Some (bacilli) like it hot: Genomics of Geobacillus species

Microbial Biotechnology

Volumn 8, Issue 1, 2015, Pages 40-48

  Studholme, David J ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BIOTECHNOLOGY; GENE SEQUENCE; GENETIC ANALYSIS; GENOMICS; GEOBACILLUS; HETEROLOGOUS EXPRESSION; NONHUMAN; PHYLOGENY; CHEMISTRY; CLASSIFICATION; GENETICS; HEAT; ISOLATION AND PURIFICATION; MOLECULAR GENETICS;

BACILLI (CLASS); GEOBACILLUS;

BIOTECHNOLOGY; GENOME, BACTERIAL; GENOMICS; GEOBACILLUS; HOT TEMPERATURE; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 84922353374     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/1751-7915.12161     Document Type: Article

References (62)

1. Banat, I.M., Marchant, R., and Rahman, T.J. (2004) Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov. Int J Syst Evol Microbiol 54: 2197-2201.
2. Bartosiak-Jentys, J., Hussein, A.H., Lewis, C.J., and Leak, D.J. (2013) Modular system for assessment of glycosyl hydrolase secretion in Geobacillus thermoglucosidasius. Microbiology 159: 1267-1275.
3. Begley, M., Cotter, P.D., Hill, C., and Ross, R.P. (2009) Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins. Appl Environ Microbiol 75: 5451-5460.
4. Bhalla, A., Kainth, A.S., and Sani, R.K. (2013) Draft genome sequence of lignocellulose-degrading thermophilic bacterium Geobacillus sp. strain WSUCF1. Genome Announc 1: pii: e00595-13. doi:10.1128/genomeA.00595-13.
5. Bhalla, A., Bischoff, K.M., Uppugundla, N., Balan, V., and Sani, R.K. (2014) Novel thermostable endo-xylanase cloned and expressed from bacterium Geobacillus sp. WSUCF1. Bioresour Technol 165: 314-318.
6. Blanchard, K., Robic, S., and Matsumura, I. (2014) Transformable facultative thermophile Geobacillus stearothermophilus NUB3621 as a host strain for metabolic engineering. Appl Microbiol Biotechnol 98: 6715-6723.
7. Boonmak, C., Takahasi, Y., and Morikawa, M. (2013) Draft genome sequence of Geobacillus thermoleovorans strain B23. Genome Announc 1: pii: e00944-13. doi:10.1128/genomeA.00944-13.
8. Boonmak, C., Takahashi, Y., and Morikawa, M. (2014) Cloning and expression of three ladA-type alkane monooxygenase genes from an extremely thermophilic alkane-degrading bacterium Geobacillus thermoleovorans B23. Extremophiles 18: 515-523.
9. Bryant, D., and Moulton, V. (2004) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21: 255-265.
10. Burgess, S.A., Lindsay, D., and Flint, S.H. (2010) Thermophilic bacilli and their importance in dairy processing. Int J Food Microbiol 144: 215-225.
11. Chen, X.-G., Stabnikova, O., Tay, J.-H., Wang, J.-Y., and Tay, S.T.-L. (2004) Thermoactive extracellular proteases of Geobacillus caldoproteolyticus, sp. nov., from sewage sludge. Extremophiles 8: 489-498.
12. Chen, Z.F., Wojcik, S.F., and Welker, N.E. (1986) Genetic analysis of Bacillus stearothermophilus by protoplast fusion. J Bacteriol 165: 994-1001.
13. Coorevits, A., Dinsdale, A.E., Halket, G., Lebbe, L., De Vos, P., Van Landschoot, A., and Logan, N.A. (2012) Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G.stearothermophilus, G.jurassicus, G.toebii, G.thermodenitrificans and G.thermoglucosidans (nom. corrig., formerly 'thermoglucosidasius'); transfer of Bacillus thermantarcticus. Int J Syst Evol Microbiol 62: 1470-1485.
14. Couñago, R., and Shamoo, Y. (2005) Gene replacement of adenylate kinase in the gram-positive thermophile Geobacillus stearothermophilus disrupts adenine nucleotide homeostasis and reduces cell viability. Extremophiles 9: 135-144.
15. Cripps, R.E., Eley, K., Leak, D.J., Rudd, B., Taylor, M., Todd, M., etal. (2009) Metabolic engineering of Geobacillus thermoglucosidasius for high yield ethanol production. Metab Eng 11: 398-408.
16. De Maayer, P., Williamson, C.E., Vennard, C.T., Danson, M.J., and Cowan, D.A. (2014) Draft genome sequences of Geobacillus sp. strains CAMR5420 and CAMR12739. Genome Announc 2: pii: e00567-14. doi:10.1128/genomeA.00567-14.
17. Delcher, A.L., Phillippy, A., Carlton, J., and Salzberg, S.L. (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30: 2478-2483.
