Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering

Microbiology (United Kingdom)

Volumn 160, Issue , 2014, Pages 2341-2351

  Juhas, Mario ^a   Reuß, Daniel R ^b   Zhu, Bingyao ^b   Commichau, Fabian M ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; BACTERIAL PROTEIN;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL CELL; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; ESCHERICHIA COLI; ESSENTIAL GENE; GENE INSERTION SEQUENCE; GENE MUTATION; GENETIC ENGINEERING; NONHUMAN; GENETICS; METABOLIC ENGINEERING; METABOLISM; MICROBIOLOGY;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; ESCHERICHIA COLI; GENES, ESSENTIAL; GENOME, BACTERIAL; INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING;

EID: 84932150341     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.079376-0     Document Type: Article

References (110)

1. Ajikumar, P. K., Xiao, W. H., Tyo, K. E., Wang, Y., Simeon, F., Leonard, E., Mucha, O., Phon, T. H., Pfeifer, B. & Stephanopoulos, G. (2010). Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 330, 70–74.
2. Akanuma, G., Nanamiya, H., Natori, Y., Yano, K., Suzuki, S., Omata, S., Ishizuka, M., Sekine, Y. & Kawamura, F. (2012). Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation. J Bacteriol 194, 6282–6291.
3. Annaluru, N., Muller, H., Mitchell, L. A., Ramalingam, S., Stracquadanio, G., Richardson, S. M., Dymond, J. S., Kuang, Z., Scheifele, L. Z. & other authors (2014). Total synthesis of a functional designer eukaryotic chromosome. Science 344, 55–58.
4. Ara, K., Ozaki, K., Nakamura, K., Yamane, K., Sekiguchi, J. & Ogasawara, N. (2007). Bacillus minimum genome factory: effective utilization of microbial genome information. Biotechnol Appl Biochem 46, 169–178.
5. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L. & Mori, H. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2, 2006.0008.
6. Bergmiller, T., Ackermann, M. & Silander, O. K. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genet 8, e1002803.
7. Bielaszewska, M., Mellmann, A., Zhang, W., Koöck, R., Fruth, A., Bauwens, A., Peters, G. & Karch, H. (2011). Characterisation of theEscherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. Lancet Infect Dis 11, 671–676.
8. Blattner, F. R., Plunkett, G., Bloch, C. A. & other authors (1997). The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1462.
9. Boutros, M. & Ahringer, J. (2008). The art and design of genetic screens: RNA interference. Nat Rev Genet 9, 554–566.
10. Buescher, J. M., Liebermeister, W., Jules, M., Uhr, M., Muntel, J., Botella, E., Hessling, B., Kleijn, R. J., Le Chat, L. & other authors (2012). Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 335, 1099–1103.
11. Bumann, D. (2008). Has nature already identified all useful antibacterial targets? Curr Opin Microbiol 11, 387–392.
12. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A. & other authors (2014). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42 (D1), D459–D471.
13. Chen, X., Zhou, L., Tian, K., Kumar, A., Singh, S., Prior, B. A. & Wang, Z. (2013). Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production. Biotechnol Adv 31, 1200–1223.
14. Christen, B., Abeliuk, E., Collier, J. M., Kalogeraki, V. S., Passarelli, B., Coller, J. A., Fero, M. J., McAdams, H. H. & Shapiro, L. (2011). The essential genome of a bacterium. Mol Syst Biol 7, 528.
15. Clements, A., Young, J. C., Constantinou, N. & Frankel, G. (2012). Infection strategies of enteric pathogenic Escherichia coli. Gut Microbes 3, 71–87.
16. Clomburg, J. M. & Gonzalez, R. (2010). Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 86, 419–434.
17. Clomburg, J. M. & Gonzalez, R. (2011). Metabolic engineering of Escherichia coli for the production of 1,2-propanediol from glycerol. Biotechnol Bioeng 108, 867–879.
18. Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O. & Stülke, J. (2007). A regulatory protein–protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65, 642–654.
19. Commichau, F. M., Pietack, N. & Stülke, J. (2013). Essential genes in Bacillus subtilis: a re-evaluation after ten years. Mol Biosyst 9, 1068–1075.
20. Commichau, F. M., Alzinger, A., Sande, R., Bretzel, W., Meyer, F. M., Chevreux, B., Wyss, M., Hohmann, H. P. & Prágai, Z. (2014). Overexpression of a non-native deoxyxylulose-dependent vitamin B6 pathway in Bacillus subtilis for the production of pyridoxine. Metab Eng 25, 38–49.
