Publikationsserver der Universitätsbibliothek Marburg

Titel:Konstruktion, Charakterisierung und Optimierung des synthetischen, sekundären Chromosoms synVicII in Escherichia coli
Autor:Messerschmidt, Sonja
Weitere Beteiligte: Waldminghaus, Torsten (Prof. Dr.)
Veröffentlicht:2016
URI:https://archiv.ub.uni-marburg.de/diss/z2016/0944
DOI: https://doi.org/10.17192/z2016.0944
URN: urn:nbn:de:hebis:04-z2016-09440
DDC: Biowissenschaften, Biologie
Titel (trans.):Construction, characterization and optimization of the synthetic, secondary chromosome synVicII in Escherichia coli
Publikationsdatum:2016-12-15
Lizenz:https://creativecommons.org/licenses/by-nc-nd/4.0/

Dokument

Schlagwörter:
Replikation, Synthetic Microbiology, Escherichia coli, secondary replicon, sekundäres Replikon, DNA replication, Synthetische Biologie

Zusammenfassung:
Synthetische, sekundäre Chromosomen sind ein wertvolles Werkzeug, um Chromosomenorganisationssysteme zu untersuchen. Anhand ihres Designs, ihrer Assemblierung und ihrer Charakterisierung können auch wichtige Konstruktionsregeln für synthetische Chromosomen abgeleitet werden. In der Biotechnologie könnten außerdem synthetische, sekundäre Chromosomen genutzt werden, um Mikroorganismen genetisch zu verändern. Für alle Anwendungen ist es wichtig, dass das verwendete synthetische, sekundäre Replikon gut charakterisiert und beschrieben worden ist. In dieser Arbeit wurde das synthetische, sekundäre Chromosom synVicII im monochromosomalen Bakterium Escherichia coli etabliert und charakterisiert. Als Vorbild für synVicII diente das natürlich vorkommende sekundäre Chromosom II von Vibrio cholerae, einem Bakterium, welches zwei unterschiedlich große Chromosomen besitzt. So wurden der Replikationsursprung des zweiten V. cholerae Chromosoms oriII, das Initiatorgen rctB und das eigene Chromosomen II Segregationssystem parABII in synVicII integriert. Transformation in E. coli bewies, dass synVicII erfolgreich in E. coli replizieren kann. Für die effiziente Assemblierung, Modifizierung und den Transfer von synVicII wurden verschiedene Elemente eingebaut: Beispielsweise macht ein integrierter oriT synVicII konjugierbar, ein Hefereplikationsursprung und ein Selektionsmarker erlauben die Assemblierung in S. cerevisiae und eine Flp-FRT-Kassette erlaubt die Entfernung von nur für die Konstruktion wichtigen Elementen. SynVicII wurde ModularCloning kompatibel entwickelt, sodass schnell und effizient neue DNA-Sequenzen eingebaut werden können. Im zweiten Teil dieser Arbeit wurde synVicII auf wesentliche Charakteristika bakterieller Chromosomen wie die Stabilität, die Kopienzahl und die genetische Integrität untersucht. Mit einem neu entwickelten Durchflusszytometrie-basierten Stabilitätstest konnte gezeigt werden, dass synVicII deutlich stabiler als ein oriC-basiertes Replikon, synEsc, ist. Ein Plattentest bestätigte die mit dem neu entwickelten Durchflusszytometrie-basierten Stabilitätstest bestimmte Replikonverlustrate von synVicII. Der Plattentest demonstrierte auch, dass synVicII instabiler als ein 100 % stabiles synF-Plasmid ist. Mit einem neu entwickelten Evolutionsexperiment konnten neue stabilere synVicII-Varianten entwickelt und identifiziert werden. synVicII besitzt in E. coli eine vergleichbar niedrige Kopienzahl relativ zu oriC, was anhand von qPCR und Microarray-Analysen geklärt werden konnte. Die Kopienzahl-Analyse deutete sogar darauf hin, dass synVicII in E. coli ähnlich wie das zweite Chromosom in V. cholerae repliziert. Demnach startet synVicII vermutlich später die DNA-Replikation als das E. coli Chromosom. Southern Blot Analysen demonstrierten, dass synVicII im Gegensatz zu synEsc nicht in das E. coli Chromosom integriert. Neben sekundären Chromosomen könnten auch noch zusätzlich tertiäre Chromosomen in der Biotechnologie zum Einsatz kommen. Deswegen wurde die Diversität der sekundären Chromosomen von Vibrionaceae untersucht. Marker-Frequency-Analysen deuten darauf hin, dass alle sekundären Chromosomen in den 11 untersuchten Vertretern der Vibrionaceae die DNA-Replikation später initiieren als das erste Chromosom und beide Chromosomen zusammen terminieren. Neun neue synthetische Chromosomen mit verschiedenen Vibrionaceae Replikationsursprüngen wurden assembliert und ihre Eignung als tertiäres Chromosom initial getestet. Mit Konjugationstests wurde demonstriert, dass alle verwendeten Vibrionaceae Replikationsursprünge untereinander nicht kompatibel sind. Zusammengefasst besitzt synVicII mit seinen bisherigen charakterisierten Chromosomeneigenschaften schon großes Potenzial, um in der Grundlagenforschung und Biotechnologie eingesetzt werden zu können.

