosyst Eng 30, 419-427.
51. Qureshi, N., Saha, B. C., Dien, B., Hector, R. E. & Cotta, M. A. (2010). Production of butanol (a biofuel) from agricultural residues: Part I-Use of barley straw hydrolysate. Biomass Bioenergy 34, 559-565.
52. Reid, S. J., Rafudeen, M. S. & Leat, N. G. (1999). The genes controlling sucrose utilization in Clostridium beijerinckii NCIMB 8052 constitute an operon. Microbiology 145, 1461-1472.
53. Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G. & Mesirov, J. P. (2011). Integrative genomics viewer. Nat Biotechnol 29, 24-26.
54. Schultz, A. C., Nygaard, P. & Saxild, H. H. (2001). Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator. J Bacteriol 183, 3293-3302.
55. Soucaille, P., Joliff, G., Izard, A. & Goma, G. (1987). Butanol tolerance and autobacteriocin production by Clostridium acetobutylicum. Curr Microbiol 14, 295-299.
56. Stackebrandt, E. & Rainey, F. A. (1997). Phylogenetic relationships. In The Clostridia: Molecular Biology and Pathogenesis, pp. 3-19. Edited by I. R. Julian, A. M. Bruce, J. G. Songer, W. T. Richard & W. T. Richard. San Diego, CA: Academic Press.
57. Tangney, M., Rousse, C., Yazdanian, M. & Mitchell, W. J. (1998). Note: sucrose transport and metabolism in Clostridium beijerinckii NCIMB 8052. J Appl Microbiol 84, 914-919.
58. Terzaghi, B. E. & Sandine, W. E. (1975). Improved medium for lactic streptococci and their bacteriophages. Appl Microbiol 29, 807-813.
59. Treangen, T. J. & Salzberg, S. L. (2012). Repetitive DNA and nextgeneration sequencing: computational challenges and solutions. Nat Rev Genet 13, 36-46.
60. Van Der Westhuizen, A., Jones, D. T. & Woods, D. R. (1982). Autolytic activity and butanol tolerance of Clostridium acetobutylicum. Appl Environ Microbiol 44, 1277-1281.
61. Wang, Y. & Blaschek, H. P. (2011). Optimization of butanol production from tropical maize stalk juice by fermentation with Clostridium beijerinckii NCIMB 8052. Bioresour Technol 102, 9985-9990.
62. Wilson, K. (1994). Preparation of genomic DNA from bacteria. In: Current Protocols in Molecular Biology, pp. 2.4.1-2.4.5. Edited by F. A. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Wiley.
63. Wlodawer, A., Li, M., Gustchina, A., Oyama, H., Dunn, B. M. & Oda, K. (2003). Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases. Acta Biochim Pol 50, 81-102.
64. Xi, H., Schneider, B. L. & Reitzer, L. (2000). Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage. J Bacteriol 182, 5332-5341.
65. Xiao, H., Gu, Y., Ning, Y., Yang, Y., Mitchell, W. J., Jiang, W. & Yang, S. (2011). Confirmation and elimination of xylose metabolism bottlenecks in glucose phosphoenolpyruvate-dependent phosphotransferase system-deficient Clostridium acetobutylicum for simultaneous utilization of glucose, xylose, and arabinose. Appl Environ Microbiol 77, 7886-7895.