1887

Abstract

Investigation of essential genes, besides contributing to understanding the fundamental principles of life, has numerous practical applications. Essential genes can be exploited as building blocks of a tightly controlled cell ‘chassis’. and K-12 are both well-characterized model bacteria used as hosts for a plethora of biotechnological applications. Determination of the essential genes that constitute the and minimal genomes is therefore of the highest importance. Recent advances have led to the modification of the original and essential gene sets identified 10 years ago. Furthermore, significant progress has been made in the area of genome minimization of both model bacteria. This review provides an update, with particular emphasis on the current essential gene sets and their comparison with the original gene sets identified 10 years ago. Special attention is focused on the genome reduction analyses in and and the construction of minimal cell factories for industrial applications.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.079376-0
2014-11-01
2019-11-12
Loading full text...

Full text loading...

/deliver/fulltext/micro/160/11/2341.html?itemId=/content/journal/micro/10.1099/mic.0.079376-0&mimeType=html&fmt=ahah

References

  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  6. Bergmiller T., Ackermann M., Silander O. K.. ( 2012;). Patterns of evolutionary conservation of essential genes correlate with their compensability. . PLoS Genet 8:, e1002803. [CrossRef]
    [Google Scholar]
  7. Bielaszewska M., Mellmann A., Zhang W., Köck R., Fruth A., Bauwens A., Peters G., Karch H.. ( 2011;). Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. . Lancet Infect Dis 11:, 671–676. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  9. Boutros M., Ahringer J.. ( 2008;). The art and design of genetic screens: RNA interference. . Nat Rev Genet 9:, 554–566. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  11. Bumann D.. ( 2008;). Has nature already identified all useful antibacterial targets?. Curr Opin Microbiol 11:, 387–392. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  15. Clements A., Young J. C., Constantinou N., Frankel G.. ( 2012;). Infection strategies of enteric pathogenic Escherichia coli. . Gut Microbes 3:, 71–87. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  22. Copley S. D.. ( 2012;). Moonlighting is mainstream: paradigm adjustment required. . Bioessays 34:, 578–588. [CrossRef]
    [Google Scholar]
  23. Corrigan R. M., Gründling A.. ( 2013;). Cyclic di-AMP: another second messenger enters the fray. . Nat Rev Microbiol 11:, 513–524. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  28. Esvelt K. M., Wang H. H.. ( 2013;). Genome-scale engineering for systems and synthetic biology. . Mol Syst Biol 9:, 641. [CrossRef]
    [Google Scholar]
  29. Fehér T., Papp B., Pal C., Pósfai G.. ( 2007;). Systematic genome reductions: theoretical and experimental approaches. . Chem Rev 107:, 3498–3513. [CrossRef]
    [Google Scholar]
  30. Fehér T., Burland V., Pósfai G.. ( 2012;). In the fast lane: large-scale bacterial genome engineering. . J Biotechnol 160:, 72–79. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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 reduced-genome Escherichia coli. . J Biosci Bioeng 116:, 52–58. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  43. Hung C. L., Hua G. J.. ( 2014;). Local alignment tool based on Hadoop framework and GPU architecture. . Biomed Res Int 2014:, 541490. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  45. Itaya M.. ( 2010;). A synthetic DNA transplant. . Nat Biotechnol 28:, 687–689. [CrossRef]
    [Google Scholar]
  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.
    [Google Scholar]
  47. Jewett M. C., Forster A. C.. ( 2010;). Update on designing and building minimal cells. . Curr Opin Biotechnol 21:, 697–703. [CrossRef]
    [Google Scholar]
  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] [CrossRef]
    [Google Scholar]
  49. Juhas M., Eberl L., Glass J. I.. ( 2011;). Essence of life: essential genes of minimal genomes. . Trends Cell Biol 21:, 562–568. [CrossRef]
    [Google Scholar]
  50. Juhas M., Eberl L., Church G. M.. ( 2012a;). Essential genes as antimicrobial targets and cornerstones of synthetic biology. . Trends Biotechnol 30:, 601–607. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  53. Kato J., Hashimoto M.. ( 2007;). Construction of consecutive deletions of the Escherichia coli chromosome. . Mol Syst Biol 3:, 132. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  59. Kolisnychenko V., Plunkett G., Herring C. D., Fehér T., Pósfai J., Blattner F. R., Pósfai G.. ( 2002;). Engineering a reduced Escherichia coli genome. . Genome Res 12:, 640–647. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  61. Kunst F., Ogasawara N., Moszer I., Albertini A. M., Alloni G., Azevedo V., Bertero M. G., Bessières P., Bolotin A.. & other authors ( 1997;). The complete genome sequence of the gram-positive bacterium Bacillus subtilis. . Nature 390:, 249–256. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  68. Leimbach A., Hacker J., Dobrindt U.. ( 2013;). E. coli as an all-rounder: the thin line between commensalism and pathogenicity. . Curr Top Microbiol Immunol 358:, 3–32.
    [Google Scholar]
  69. Li M. Z., Elledge S. J.. ( 2007;). Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. . Nat Methods 4:, 251–256. [CrossRef]
    [Google Scholar]
  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 genome-reduced Bacillus subtilis strain MGB874. . Appl Environ Microbiol 77:, 8370–8381. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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.
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  76. Mehne F. M., Gunka K., Eilers H., Herzberg C., Kaever V., Stülke 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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  79. Mizoguchi H., Mori H., Fujio T.. ( 2007;). Escherichia coli minimum genome factory. . Biotechnol Appl Biochem 46:, 157–167. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  83. Nandagopal N., Elowitz M. B.. ( 2011;). Synthetic biology: integrated gene circuits. . Science 333:, 1244–1248. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  88. Pósfai G., Plunkett G., Fehér T.. & other authors ( 2006;). Emergent properties of reduced-genome Escherichia coli. . Science 312:, 1044–1046. [CrossRef]
    [Google Scholar]
  89. Quan J., Tian J.. ( 2009;). Circular polymerase extension cloning of complex gene libraries and pathways. . PLoS ONE 4:, e6441. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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 hemolytic-uremic syndrome in Germany. . N Engl J Med 365:, 709–717. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  97. Simonen M., Palva I.. ( 1993;). Protein secretion in Bacillus species. . Microbiol Rev 57:, 109–137.
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  107. Zhang Y., Werling U., Edelmann W.. ( 2012;). SLiCE: a novel bacterial cell extract-based DNA cloning method. . Nucleic Acids Res 40:, e55. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
  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. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.079376-0
Loading
/content/journal/micro/10.1099/mic.0.079376-0
Loading

Data & Media loading...

Supplements

Supplementary Data 

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error