21. Conrad, T. M., Frazier, M., Joyce, A. R., Cho, B. K., Knight, E. M., Lewis, N. E., Landick, R. & Palsson, B. (2010). RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci U S A 107, 20500–20505.
22. Copley, S. D. (2012). Moonlighting is mainstream: paradigm adjustment required. Bioessays 34, 578–588.
23. Corrigan, R. M. & Gründling, A. (2013). Cyclic di-AMP: another second messenger enters the fray. Nat Rev Microbiol 11, 513–524.
24. de Berardinis, V., Vallenet, D., Castelli, V., Besnard, M., Pinet, A., Cruaud, C., Samair, S., Lechaplais, C., Gyapay, G. & other authors (2008). A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol 4, 174.
25. de Kok, S., Stanton, L. H., Slaby, T. & other authors (2014). Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth Biol 3, 97–106.
26. Dorenbos, R., Stein, T., Kabel, J., Bruand, C., Bolhuis, A., Bron, S., Quax, W. J. & Van Dijl, J. M. (2002). Thiol-disulfide oxidoreductases are essential for the production of the lantibiotic sublancin 168. J Biol Chem 277, 16682–16688.
27. Durand, S., Gilet, L. & Condon, C. (2012). The essential function of B. subtilis RNase III is to silence foreign toxin genes. PLoS Genet 8, e1003181.
28. Esvelt, K. M. & Wang, H. H. (2013). Genome-scale engineering for systems and synthetic biology. Mol Syst Biol 9, 641.
29. Fehér, T., Papp, B., Pal, C. & Pósfai, G. (2007). Systematic genome reductions: theoretical and experimental approaches. Chem Rev 107, 3498–3513.
30. Fehér, T., Burland, V. & Pósfai, G. (2012). In the fast lane: large-scale bacterial genome engineering. J Biotechnol 160, 72–79.
31. Figaro, S., Durand, S., Gilet, L., Cayet, N., Sachse, M. & Condon, C. (2013). Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence. J Bacteriol 195, 2340–2348.
32. French, C. T., Lao, P., Loraine, A. E., Matthews, B. T., Yu, H. & Dybvig, K. (2008). Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol 69, 67–76.
33. Gerdes, S., Scholle, M., Campbell, J., Balazsi, G., Ravasz, E., Daugherty, M. D., Somera, A. L., Kyrpides, N. C., Anderson, I. & other authors (2003). Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185, 5673–5684.
34. Gibson, D., Young, L., Chuang, R., Venter, J., Hutchison, C. & Smith, H. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6, 343–345.
35. Gibson, D., Glass, J., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L. & other authors (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56.
36. Gunka, K., Stannek, L., Care, R. A. & Commichau, F. M. (2013). Selection-driven accumulation of suppressor mutants in Bacillus subtilis: the apparent high mutation frequency of the cryptic gudB gene and the rapid clonal expansion of gudB+ suppressors are due to growth under selection. PLoS ONE 8, e66120.
37. Hao, T., Han, B., Ma, H., Fu, J., Wang, H., Wang, Z., Tang, B., Chen, T. & Zhao, X. (2013). In silico metabolic engineering of Bacillus subtilis for improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol and isobutanol. Mol Biosyst 9, 2034–2044.
38. Hashimoto, M., Ichimura, T., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., Ote, T., Yamakawa, T., Yamazaki, Y. & other authors (2005). Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55, 137–149.
39. Hemm, M. R., Paul, B. J., Schneider, T. D., Storz, G. & Rudd, K. E. (2008). Small membrane proteins found by comparative genomics and ribosome binding site models. Mol Microbiol 70, 1487–1501.
40. Hemm, M. R., Paul, B. J., Miranda-Ríos, J., Zhang, A., Soltanzad, N. & Storz, G. (2010). Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies. J Bacteriol 192, 46–58.
41. Hirokawa, Y., Kawano, H., Tanaka-Masuda, K., Nakamura, N., Nakagawa, A., Ito, M., Mori, H., Oshima, T. & Ogasawara, N. (2013). Genetic manipulations restored the growth fitness of reducedgenome Escherichia coli. J Biosci Bioeng 116, 52–58.
42. Hobbs, E. C., Astarita, J. L. & Storz, G. (2010). Small RNAs and small proteins involved in resistance to cell envelope stress and acid shock in Escherichia coli: analysis of a bar-coded mutant collection. J Bacteriol 192, 59–67.
43. Hung, C. L. & Hua, G. J. (2014). Local alignment tool based on Hadoop framework and GPU architecture. Biomed Res Int 2014, 541490.