18. Dinsdale, A.E., Halket, G., Coorevits, A., Van Landschoot, A., Busse, H.-J., De Vos, P., and Logan, N.A. (2011) Emended descriptions of Geobacillus thermoleovorans and Geobacillus thermocatenulatus. Int J Syst Evol Microbiol 61: 1802-1810.
19. Doi, K., Mori, K., Martono, H., Nagayoshi, Y., Fujino, Y., Tashiro, K., etal. (2013) Draft genome sequence of Geobacillus kaustophilus GBlys, a lysogenic strain with bacteriophage OH2. Genome Announc 1: pii: e00634-13. doi:10.1128/genomeA.00634-13.
20. Feng, L., Wang, W., Cheng, J., Ren, Y., Zhao, G., Gao, C., etal. (2007) Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci USA 104: 5602-5607.
21. Fridjonsson, O., Watzlawick, H., Gehweiler, A., and Mattes, R. (1999) Thermostable alpha-galactosidase from Bacillus stearothermophilus NUB3621: cloning, sequencing and characterization. FEMS Microbiol Lett 176: 147-153.
22. Garg, N., Tang, W., Goto, Y., Nair, S.K., and van der Donk, W.A. (2012) Lantibiotics from Geobacillus thermodenitrificans. Proc Natl Acad Sci USA 109: 5241-5246.
23. Haki, G.D., and Rakshit, S.K. (2003) Developments in industrially important thermostable enzymes: a review. Bioresour Technol 89: 17-34.
24. Huson, D.H. (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
25. Imanaka, T., Fujii, M., Aramori, I., and Aiba, S. (1982) Transformation of Bacillus stearothermophilus with plasmid DNA and characterization of shuttle vector plasmids between Bacillus stearothermophilus and Bacillus subtilis. J Bacteriol 149: 824-830.
26. Li, Y., Wu, J., Wang, W., Ding, P., and Feng, L. (2012) Proteomics analysis of aromatic catabolic pathways in thermophilic Geobacillus thermodenitrificans NG80-2. J Proteomics 75: 1201-1210.
27. Liao, H., McKenzie, T., and Hageman, R. (1986) Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc Natl Acad Sci USA 83: 576-580.
28. Marchant, R., Sharkey, F.H., Banat, I.M., Rahman, T.J., and Perfumo, A. (2006) The degradation of n-hexadecane in soil by thermophilic geobacilli. FEMS Microbiol Ecol 56: 44-54.
29. Marks, T.J., and Hamilton, P.T. (2014) Characterization of a thermophilic bacteriophage of Geobacillus kaustophilus. Arch Virol. doi:10.1007/s00705-014-2101-8.
30. Mead, D.A., Lucas, S., Copeland, A., Lapidus, A., Cheng, J.-F., Bruce, D.C., etal. (2012) Complete genome sequence of Paenibacillus strain Y4.12MC10, a novel Paenibacillus lautus strain isolated from Obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 6: 381-400.
31. Muhd Sakaff, M.K.L., Abdul Rahman, A.Y., Saito, J.A., Hou, S., and Alam, M. (2012) Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5. J Bacteriol 194: 1239.
32. Mukerjee-Dhar, G., Shimura, M., Miyazawa, D., Kimbara, K., and Hatta, T. (2005) bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC. Microbiology 151: 4139-4151.
33. Narumi, I., Sawakami, K., Nakamoto, S., Nakayama, N., Yanagisawa, T., Takahashi, N., and Kihara, H. (1992) A newly isolated Bacillus stearotheromophilus K1041 and its transformation by electroporation. Biotechnol Tech 6: 83-86.
34. Nazina, T.N., Tourova, T.P., Poltaraus, A.B., Novikova, E., V, Grigoryan, A.A., Ivanova, A.E., etal. (2001) Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Int J Syst Evol Microbiol 51: 433-446.
35. Nicholson, W.L. (2003) Using thermal inactivation kinetics to calculate the probability of extreme spore longevity: implications for paleomicrobiology and lithopanspermia. Orig Life Evol Biosph 33: 621-631.
36. Niehaus, F., Bertoldo, C., Kähler, M., and Antranikian, G. (1999) Extremophiles as a source of novel enzymes for industrial application. Appl Microbiol Biotechnol 51: 711-729.
37. Pore, S.D., Arora, P., and Dhakephalkar, P.K. (2014) Draft genome sequence of Geobacillus sp. strain FW23, isolated from a formation water sample. Genome Announc 2: pii: e00352-14. doi:10.1128/genomeA.00352-14.
38. R Development Core Team, R. (2013) R: a language and environment for statistical computing. R Found Stat Comput 1: 409.
39. Sandalli, C., Singh, K., Modak, M.J., Ketkar, A., Canakci, S., Demir, I., and Belduz, A.O. (2009) A new DNA polymerase I from Geobacillus caldoxylosilyticus TK4: cloning, characterization, and mutational analysis of two aromatic residues. Appl Microbiol Biotechnol 84: 105-117.