Bibliographie / References

  1. Venkova-Canova, T., Saha, A. and Chattoraj, D.K., 2012. A 29-mer site regulates transcription of the initiator gene as well as function of the replication origin of Vibrio cholerae chromosome II. Plasmid. 67, 102-10.
  2. Val, M.E., Marbouty, M., de Lemos Martins, F., Kennedy, S.P., Kemble, H., Bland, M.J., Possoz, C., Koszul, R., Skovgaard, O. and Mazel, D., 2016. A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae. Sci Adv. 2, e1501914.
  3. Borodina, I. and Nielsen, J., 2014. Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnol J. 9, 609-620.
  4. Zhang, G., Wang, W., Deng, A., Sun, Z., Zhang, Y., Liang, Y., Che, Y. and Wen, T., 2012. A mimicking-ofDNA-methylation-patterns pipeline for overcoming the restriction barrier of bacteria. PLoS Genet. 8, e1002987.
  5. Mulcair, M.D., Schaeffer, P.M., Oakley, A.J., Cross, H.F., Neylon, C., Hill, T.M. and Dixon, N.E., 2006. A molecular mousetrap determines polarity of termination of DNA replication in E. coli. Cell. 125, 1309-19.
  6. Jang, K.H., Chambers, P.J. and Britz, M.L., 1996. Analysis of nucleotide methylation in DNA from Corynebacterium glutamicum and related species. FEMS Microbiol Lett. 136, 309-15.
  7. Asai, T., Bates, D.B., Boye, E. and Kogoma, T., 1998. Are minichromosomes valid model systems for DNA replication control? Lessons learned from Escherichia coli. Mol Microbiol. 29, 671-5.
  8. Duigou, S., Yamaichi, Y. and Waldor, M.K., 2008. ATP negatively regulates the initiator protein of Vibrio cholerae chromosome II replication. Proc Natl Acad Sci U S A. 105, 10577-82.
  9. Juhas, M., Reuss, D.R., Zhu, B. and Commichau, F.M., 2014. Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering. Microbiology. 160, 2341-51.
  10. Westers, L., Westers, H. and Quax, W.J., 2004. Bacillus subtilis as cell factory for pharmaceutical proteins: a biotechnological approach to optimize the host organism. Biochimica Et Biophysica Acta-Molecular Cell Research. 1694, 299-310.
  11. Ochman, H., 2002. Bacterial evolution: chromosome arithmetic and geometry. Curr Biol. 12, R427-8.
  12. Jain, A. and Srivastava, P., 2013. Broad host range plasmids. FEMS Microbiol Lett. 348, 87-96.
  13. Leonard, A.C. and Helmstetter, C.E., 1986. Cell cycle-specific replication of Escherichia coli minichromosomes. Proc Natl Acad Sci U S A. 83, 5101-5.
  14. Steiner, W.W. and Kuempel, P.L., 1998. Cell division is required for resolution of dimer chromosomes at the dif locus of Escherichia coli. Mol Microbiol. 27, 257-68.
  15. Wadood, A., Dohmoto, M., Sugiura, S. and Yamaguchi, K., 1997. Characterization of copy number mutants of plasmid pSC101. J Gen Appl Microbiol. 43, 309-316.
  16. Cello, J., Paul, A.V. and Wimmer, E., 2002. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 297, 1016-8.
  17. Lobner-Olesen, A. and von Freiesleben, U., 1996. Chromosomal replication incompatibility in Dam methyltransferase deficient Escherichia coli cells. EMBO J. 15, 5999-6008.
  18. Baek, J.H. and Chattoraj, D.K., 2014. Chromosome I controls chromosome II replication in Vibrio cholerae. PLoS Genet. 10, e1004184.
  19. Cooper, S. and Helmstetter, C.E., 1968. Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Biol. 31, 519-40.
  20. Ramachandran, R., Jha, J. and Chattoraj, D.K., 2014. Chromosome segregation in Vibrio cholerae. J Mol Microbiol Biotechnol. 24, 360-70.
  21. Mitchell, L.A. and Boeke, J.D., 2014. Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proc Natl Acad Sci U S A. 111, 17003-10.
  22. Galanie, S., Thodey, K., Trenchard, I.J., Filsinger Interrante, M. and Smolke, C.D., 2015. Complete biosynthesis of opioids in yeast. Science. 349, 1095-100.
  23. Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., Merryman, C., Young, L., Noskov, V.N., Glass, J.I., Venter, J.C., Hutchison, C.A., 3rd and Smith, H.O., 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 319, 1215- 20.
  24. Starkenburg, S.R., Larimer, F.W., Stein, L.Y., Klotz, M.G., Chain, P.S., Sayavedra-Soto, L.A., PoretPeterson, A.T., Gentry, M.E., Arp, D.J., Ward, B. and Bottomley, P.J., 2008. Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Appl Environ Microbiol. 74, 2852-63.
  25. Haldimann, A. and Wanner, B.L., 2001. Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J Bacteriol. 183, 6384- 93.
  26. Jones, K.L. and Keasling, J.D., 1998. Construction and characterization of F plasmid-based expression vectors. Biotechnol Bioeng. 59, 659-65.