44. Hunt, A., Rawlins, J. P., Thomaides, H. B. & Errington, J. (2006). Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895–2907.
45. Itaya, M. (2010). A syntheticDNA transplant. Nat Biotechnol 28, 687–689.
46. Jensen, K. F. (1993). The Escherichia coli K-12 ‘‘wild types’’ W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol 175, 3401–3407.
47. Jewett, M. C. & Forster, A. C. (2010). Update on designing and building minimal cells. Curr Opin Biotechnol 21, 697–703.
48. Juhas, M. (2013). Horizontal gene transfer in human pathogens. Crit Rev Microbiol 1–8. doi:10.3109/1040841X.2013.804031 [Epub ahead of print]
49. Juhas, M., Eberl, L. & Glass, J. I. (2011). Essence of life: essential genes of minimal genomes. Trends Cell Biol 21, 562–568.
50. Juhas, M., Eberl, L. & Church, G. M. (2012a). Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol 30, 601–607.
51. Juhas, M., Stark, M., von Mering, C., Lumjiaktase, P., Crook, D. W., Valvano, M. A. & Eberl, L. (2012b). High confidence prediction of essential genes in Burkholderia cenocepacia. PLoS ONE 7, e40064.
52. Juhas, M., Davenport, P. W., Brown, J. R., Yarkoni, O. & Ajioka, J. W. (2013). Meeting report: The Cambridge BioDesign TechEvent – Synthetic Biology, a new ‘‘Age of Wonder’’? Biotechnol J 8, 761–763.
53. Kato, J. & Hashimoto, M. (2007). Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol 3, 132.
54. Kato, J. & Hashimoto, M. (2008). Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome. Methods Mol Biol 416, 279–293.
55. Keseler, I. M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama- Castro, S., Bonavides-Martinez, C., Fulcher, C., Huerta, A. M., Kothari, A. & other authors (2013). EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 41 (D1), D605–D612.
56. Kim, J. & Copley, S. D. (2012). Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network. Proc Natl Acad Sci U S A 109, E2856–E2864.
57. Kobayashi, K., Ehrlich, S., Albertini, A., Amati, G., Andersen, K. K., Arnaud, M., Asai, K., Ashikaga, S., Aymerich, S. & other authors (2003). Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100, 4678–4683.
58. Kohlstedt, M., Sappa, P. K., Meyer, H., Maaß, S., Zaprasis, A., Hoffmann, T., Becker, J., Steil, L., Hecker, M. & other authors (2014). Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective. Environ Microbiol 16, 1898–1917.
59. Kolisnychenko, V., Plunkett, G., Herring, C. D., Fehér, T., Pósfai, J., Blattner, F. R. & Po´ sfai, G. (2002). Engineering a reduced Escherichia coli genome. Genome Res 12, 640–647.
60. Kosuri, S., Eroshenko, N., Leproust, E. M., Super, M., Way, J., Li, J. B. & Church, G. M. (2010). Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol 28, 1295–1299.
61. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessiéres, P., Bolotin, A. & other authors (1997). The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390, 249–256.
62. Lam, C. M., Suárez Diez, M., Godinho, M. & Martins dos Santos, V. A. (2012). Programmable bacterial catalysis – designing cells for biosynthesis of value-added compounds. FEBS Lett 586, 2184–2190.
63. Langridge, G. C., Phan, M. D., Turner, D. J., Perkins, T. T., Parts, L., Haase, J., Charles, I., Maskell, D. J., Peters, S. E. & other authors (2009). Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome Res 19, 2308–2316.
64. Lartigue, C., Glass, J., Alperovich, N., Pieper, R., Parmar, P., Hutchison, C., Smith, H. & Venter, J. (2007). Genome transplantation in bacteria: changing one species to another. Science 317, 632–638.
65. Lartigue, C., Vashee, S., Algire, M., Chuang, R.-Y., Benders, G. A., Ma, L., Noskov, V. N., Denisova, E. A., Gibson, D. G. & other authors (2009). Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325, 1693–1696.
66. Lawther, R. P., Calhoun, D. H., Adams, C. W., Hauser, C. A., Gray, J. & Hatfield, G. W. (1981). Molecular basis of valine resistance in Escherichia coli K-12. Proc Natl Acad Sci U S A 78, 922–925.
67. Lee, J. H., Sung, B. H., Kim, M. S., Blattner, F. R., Yoon, B. H., Kim, J. H. & Kim, S. C. (2009). Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production. Microb Cell Fact 8, 2.
