Modification of the genome of rhodobacter sphaeroides and construction of synthetic operons

Methods in Enzymology

Volumn 497, Issue , 2011, Pages 519-538

  Jaschke, Paul R ^a   Saer, Rafael G ^a   Noll, Stephan ^b   Beatty, J Thomas ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b Gene Bridges GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; DNA MODIFICATION; EXPRESSION VECTOR; GENE CONTROL; GENE DELETION; GENE DISRUPTION; GENE MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; PROTEIN EXPRESSION; RHODOBACTER SPHAEROIDES;

BACTERIAL PROTEINS; GENE DELETION; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MEMBRANE PROTEINS; MULTIGENE FAMILY; OPERON; PHOTOSYNTHESIS; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; RHODOBACTER SPHAEROIDES; SYNTHETIC BIOLOGY;

PROTEOBACTERIA; RHODOBACTER SPHAEROIDES;

EID: 79957440851     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385075-100023-8     Document Type: Article

References (88)

1. K. Abremski, A. Wierzbicki, B. Frommer, and R.H. Hoess Bacteriophage P1 Cre-LoxP site-specific recombinationSite-specific DNA topoisomerase activity of the Cre recombination protein J. Biol. Chem. 261 1986 391 396 (Pubitemid 16103959)
2. E.C. Abresch, H.L.A. Axelrod, J.T. Beatty, J.A. Johnson, R. Nechushtai, and M.L. Paddock Characterization of a highly purified, fully active, crystallizable RC/LH1/PufX core complex from Rhodobacter sphaeroides Photosynth. Res. 86 2005 61 70 (Pubitemid 41361261)
3. M. Aklujkar, A.L. Harmer, R.C. Prince, and J.T. Beatty The orf162b sequence of Rhodobacter capsulatus encodes a protein required for optimal levels of photosynthetic pigmentprotein complexes J. Bacteriol. 182 2000 5440 5447
4. M. Aklujkar, R.C. Prince, and J.T. Beatty The PuhB protein of Rhodobacter capsulatus functions in photosynthetic reaction center assembly with a secondary effect on light-harvesting complex 1 J. Bacteriol. 187 2005 1334 1343 (Pubitemid 40305268)
5. H. Arai, J.H. Roh, and S. Kaplan Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1 J. Bacteriol. 190 2008 286 299
6. F. Barany Single-stranded hexameric linkersA system for in-phase insertion mutagenesis and protein engineering Gene 37 1985 111 123 (Pubitemid 16253445)
7. C.E. Bauer, A. Setterdahl, J. Wu, and B.R. Robinson Regulation of gene expression in response to oxygen tension C.N. Hunter, F. Daldal, M.C. Thurnauer, J.T. Beatty, The Purple Phototrophic Bacteria 2009 Springer Science Dordrecht, The Netherlands 707 725
8. D.C. Brune Sulfur compounds as photosynthetic electron donors R.E. Blankenship, M.T. Madigan, C.E. Bauer, Anoxygenic Photosynthetic Bacteria 1995 Kluwer Academic Dordrecht, The Netherlands 847 870
9. S.J. Callister, C.D. Nicora, X. Zeng, J.H. Roh, M.A. Dominguez, C.L. Tavano, M.E. Monroe, S. Kaplan, T.J. Donohue, R.D. Smith, and M.S. Lipton Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes J. Microbiol. Methods 67 2006 424 436 (Pubitemid 44740199)
10. G. Cannarozzi, N.N. Schraudolph, M. Faty, P. von Rohr, M.T. Friberg, A.C. Roth, P. Gonnet, G. Gonnet, and Y. Barral A role for codon order in translation dynamics Cell 141 2010 355 367
11. C.-Y.A. Chen, J.T. Beatty, S.N. Cohen, and J.G. Belasco An intercistronic stem-loop structure functions as an mRNA decay terminator necessary but insufficient for puf mRNA stability Cell 52 1988 609 619
12. X.Y. Chen, V. Yurkov, M.L. Paddock, M.Y. Okamura, and J.T. Beatty A puhA gene deletion and plasmid complementation system for site directed mutagenesis studies of the reaction center H protein of Rhodobacter sphaeroides Photosynth. Res. 55 1998 369 373 (Pubitemid 28351428)