40. Schmidt-Dannert, C., Pleiss, J., and Schmid, R.D. (1998) A toolbox of recombinant lipases for industrial applications. Ann N Y Acad Sci 864: 14-22.
41. Seo, M.-J., Lee, B.-S., Pyun, Y.-R., and Park, H. (2011) Isolation and characterization of N-acylhomoserine lactonase from the thermophilic bacterium, Geobacillus caldoxylosilyticus YS-8. Biosci Biotechnol Biochem 75: 1789-1795.
42. Shintani, M., Ohtsubo, Y., Fukuda, K., Hosoyama, A., Ohji, S., Yamazoe, A., etal. (2014) Complete genome sequence of the thermophilic polychlorinated biphenyl degrader Geobacillus sp. strain JF8 (NBRC 109937). Genome Announc 2: e01213-13.
43. Siddiqui, M.A., Rashid, N., Ayyampalayam, S., and Whitman, W.B. (2014) Draft genome sequence of Geobacillus thermopakistaniensis strain MAS1. Genome Announc 2: pii: e00559-14. doi:10.1128/genomeA.00559-14.
44. Studholme, D.J. (1998) Metabolic engineering of thermophilic Bacillus species for ethanol production. PhD Thesis. London: Deparment of Biochemistry, Imperial College.
45. Studholme, D.J., Jackson, R.A., and Leak, D.J. (1999) Phylogenetic analysis of transformable strains of thermophilic Bacillus species. FEMS Microbiol Lett 172: 85-90.
46. Suzuki, H., Okazaki, F., Kondo, A., and Yoshida, K. (2013) Genome mining and motif modifications of glycoside hydrolase family 1 members encoded by Geobacillus kaustophilus HTA426 provide thermostable 6-phospho-β-glycosidase and β-fucosidase. Appl Microbiol Biotechnol 97: 2929-2938.
47. Tabachnikov, O., and Shoham, Y. (2013) Functional characterization of the galactan utilization system of Geobacillus stearothermophilus. FEBS J 280: 950-964.
48. Takami, H., Takaki, Y., Chee, G.-J., Nishi, S., Shimamura, S., Suzuki, H., etal. (2004) Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res 32: 6292-6303.
49. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725-2729.
50. Taylor, M.P., Eley, K.L., Martin, S., Tuffin, M.I., Burton, S.G., and Cowan, D.A. (2009) Thermophilic ethanologenesis: future prospects for second-generation bioethanol production. Trends Biotechnol 27: 398-405.
51. Taylor, M.P., Zyl, L., van Tuffin, I.M., Leak, D.J., and Cowan, D.A. (2011) Genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts. Microb Biotechnol 4: 438-448.
52. Thompson, A.H., Studholme, D.J., Green, E.M., and Leak, D.J. (2008) Heterologous expression of pyruvate decarboxylase in Geobacillus thermoglucosidasius. Biotechnol Lett 30: 1359-1365.
53. Vallier, H., and Welker, N.E. (1990) Genetic map of the Bacillus stearothermophilus NUB36 chromosome. J Bacteriol 172: 793-801.
54. Wiegand, S., Rabausch, U., Chow, J., Daniel, R., Streit, W.R., and Liesegang, H. (2013) Complete genome sequence of Geobacillus sp. strain GHH01, a thermophilic lipase-secreting bacterium. Genome Announc 1: e0009213. doi:10.1128/genomeA.00092-13.
55. Wiegel, J., Ljungdahl, L.G., and Demain, A.L. (1985) The importance of thermophilic bacteria in biotechnology. Crit Rev Biotechnol 3: 39-108.
56. Wu, L., and Welker, N.E. (1991) Temperature-induced prote in synthesis in Bacillus stearothermophilus NUB36. J Bacteriol 173: 4889-4892.
57. Wu, L.J., and Welker, N.E. (1989) Protoplast transformation of Bacillus stearothermophilus NUB36 by plasmid DNA. J Gen Microbiol 135: 1315-1324.
58. Xu, K., Su, F., Tao, F., Li, C., Ni, J., and Xu, P. (2013) Genome sequences of two morphologically distinct and thermophilic Bacillus coagulans strains, H-1 and XZL9. Genome Announc 1: 4563-4564.
59. Yao, N., Ren, Y., and Wang, W. (2013) Genome sequence of a thermophilic Bacillus, Geobacillus thermodenitrificans DSM465. Genome Announc 1: pii: e01046-13. doi:10.1128/genomeA.01046-13.
60. Zeigler, D.R. (2005) Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus. Int J Syst Evol Microbiol 55: 1171-1179.
61. Zeigler, D.R. (2014) The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet? Microbiology 160: 1-11.
62. Zhao, Y., Caspers, M.P., Abee, T., Siezen, R.J., and Kort, R. (2012) Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment. J Bacteriol 194: 4118.