  27. Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R.Y., Algire, M.A., Benders, G.A., Montague, M.G., Ma, L., Moodie, M.M., Merryman, C., Vashee, S., Krishnakumar, R., AssadGarcia, N., Andrews-Pfannkoch, C., Denisova, E.A., Young, L., Qi, Z.Q., Segall-Shapiro, T.H., Calvey, C.H., Parmar, P.P., Hutchison, C.A., 3rd, Smith, H.O. and Venter, J.C., 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 329, 52-6.
  28. Cooper, S. and Keasling, J.D., 1998. Cycle-specific replication of chromosomal and F-plasmid origins. FEMS Microbiol Lett. 163, 217-22.
  29. Lobner-Olesen, A., Skovgaard, O. and Marinus, M.G., 2005. Dam methylation: coordinating cellular processes. Curr Opin Microbiol. 8, 154-60.
  30. Kennedy, S.P., Chevalier, F. and Barre, F.X., 2008. Delayed activation of Xer recombination at dif by FtsK during septum assembly in Escherichia coli. Mol Microbiol. 68, 1018-28.
  31. Hutchison, C.A., 3rd, Chuang, R.Y., Noskov, V.N., Assad-Garcia, N., Deerinck, T.J., Ellisman, M.H., Gill, J., Kannan, K., Karas, B.J., Ma, L., Pelletier, J.F., Qi, Z.Q., Richter, R.A., Strychalski, E.A., Sun, L., Suzuki, Y., Tsvetanova, B., Wise, K.S., Smith, H.O., Glass, J.I., Merryman, C., Gibson, D.G. and Venter, J.C., 2016. Design and synthesis of a minimal bacterial genome. Science. 351, aad6253.
  32. Ravasi, P., Peiru, S., Gramajo, H. and Menzella, H.G., 2012. Design and testing of a synthetic biology framework for genetic engineering of Corynebacterium glutamicum. Microb Cell Fact. 11, 147.
  33. Ostrov, N., Landon, M., Guell, M., Kuznetsov, G., Teramoto, J., Cervantes, N., Zhou, M., Singh, K., Napolitano, M.G., Moosburner, M., Shrock, E., Pruitt, B.W., Conway, N., Goodman, D.B., Gardner, C.L., Tyree, G., Gonzales, A., Wanner, B.L., Norville, J.E., Lajoie, M.J. and Church, G.M., 2016. Design, synthesis, and testing toward a 57-codon genome. Science. 353, 819-22.
  34. Lobner-Olesen, A. and Boye, E., 1992. Different effects of mioC transcription on initiation of chromosomal and minichromosomal replication in Escherichia coli. Nucleic Acids Res. 20, 3029-36.
  35. Yamaichi, Y., Fogel, M.A., McLeod, S.M., Hui, M.P. and Waldor, M.K., 2007a. Distinct centromere-like parS sites on the two chromosomes of Vibrio spp. J Bacteriol. 189, 5314-24.
  36. Egan, E.S. and Waldor, M.K., 2003. Distinct replication requirements for the two Vibrio cholerae chromosomes. Cell. 114, 521-30.
  37. Lobner-Olesen, A., 1999. Distribution of minichromosomes in individual Escherichia coli cells: implications for replication control. EMBO J. 18, 1712-21.
  38. Thompson, J.R., Randa, M.A., Marcelino, L.A., Tomita-Mitchell, A., Lim, E. and Polz, M.F., 2004. Diversity and dynamics of a north atlantic coastal Vibrio community. Appl Environ Microbiol. 70, 4103-10.
  39. Demarre, G. and Chattoraj, D.K., 2010. DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle. PLoS Genet. 6, e1000939.
  40. Messer, W. and Weigel, C., 1997. DnaA initiator--also a transcription factor. Mol Microbiol. 24, 1-6.
  41. Touzain, F., Petit, M.A., Schbath, S. and El Karoui, M., 2011. DNA motifs that sculpt the bacterial chromosome. Nat Rev Microbiol. 9, 15-26.
  42. Milbredt, S., Farmani, N., Sobetzko, P. and Waldminghaus, T., 2016. DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins. ACS Synth Biol.
  43. Heidelberg, J.F., Eisen, J.A., Nelson, W.C., Clayton, R.A., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Umayam, L., Gill, S.R., Nelson, K.E., Read, T.D., Tettelin, H., Richardson, D., Ermolaeva, M.D., Vamathevan, J., Bass, S., Qin, H., Dragoi, I., Sellers, P., McDonald, L., Utterback, T., Fleishmann, R.D., Nierman, W.C., White, O., Salzberg, S.L., Smith, H.O., Colwell, R.R., Mekalanos, J.J., Venter, J.C. and Fraser, C.M., 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 406, 477-83.
  44. Brezellec, P., Hoebeke, M., Hiet, M.S., Pasek, S. and Ferat, J.L., 2006. DomainSieve: a protein domainbased screen that led to the identification of dam-associated genes with potential link to DNA maintenance. Bioinformatics. 22, 1935-41.
  45. Bramhill, D. and Kornberg, A., 1988. Duplex opening by DnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell. 52, 743-55.
  46. Hiraga, S., 2000. Dynamic localization of bacterial and plasmid chromosomes. Annu Rev Genet. 34, 21-59.
  47. Messerschmidt, S.J. and Waldminghaus, T., 2014. Dynamic organization: chromosome domains in Escherichia coli. J Mol Microbiol Biotechnol. 24, 301-15.