13. J. Chory, T.J. Donohue, A.R. Varga, L.A. Staehelin, and S. Kaplan Induction of the photosynthetic membranes of Rhodopseudomonas sphaeroides: Biochemical and morphological studies J. Bacteriol. 159 1984 540 554 (Pubitemid 14056090)
14. M. Choudhary, and S. Kaplan DNA sequence analysis of the photosynthesis region of Rhodobacter sphaeroides 2.4.1 Nucleic Acids Res. 28 2000 862 867 (Pubitemid 30085310)
15. W. Curtis, J. Chapelle, B.E. Logan, and H. Salis Development of Rhodobacter as a versatile platform for fuels production 2010 (PI: W. Curtis; with J. Chapelle, B.E. Logan, H. Salis). ArpaE, June 2010May 2013. The Pennsylvania State University
16. J. Davison, M. Heusterspreute, N. Chevalier, V. Hathi, and F. Brunel Vectors with restriction site banks. pJRD215, a wide-host-range cosmid vector with multiple cloning sites Gene 51 1987 275 280 (Pubitemid 17061193)
17. G. Ditta, T. Schmidhauser, E. Yakobson, P. Lu, X.W. Liang, D.R. Finlay, D. Guiney, and D.R. Helinski Plasmids related to the broad host range vector, pRK290, useful for gene cloning and for monitoring gene expression Plasmid 13 1985 149 153 (Pubitemid 15110380)
18. T.J. Donohue, J.H. Hoger, and S. Kaplan Cloning and expression of the Rhodobacter sphaeroides reaction center H gene J. Bacteriol. 168 1986 953 961 (Pubitemid 17172798)
19. C. Duport, C. Meyer, I. Naud, and Y. Jouanneau A new gene-expression system based on a fructose-dependent promoter from Rhodobacter capsulatus Gene 145 1994 103 108 (Pubitemid 24224971)
20. J.M. Eraso, and S. Kaplan Redox flow as an instrument of gene regulation Methods Enzymol. 348 2002 216 229 (Pubitemid 41103112)
21. J.M. Eraso, and S. Kaplan Regulation of gene expression by PrrA in Rhodobacter sphaeroides 2.4.1: Role of polyamines and DNA topology J. Bacteriol. 191 2009 4341 4352
22. J.M. Eraso, J.H. Roh, X. Zeng, S.J. Callister, M.S. Lipton, and S. Kaplan Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: Combined transcriptome and proteome analysis J. Bacteriol. 190 2008 4831 4848 (Pubitemid 351991051)
23. M. Gabrielsen, A.T. Gardiner, and R.J. Cogdell Peripheral complexes of purple bacteria C.N. Hunter, F. Daldal, M.C. Thurnauer, J.T. Beatty, The Purple Phototrophic Bacteria 2009 Springer Science 135 153
24. P. Gay, D. Le Coq, M. Steinmetz, E. Ferrari, and J.A. Hoch Cloning structural gene sacB, which codes for exoenzyme levansucrase of Bacillus subtilis: Expression of the gene in Escherichia coli J. Bacteriol. 153 1983 1424 1431 (Pubitemid 13126628)
25. P. Gay, D. Lecoq, M. Steinmetz, T. Berkelman, and C.I. Kado Positive selection procedure for entrapment of insertion-sequence elements in Gram-negative bacteria J. Bacteriol. 164 1985 918 921 (Pubitemid 16191873)
26. S.M. Herter, C.M. Kortlke, and G. Drew Complex I of Rhodobacter capsulatus and its role in reverted electron transport Arch. Microbiol. 169 1997 98 105
27. I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster Fast folding and comparison of RNA secondary structures Monatsh. Chem. 125 1994 167 188
28. Z.L. Hu, Z.P. Zhao, Y. Pan, Y. Tu, and G.P. Chen A powerful hybrid puc operon promoter tightly regulated by both IPTG and low oxygen level Biochemistry (Moscow) 75 2010 519 525
29. F. Italiano, A. Buccolieri, L. Giotta, A. Agostiano, L. Valli, F. Milano, and M. Trotta Response of the carotenoidless mutant Rhodobacter sphaeroides growing cells to cobalt and nickel exposure Int. Biodeter. Biodegrad. 63 2009 948 957