68. Leimbach, A., Hacker, J. & Dobrindt, U. (2013). E. coli as an allrounder: the thin line between commensalism and pathogenicity. Curr Top Microbiol Immunol 358,3–32.
69. Li, M. Z. & Elledge, S. J. (2007). Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4, 251–256.
70. Manabe, K., Kageyama, Y., Morimoto, T., Ozawa, T., Sawada, K., Endo, K., Tohata, M., Ara, K., Ozaki, K. & Ogasawara, N. (2011). Combined effect of improved cell yield and increased specific productivity enhances recombinant enzyme production in genomereduced Bacillus subtilis strain MGB874. Appl Environ Microbiol 77, 8370–8381.
71. Manabe, K., Kageyama, Y., Morimoto, T., Shimizu, E., Takahashi, H., Kanaya, S., Ara, K., Ozaki, K. & Ogasawara, N. (2013). Improved production of secreted heterologous enzyme in Bacillus subtilis strain MGB874 via modification of glutamate metabolism and growth conditions. Microb Cell Fact 12, 18.
72. Matzas, M., Stähler, P. F., Kefer, N., Siebelt, N., Boisguérin, V., Leonard, J. T., Keller, A., Stähler, C. F., Häberle, P. & other authors (2010). High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol 28, 1291–1294.
73. McCutcheon, J. P. & Moran, N. A. (2010). Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution. Genome Biol Evol 2, 708–718.
74. McIntosh, B. K., Renfro, D. P., Knapp, G. S., Lairikyengbam, C. R., Liles, N. M., Niu, L., Supak, A. M., Venkatraman, A., Zweifel, A. E. & other authors (2012). EcoliWiki: a wiki-based community resource for Escherichia coli. Nucleic Acids Res 40 (D1), D1270–D1277.
75. McKenney, P. T., Driks, A. & Eichenberger, P. (2013). The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nat Rev Microbiol 11, 33–44.
76. Mehne, F. M., Gunka, K., Eilers, H., Herzberg, C., Kaever, V. & Stu¨ lke, J. (2013). Cyclic di-AMP homeostasis in Bacillus subtilis: both lack and high level accumulation of the nucleotide are detrimental for cell growth. J Biol Chem 288, 2004–2017.
77. Mellmann, A., Harmsen, D., Cummings, C. A., Zentz, E. B., Leopold, S. R., Rico, A., Prior, K., Szczepanowski, R., Ji, Y. & other authors (2011). Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS ONE 6, e22751.
78. Michna, R. H., Commichau, F. M., Tödter, D., Zschiedrich, C. P. & Stülke, J. (2014). SubtiWiki – a database for the model organism Bacillus subtilis that links pathway, interaction and expression information. Nucleic Acids Res 42 (D1), D692–D698.
79. Mizoguchi, H., Mori, H. & Fujio, T. (2007). Escherichia coli minimum genome factory. Biotechnol Appl Biochem 46, 157–167.
80. Mizoguchi, H., Sawano, Y., Kato, J. & Mori, H. (2008). Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome. DNA Res 15, 277–284.
81. Morimoto, T., Kadoya, R., Endo, K., Tohata, M., Sawada, K., Liu, S., Ozawa, T., Kodama, T., Kakeshita, H. & other authors (2008). Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res 15, 73–81.
82. Moya, A., Gil, R., Latorre, A., Peretó, J., Pilar Garcillán-Barcia, M. & de la Cruz, F. (2009). Toward minimal bacterial cells: evolution vs. design. FEMS Microbiol Rev 33, 225–235.
83. Nandagopal, N. & Elowitz, M. B. (2011). Synthetic biology: integrated gene circuits. Science 333, 1244–1248.
84. Nicolas, P., Mäder, U., Dervyn, E., Rochat, T., Leduc, A., Pigeonneau, N., Bidnenko, E., Marchadier, E., Hoebeke, M. & other authors (2012). Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335, 1103–1106.
85. O’Connor, M. & Gregory, S. T. (2011). Inactivation of the RluD pseudouridine synthase has minimal effects on growth and ribosome function in wild-type Escherichia coli and Salmonella enterica. J Bacteriol 193, 154–162.
86. Park, S. J., Lee, T. W., Lim, S. C., Kim, T. W., Lee, H., Kim, M. K., Lee, S. H., Song, B. K. & Lee, S. Y. (2012). Biosynthesis of polyhydroxyalkanoates containing 2-hydroxybutyrate from unrelated carbon source by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 93, 273–283.
87. Pitera, D. J., Paddon, C. J., Newman, J. D. & Keasling, J. D. (2007). Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab Eng 9, 193–207.