  48. Olsson, J., Dasgupta, S., Berg, O.G. and Nordstrom, K., 2002. Eclipse period without sequestration in Escherichia coli. Mol Microbiol. 44, 1429-40.
  49. Crooke, E., Hwang, D.S., Skarstad, K., Thony, B. and Kornberg, A., 1991. E. coli minichromosome replication: regulation of initiation at oriC. Res Microbiol. 142, 127-30.
  50. Campbell, J.L. and Kleckner, N., 1990. E. coli oriC and the dnaA gene promoter are sequestered from Dam methyltransferase following the passage of the chromosomal replication fork. Cell. 62, 967-79.
  51. Slater, S., Wold, S., Lu, M., Boye, E., Skarstad, K. and Kleckner, N., 1995. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell. 82, 927-36.
  52. Posfai, G., Plunkett, G., 3rd, Feher, T., Frisch, D., Keil, G.M., Umenhoffer, K., Kolisnychenko, V., Stahl, B., Sharma, S.S., de Arruda, M., Burland, V., Harcum, S.W. and Blattner, F.R., 2006. Emergent properties of reduced-genome Escherichia coli. Science. 312, 1044-6.
  53. Sturino, J.M. and Klaenhammer, T.R., 2006. Engineered bacteriophage-defence systems in bioprocessing. Nat Rev Microbiol. 4, 395-404.
  54. Rodriguez, A., Martinez, J.A., Flores, N., Escalante, A., Gosset, G. and Bolivar, F., 2014. Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds. Microb Cell Fact. 13, 126.
  55. Gibson, D.G., Young, L., Chuang, R.Y., Venter, J.C., Hutchison, C.A., 3rd and Smith, H.O., 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 6, 343- 5.
  56. Holloway, B., Low, K.B. and Neidhardt, F.C., 1987. Escherichia coli and Salmonella typhimurium : Cellular and Molecular biology. American Society for Microbiology, Washington, DC, USA. pp. 1145-1153.
  57. Liang, X., Baek, C.H. and Katzen, F., 2013. Escherichia coli with Two Linear Chromosomes. ACS Synth Biol.
  58. Venkova-Canova, T., Baek, J.H., Fitzgerald, P.C., Blokesch, M. and Chattoraj, D.K., 2013. Evidence for two different regulatory mechanisms linking replication and segregation of Vibrio cholerae chromosome II. PLoS Genet. 9, e1003579.
  59. Guha, S. and Guschlbauer, W., 1992. Expression of Escherichia coli dam gene in Bacillus subtilis provokes DNA damage response: N6-methyladenine is removed by two repair pathways. Nucleic Acids Res. 20, 3607-15.
  60. Val, M.E., Kennedy, S.P., El Karoui, M., Bonne, L., Chevalier, F. and Barre, F.X., 2008. FtsK-dependent dimer resolution on multiple chromosomes in the pathogen Vibrio cholerae. PLoS Genet. 4, e1000201.
  61. Perals, K., Cornet, F., Merlet, Y., Delon, I. and Louarn, J.M., 2000. Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol Microbiol. 36, 33-43.
  62. Val, M.E., Kennedy, S.P., Soler-Bistue, A.J., Barbe, V., Bouchier, C., Ducos-Galand, M., Skovgaard, O. and Mazel, D., 2014. Fuse or die: how to survive the loss of Dam in Vibrio cholerae. Mol Microbiol. 91, 665-78.
  63. Raymond, C.K., Pownder, T.A. and Sexson, S.L., 1999. General method for plasmid construction using homologous recombination. Biotechniques. 26, 134-8, 140-1.
  64. Berenstein, D., Olesen, K., Speck, C. and Skovgaard, O., 2002. Genetic organization of the Vibrio harveyi DnaA gene region and analysis of the function of the V. harveyi DnaA protein in Escherichia coli. J Bacteriol. 184, 2533-8.
  65. Val, M.E., Skovgaard, O., Ducos-Galand, M., Bland, M.J. and Mazel, D., 2012. Genome engineering in Vibrio cholerae: a feasible approach to address biological issues. PLoS Genet. 8, e1002472.
  66. White, O., Eisen, J.A., Heidelberg, J.F., Hickey, E.K., Peterson, J.D., Dodson, R.J., Haft, D.H., Gwinn, M.L., Nelson, W.C., Richardson, D.L., Moffat, K.S., Qin, H., Jiang, L., Pamphile, W., Crosby, M., Shen, M., Vamathevan, J.J., Lam, P., McDonald, L., Utterback, T., Zalewski, C., Makarova, K.S., Aravind, L., Daly, M.J., Minton, K.W., Fleischmann, R.D., Ketchum, K.A., Nelson, K.E., Salzberg, S., Smith, H.O., Venter, J.C. and Fraser, C.M., 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. 286, 1571-7.
  67. Slater, S.C., Goldman, B.S., Goodner, B., Setubal, J.C., Farrand, S.K., Nester, E.W., Burr, T.J., Banta, L., Dickerman, A.W., Paulsen, I., Otten, L., Suen, G., Welch, R., Almeida, N.F., Arnold, F., Burton, O.T., Du, Z., Ewing, A., Godsy, E., Heisel, S., Houmiel, K.L., Jhaveri, J., Lu, J., Miller, N.M., Norton, S., Chen, Q., Phoolcharoen, W., Ohlin, V., Ondrusek, D., Pride, N., Stricklin, S.L., Sun, J., Wheeler, C., Wilson, L., Zhu, H. and Wood, D.W., 2009. Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol. 191, 2501-11.
  68. Downie, J.A. and Young, J.P., 2001. Genome sequencing. The ABC of symbiosis. Nature. 412, 597-8.
  69. Oshima, T., Wada, C., Kawagoe, Y., Ara, T., Maeda, M., Masuda, Y., Hiraga, S. and Mori, H., 2002. Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli. Mol Microbiol. 45, 673-95.
  70. Lajoie, M.J., Rovner, A.J., Goodman, D.B., Aerni, H.R., Haimovich, A.D., Kuznetsov, G., Mercer, J.A., Wang, H.H., Carr, P.A., Mosberg, J.A., Rohland, N., Schultz, P.G., Jacobson, J.M., Rinehart, J., Church, G.M. and Isaacs, F.J., 2013. Genomically recoded organisms expand biological functions. Science. 342, 357-60.
  71. Lessie, T.G., Hendrickson, W., Manning, B.D. and Devereux, R., 1996. Genomic complexity and plasticity of Burkholderia cepacia. FEMS Microbiol Lett. 144, 117-28.
  72. Russell, D.W. and Zinder, N.D., 1987. Hemimethylation prevents DNA replication in E. coli. Cell. 50, 1071-9.
  73. Liebl, W., Bayerl, A., Schein, B., Stillner, U. and Schleifer, K.H., 1989. High efficiency electroporation of intact Corynebacterium glutamicum cells. FEMS Microbiol Lett. 53, 299-303.
  74. Schafer, A., Kalinowski, J., Simon, R., Seep-Feldhaus, A.H. and Puhler, A., 1990. High-frequency conjugal plasmid transfer from gram-negative Escherichia coli to various gram-positive coryneform bacteria. J Bacteriol. 172, 1663-6.
  75. van Steensel, B. and Henikoff, S., 2000. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nat Biotechnol. 18, 424-8.
  76. El-Hajj, Z.W., Tryfona, T., Allcock, D.J., Hasan, F., Lauro, F.M., Sawyer, L., Bartlett, D.H. and Ferguson, G.P., 2009. Importance of proteins controlling initiation of DNA replication in the growth of the high-pressure-loving bacterium Photobacterium profundum SS9. J Bacteriol. 191, 6383- 93.
  77. Jang, K.H. and Britz, M.L., 2000. Improved electrotransformation frequencies of Corynebacterium glutamicum using cell-surface mutants. Biotechnol Lett. 22, 539-545.
  78. Krabbe, M., Zabielski, J., Bernander, R. and Nordstrom, K., 1997. Inactivation of the replicationtermination system affects the replication mode and causes unstable maintenance of plasmid R1. Mol Microbiol. 24, 723-35.
  79. Schafer, A., Kalinowski, J. and Puhler, A., 1994. Increased fertility of Corynebacterium glutamicum recipients in intergeneric matings with Escherichia coli after stress exposure. Appl Environ Microbiol. 60, 756-9.
  80. Duigou, S., Knudsen, K.G., Skovgaard, O., Egan, E.S., Lobner-Olesen, A. and Waldor, M.K., 2006. Independent control of replication initiation of the two Vibrio cholerae chromosomes by DnaA and RctB. J Bacteriol. 188, 6419-24.
  81. Jha, J.K., Ghirlando, R. and Chattoraj, D.K., 2014. Initiator protein dimerization plays a key role in replication control of Vibrio cholerae chromosome 2. Nucleic Acids Res. 42, 10538-49.
  82. Bonamy, C., Guyonvarch, A., Reyes, O., David, F. and Leblon, G., 1990. Interspecies electrotransformation in Corynebacteria. FEMS Microbiol Lett. 54, 263-9.
  83. Harrison, P.W., Lower, R.P., Kim, N.K. and Young, J.P., 2010. Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends Microbiol. 18, 141-8.
  84. Jones, K.L., Kim, S.W. and Keasling, J.D., 2000. Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab Eng. 2, 328-38.
  85. Noack, D., Roth, M., Geuther, R., Muller, G., Undisz, K., Hoffmeier, C. and Gaspar, S., 1981. Maintenance and genetic stability of vector plasmids pBR322 and pBR325 in Escherichia coli K12 strains grown in a chemostat. Mol Gen Genet. 184, 121-4.
  86. Li, G.M., 2008. Mechanisms and functions of DNA mismatch repair. Cell Res. 18, 85-98.
  87. Kaplan, D.L. and Bastia, D., 2009. Mechanisms of polar arrest of a replication fork. Mol Microbiol. 72, 279-85.
  88. Lin, Z., Xu, Z., Li, Y., Wang, Z., Chen, T. and Zhao, X., 2014. Metabolic engineering of Escherichia coli for the production of riboflavin. Microb Cell Fact. 13, 104.