88. Pósfai, G., Plunkett, G., Fehér, T. & other authors (2006). Emergent properties of reduced-genome Escherichia coli. Science 312, 1044–1046.
89. Quan, J. & Tian, J. (2009). Circular polymerase extension cloning of complex gene libraries and pathways. PLoS ONE 4, e6441.
90. Quan, J. & Tian, J. (2011). Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc 6, 242–251.
91. Rasko, D. A., Rosovitz, M. J., Myers, G. S., Mongodin, E. F., Fricke, W. F., Gajer, P., Crabtree, J., Sebaihia, M., Thomson, N. R. & other authors (2008). The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190, 6881–6893.
92. Rasko, D. A., Webster, D. R., Sahl, J. W., Bashir, A., Boisen, N., Scheutz, F., Paxinos, E. E., Sebra, R., Chin, C.-S. & other authors (2011). Origins of the E. coli strain causing an outbreak of hemolyticuremic syndrome in Germany. N Engl J Med 365, 709–717.
93. Sandmann, G. (2002). Combinatorial biosynthesis of carotenoids in a heterologous host: a powerful approach for the biosynthesis of novel structures. ChemBioChem 3, 629–635.
94. Schallmey, M., Singh, A. & Ward, O. P. (2004). Developments in the use of Bacillus species for industrial production. Can J Microbiol 50, 1–17.
95. Seo, S. W., Yang, J., Min, B. E., Jang, S., Lim, J. H., Lim, H. G., Kim, S. C., Kim, S. Y., Jeong, J. H. & Jung, G. Y. (2013). Synthetic biology: tools to design microbes for the production of chemicals and fuels. Biotechnol Adv 31, 811–817.
96. Shi, S., Chen, T., Zhang, Z., Chen, X. & Zhao, X. (2009). Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production. Metab Eng 11, 243–252.
97. Simonen, M. & Palva, I. (1993). Protein secretion in Bacillus species. Microbiol Rev 57, 109–137.
98. Tanaka, K., Henry, C. S., Zinner, J. F., Jolivet, E., Cohoon, M. P., Xia, F., Bidnenko, V., Ehrlich, S. D., Stevens, R. L. & Noirot, P. (2013). Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res 41, 687–699.
99. Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., Bingen, E., Bonacorsi, S., Bouchier, C. & other authors (2009). Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5, e1000344.
100. Trinh, C. T., Unrean, P. & Srienc, F. (2008). Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol 74, 3634–3643.
101. Wang, Q., Zhang, Y., Yang, C., Xiong, H., Lin, Y., Yao, J., Li, H., Xie, L., Zhao, W. & other authors (2010). Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327, 1004–1007.
102. Westers, H., Dorenbos, R., van Dijl, J. M. & other authors (2003). Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol 20, 2076–2090.
103. Yano, K., Wada, T., Suzuki, S., Tagami, K., Matsumoto, T., Shiwa, Y., Ishige, T., Kawaguchi, Y., Masuda, K. & other authors (2013). Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis. Microbiology 159, 2225–2236.
104. Yim, H., Haselbeck, R., Niu, W., Pujol-Baxley, C., Burgard, A., Boldt, J., Khandurina, J., Trawick, J. D., Osterhout, R. E. & other authors (2011). Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7, 445–452.
105. Yu, B., Sung, B., Koob, M., Lee, C., Lee, J., Lee, W., Kim, M. & Kim, S. (2002). Minimization of the Escherichia coli genome using a Tn5- targeted Cre/loxP excision system. Nat Biotechnol 20, 1018–1023.
106. Yu, B. J., Kang, K. H., Lee, J. H., Sung, B. H., Kim, M. S. & Kim, S. C. (2008). Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res 36, e84.
107. Zhang, Y., Werling, U. & Edelmann, W. (2012). SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res 40, e55.
108. Zhou, L., Niu, D. D., Tian, K. M., Chen, X. Z., Prior, B. A., Shen, W., Shi, G. Y., Singh, S. & Wang, Z. X. (2012a). Genetically switched D-lactate production in Escherichia coli. Metab Eng 14, 560–568.
109. Zhou, L., Tian, K. M., Niu, D. D., Shen, W., Shi, G. Y., Singh, S. & Wang, Z. X. (2012b). Improvement of D-lactate productivity in recombinant Escherichia coli by coupling production with growth. Biotechnol Lett 34, 1123–1130.
110. Zweers, J. C., Barák, I., Becher, D., Driessen, A. J., Hecker, M., Kontinen, V. P., Saller, M. J., Vavrová, L. & van Dijl, J. M. (2008). Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes. Microb Cell Fact 7, 10.