  89. Gerding, M.A., Chao, M.C., Davis, B.M. and Waldor, M.K., 2015. Molecular Dissection of the Essential Features of the Origin of Replication of the Second Vibrio cholerae Chromosome. MBio. 6, e00973.
  90. Lowe, J., Ellonen, A., Allen, M.D., Atkinson, C., Sherratt, D.J. and Grainge, I., 2008. Molecular mechanism of sequence-directed DNA loading and translocation by FtsK. Mol Cell. 31, 498- 509.
  91. Moyed, H.S., Nguyen, T.T. and Bertrand, K.P., 1983. Multicopy Tn10 tet plasmids confer sensitivity to induction of tet gene expression. J Bacteriol. 155, 549-56.
  92. Pal, D., Venkova-Canova, T., Srivastava, P. and Chattoraj, D.K., 2005. Multipartite regulation of rctB, the replication initiator gene of Vibrio cholerae chromosome II. J Bacteriol. 187, 7167-75.
  93. Fang, F.C., Durland, R.H. and Helinski, D.R., 1993. Mutations in the gene encoding the replicationinitiation protein of plasmid RK2 produce elevated copy numbers of RK2 derivatives in Escherichia coli and distantly related bacteria. Gene. 133, 1-8.
  94. Lee, J.Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D.N. and Yang, W., 2005. MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage. Mol Cell. 20, 155-66.
  95. Tanaka, M. and Hiraga, S., 1985. Negative control of oriC plasmid replication by transcription of the oriC region. Mol Gen Genet. 200, 21-6.
  96. Hiraga, S., 1976. Novel F prime factors able to replicate in Escherichia coli Hfr strains. Proc Natl Acad Sci U S A. 73, 198-202.
  97. Messerschmidt, S.J., Schindler, D., Zumkeller, C.M., Kemter, F.S., Schallopp, N. and Waldminghaus, T., 2016. Optimization and characterization of the synthetic secondary chromosome synVicII in Escherichia coli. . Front. Bioeng. Biotechnol.
  98. Du, W.L., Dubarry, N., Passot, F.M., Kamgoue, A., Murray, H., Lane, D. and Pasta, F., 2016. Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315. PLoS Genet. 12, e1006172.
  99. Krawiec, S. and Riley, M., 1990. Organization of the bacterial chromosome. Microbiol Rev. 54, 502- 39.
  100. Yamaichi, Y., Fogel, M.A. and Waldor, M.K., 2007b. par genes and the pathology of chromosome loss in Vibrio cholerae. Proc Natl Acad Sci U S A. 104, 630-5.
  101. Kano, Y., Ogawa, T., Ogura, T., Hiraga, S., Okazaki, T. and Imamoto, F., 1991. Participation of the histone-like protein HU and of IHF in minichromosomal maintenance in Escherichia coli. Gene. 103, 25-30.
  102. Jones, S.A. and Melling, J., 1984. Persistence of Pbr322-Related Plasmids in Escherichia-Coli Grown in Chemostat Cultures. FEMS Microbiol Lett. 22, 239-243.
  103. Suwanto, A. and Kaplan, S., 1989. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. J Bacteriol. 171, 5850-9.
  104. Kroll, J., Klinter, S., Schneider, C., Voss, I. and Steinbuchel, A., 2010. Plasmid addiction systems: perspectives and applications in biotechnology. Microb Biotechnol. 3, 634-57.
  105. San Millan, A., Heilbron, K. and MacLean, R.C., 2014. Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations. ISME J. 8, 601-12.
  106. Sengupta, M. and Austin, S., 2011. Prevalence and significance of plasmid maintenance functions in the virulence plasmids of pathogenic bacteria. Infect Immun. 79, 2502-9.
  107. Zirpel, B., Stehle, F. and Kayser, O., 2015. Production of Delta9-tetrahydrocannabinolic acid from cannabigerolic acid by whole cells of Pichia (Komagataella) pastoris expressing Delta9- tetrahydrocannabinolic acid synthase from Cannabis sativa L. Biotechnol Lett. 37, 1869-75.
  108. Birchler, J.A., 2015. Promises and pitfalls of synthetic chromosomes in plants. Trends Biotechnol. 33, 189-94.
  109. Koch, B., Ma, X. and Lobner-Olesen, A., 2012. rctB mutations that increase copy number of Vibrio cholerae oriCII in Escherichia coli. Plasmid. 68, 159-69.
  110. Rosano, G.L. and Ceccarelli, E.A., 2014. Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol. 5, 172.
  111. Oldenburg, K.R., Vo, K.T., Michaelis, S. and Paddon, C., 1997. Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res. 25, 451-2.
  112. Thomason, L., Court, D.L., Bubunenko, M., Costantino, N., Wilson, H., Datta, S. and Oppenheim, A., 2007. Recombineering: genetic engineering in bacteria using homologous recombination. Curr Protoc Mol Biol. Chapter 1, Unit 1 16.
  113. Zakrzewska-Czerwinska, J., Jakimowicz, D., Zawilak-Pawlik, A. and Messer, W., 2007. Regulation of the initiation of chromosomal replication in bacteria. FEMS Microbiol Rev. 31, 378-87.
  114. del Solar, G., Giraldo, R., Ruiz-Echevarria, M.J., Espinosa, M. and Diaz-Orejas, R., 1998. Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev. 62, 434-64.
  115. Helmstetter, C.E., Thornton, M., Zhou, P., Bogan, J.A., Leonard, A.C. and Grimwade, J.E., 1997. Replication and segregation of a miniF plasmid during the division cycle of Escherichia coli. J Bacteriol. 179, 1393-9.
  116. Keasling, J.D., Palsson, B.O. and Cooper, S., 1992. Replication of mini-F plasmids during the bacterial division cycle. Res Microbiol. 143, 541-8.
  117. Koch, B., Ma, X. and Lobner-Olesen, A., 2010. Replication of Vibrio cholerae chromosome I in Escherichia coli: dependence on Dam methylation. J Bacteriol. 192, 3903-14.
  118. Stokke, C., Waldminghaus, T. and Skarstad, K., 2011. Replication patterns and organization of replication forks in Vibrio cholerae. Microbiology. 157, 695-708.
  119. Leonard, A.C. and Helmstetter, C.E., 1988. Replication patterns of multiple plasmids coexisting in Escherichia coli. J Bacteriol. 170, 1380-3.
  120. Jha, J.K., Demarre, G., Venkova-Canova, T. and Chattoraj, D.K., 2012. Replication regulation of Vibrio cholerae chromosome II involves initiator binding to the origin both as monomer and as dimer. Nucleic Acids Res. 40, 6026-38.
  121. Von Freiesleben, U., Rasmussen, K.V., Atlung, T. and Hansen, F.G., 2000. Rifampicin-resistant initiation of chromosome replication from oriC in ihf mutants. Mol Microbiol. 37, 1087-93.
  122. Lu, M., Campbell, J.L., Boye, E. and Kleckner, N., 1994. SeqA: a negative modulator of replication initiation in E. coli. Cell. 77, 413-26.
  123. Mettrick, K.A. and Grainge, I., 2016. Stability of blocked replication forks in vivo. Nucleic Acids Res. 44, 657-68.
  124. Skarstad, K. and Lobner-Olesen, A., 2003. Stable co-existence of separate replicons in Escherichia coli is dependent on once-per-cell-cycle initiation. EMBO J. 22, 140-50.
  125. Gerdes, K., Larsen, J.E. and Molin, S., 1985. Stable inheritance of plasmid R1 requires two different loci. J Bacteriol. 161, 292-8.
  126. Egan, E.S., Lobner-Olesen, A. and Waldor, M.K., 2004. Synchronous replication initiation of the two Vibrio cholerae chromosomes. Curr Biol. 14, R501-2.
  127. Dymond, J.S., Richardson, S.M., Coombes, C.E., Babatz, T., Muller, H., Annaluru, N., Blake, W.J., Schwerzmann, J.W., Dai, J., Lindstrom, D.L., Boeke, A.C., Gottschling, D.E., Chandrasegaran, S., Bader, J.S. and Boeke, J.D., 2011. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 477, 471-6.
  128. Schindler, D. and Waldminghaus, T., 2015. Synthetic chromosomes. FEMS Microbiol Rev. 39, 871-91.
  129. Schmidt, M. and de Lorenzo, V., 2012. Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett. 586, 2199-206.
  130. Messerschmidt, S.J., Kemter, F.S., Schindler, D. and Waldminghaus, T., 2015. Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. Biotechnol J. 10, 302-14.
  131. Bates, D.B., Boye, E., Asai, T. and Kogoma, T., 1997. The absence of effect of gid or mioC transcription on the initiation of chromosomal replication in Escherichia coli. Proc Natl Acad Sci U S A. 94, 12497-502.
  132. Messer, W., 2002. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev. 26, 355-74.
  133. Schafer, A., Tauch, A., Droste, N., Puhler, A. and Kalinowski, J., 1997. The Corynebacterium glutamicum cglIM gene encoding a 5-cytosine methyltransferase enzyme confers a specific DNA methylation pattern in an McrBC-deficient Escherichia coli strain. Gene. 203, 95-101.
  134. Bates, D.B., Asai, T., Cao, Y., Chambers, M.W., Cadwell, G.W., Boye, E. and Kogoma, T., 1995. The DnaA box R4 in the minimal oriC is dispensable for initiation of Escherichia coli chromosome replication. Nucleic Acids Res. 23, 3119-25.
  135. Fuller, R.S., Funnell, B.E. and Kornberg, A., 1984. The DnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell. 38, 889-900.
  136. Waldminghaus, T. and Skarstad, K., 2009. The Escherichia coli SeqA protein. Plasmid. 61, 141-50.
  137. Sivanathan, V., Allen, M.D., de Bekker, C., Baker, R., Arciszewska, L.K., Freund, S.M., Bycroft, M., Lowe, J. and Sherratt, D.J., 2006. The FtsK gamma domain directs oriented DNA translocation by interacting with KOPS. Nat Struct Mol Biol. 13, 965-72.
  138. Hansen, F.G., Christensen, B.B. and Atlung, T., 1991. The initiator titration model: computer simulation of chromosome and minichromosome control. Res Microbiol. 142, 161-7.
  139. Sherratt, D.J., 1982. The maintenance and propagation of plasmid genes in bacterial populations. The Sixth Fleming Lecture. J Gen Microbiol. 128, 655-61.
  140. Duggin, I.G., Wake, R.G., Bell, S.D. and Hill, T.M., 2008. The replication fork trap and termination of chromosome replication. Mol Microbiol. 70, 1323-33.
  141. Boye, E. and Lobner-Olesen, A., 1990. The role of Dam methyltransferase in the control of DNA replication in E. coli. Cell. 62, 981-9.
  142. Dymond, J. and Boeke, J., 2012. The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Bioeng Bugs. 3, 168-71.
  143. Woelker, B. and Messer, W., 1993. The structure of the initiation complex at the replication origin, oriC, of Escherichia coli. Nucleic Acids Res. 21, 5025-33.
  144. Zielenkiewicz, U. and Ceglowski, P., 2005. The toxin-antitoxin system of the streptococcal plasmid pSM19035. J Bacteriol. 187, 6094-105.
  145. Rasmussen, T., Jensen, R.B. and Skovgaard, O., 2007. The two chromosomes of Vibrio cholerae are initiated at different time points in the cell cycle. Embo J. 26, 3124-31.
  146. Trucksis, M., Michalski, J., Deng, Y.K. and Kaper, J.B., 1998. The Vibrio cholerae genome contains two unique circular chromosomes. Proc Natl Acad Sci U S A. 95, 14464-9.
  147. Skarstad, K., Boye, E. and Steen, H.B., 1986. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J. 5, 1711-7.
  148. Annaluru, N., Muller, H., Mitchell, L.A., Ramalingam, S., Stracquadanio, G., Richardson, S.M., Dymond, J.S., Kuang, Z., Scheifele, L.Z., Cooper, E.M., Cai, Y., Zeller, K., Agmon, N., Han, J.S., Hadjithomas, M., Tullman, J., Caravelli, K., Cirelli, K., Guo, Z., London, V., Yeluru, A., Murugan, S., Kandavelou, K., Agier, N., Fischer, G., Yang, K., Martin, J.A., Bilgel, M., Bohutski, P., Boulier, K.M., Capaldo, B.J., Chang, J., Charoen, K., Choi, W.J., Deng, P., DiCarlo, J.E., Doong, J., Dunn, J., Feinberg, J.I., Fernandez, C., Floria, C.E., Gladowski, D., Hadidi, P., Ishizuka, I., Jabbari, J., Lau, C.Y., Lee, P.A., Li, S., Lin, D., Linder, M.E., Ling, J., Liu, J., London, M., Ma, H., Mao, J., McDade, J.E., McMillan, A., Moore, A.M., Oh, W.C., Ouyang, Y., Patel, R., Paul, M., Paulsen, L.C., Qiu, J., Rhee, A., Rubashkin, M.G., Soh, I.Y., Sotuyo, N.E., Srinivas, V., Suarez, A., Wong, A., Wong, R., Xie, W.R., Xu, Y., Yu, A.T., Koszul, R., Bader, J.S., Boeke, J.D. and Chandrasegaran, S., 2014. Total synthesis of a functional designer eukaryotic chromosome. Science. 344, 55-8.
  149. Bonnassie, S., Burini, J.F., Oreglia, J., Trautwetter, A., Patte, J.C. and Sicard, A.M., 1990. Transfer of plasmid DNA to Brevibacterium lactofermentum by electrotransformation. J Gen Microbiol. 136, 2107-12.
  150. Venkova-Canova, T. and Chattoraj, D.K., 2011. Transition from a plasmid to a chromosomal mode of replication entails additional regulators. Proc Natl Acad Sci U S A. 108, 6199-204.
  151. Hiasa, H. and Marians, K.J., 1994. Tus prevents overreplication of oriC plasmid DNA. J Biol Chem. 269, 26959-68.
  152. Ren, S.X., Fu, G., Jiang, X.G., Zeng, R., Miao, Y.G., Xu, H., Zhang, Y.X., Xiong, H., Lu, G., Lu, L.F., Jiang, H.Q., Jia, J., Tu, Y.F., Jiang, J.X., Gu, W.Y., Zhang, Y.Q., Cai, Z., Sheng, H.H., Yin, H.F., Zhang, Y., Zhu, G.F., Wan, M., Huang, H.L., Qian, Z., Wang, S.Y., Ma, W., Yao, Z.J., Shen, Y., Qiang, B.Q., Xia, Q.C., Guo, X.K., Danchin, A., Saint Girons, I., Somerville, R.L., Wen, Y.M., Shi, M.H., Chen, Z., Xu, J.G. and Zhao, G.P., 2003. Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature. 422, 888-93.
  153. Wendisch, V.F., Jorge, J.M., Perez-Garcia, F. and Sgobba, E., 2016. Updates on industrial production of amino acids using Corynebacterium glutamicum. World J Microbiol Biotechnol. 32, 105.
  154. Okada, K., Iida, T., Kita-Tsukamoto, K. and Honda, T., 2005. Vibrios commonly possess two chromosomes. J Bacteriol. 187, 752-7.
  155. Cooper, V.S., Vohr, S.H., Wrocklage, S.C. and Hatcher, P.J., 2010. Why genes evolve faster on secondary chromosomes in bacteria. PLoS Comput Biol. 6, e1000732.


* Das Dokument ist im Internet frei zugänglich - Hinweise zu den Nutzungsrechten