30. P.R. Jaschke, and J.T. Beatty The photosystem of Rhodobacter sphaeroides assembles with zinc-bacteriochlorophyll in a bchD (magnesium-chelatase) mutant Biochemistry 46 2007 12491 12500 (Pubitemid 350022401)
31. 2 assimilation) promoter of Ralstonia eutropha J. Bacteriol. 181 1999 4374 4380 (Pubitemid 29331396)
32. J.F. Kane Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli Curr. Opin. Biotech. 6 1995 494 500
33. N.T. Keen, S. Tamaki, D. Kobayashi, and D. Trollinger Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria Gene 70 1988 191 197 (Pubitemid 18263496)
34. C.L. Kingsford, K. Ayanbule, and S.L. Salzberg Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake Genome Biol. 8 2007 R22
35. S. Klamt, H. Grammel, R. Straube, R. Ghosh, and E.D. Gilles Modeling the electron transport chain of purple non-sulfur bacteria Mol. Syst. Biol. 4 2008 156
36. M. Kobayashi Waste remediation and treatment using anoxygenic phototrophic bacteria R.E.M. Blankenship, T. Michael, C.E. Bauer, Anoxygenic Photosynthetic Bacteria 1995 Springer Dordrecht, The Netherlands 1269 1282
37. J. Kohler Single molecule spectroscopy of pigment protein complexes from purple bacteria B. Grimm, R.J. Porra, W. Rudiger, H. Scheer, Chlorophylls and Bacteriochlorophylls: Biochemistry, Biophysics, Functions and Applications Vol. 25 2006 Springer Dordrecht 309 321
38. M.E. Kovach, R.W. Phillips, P.H. Elzer, R.M. Roop 2nd, and K.M. Peterson pBBR1MCS: A broad-host-range cloning vector Biotechniques 16 1994 800 802 (Pubitemid 2103380)
39. P.D. Laible, H.N. Scott, L. Henry, and D.K. Hanson Towards higher-throughput membrane protein production for structural genomics initiatives J. Struct. Funct. Genomics 5 2004 167 172 (Pubitemid 39030632)
40. P.D. Laible, D.L. Mielke, and D.K. Hanson Foreign gene expression in photosynthetic bacteria C.N. Hunter, F. Daldal, M.C. Thurnauer, J.T. Beatty, The Purple Phototrophic Bacteria 2009 Springer Science Dordrecht, The Netherlands 839 860
41. N. Lebedev, S.A. Trammell, S. Tsoi, A. Spano, J.H. Kim, J. Xu, M.E. Twigg, and J.M. Schnur Increasing efficiency of photoelectronic conversion by encapsulation of photosynthetic reaction center proteins in arrayed carbon nanotube electrode Langmuir 24 2008 8871 8876
42. J.K. Lee, and S. Kaplan Transcriptional regulation of puc operon expression in Rhodobacter sphaeroides. Analysis of the cis-acting downstream regulatory sequence J. Biol. Chem. 270 1995 20453 20458
43. S.F. Lee, Y.J. Li, and S.A. Halperin Overcoming codon-usage bias in heterologous protein expression in Streptococcus gordonii Microbiology 155 2009 3581 3588
44. O. Lenz, E. Schwartz, J. Dernedde, M. Eitinger, and B. Friedrich The Alcaligenes eutrophus H16 hoxX gene participates in hydrogenase regulation J. Bacteriol. 176 1994 4385 4393 (Pubitemid 24226477)
45. M.M.-Y. Leung CtrA and GtaR: Two systems that regulate the gene transfer agent in Rhodobacter capsulatus 2010 Microbiology and Immunology. University of British Columbia, Vancouver
46. S. Lin, P.R. Jaschke, H.Y. Wang, M. Paddock, A. Tufts, J.P. Allen, F.I. Rosell, A.G. Mauk, N.W. Woodbury, and J.T. Beatty Electron transfer in the Rhodobacter sphaeroides reaction center assembled with zinc bacteriochlorophyll Proc. Natl. Acad. Sci. USA 106 2009 8537 8542
47. M.T. Madigan Microbiology of nitrogen fixation by anoxygenic photosynthetic bacteria R.E. Blankenship, M.T. Madigan, C.E. Bauer, Anoxygenic Photosynthetic Bacteria 1995 Kluwer Academic Dordrecht, The Netherlands 915 928
48. J.S. McCaskill The equilibrium partition-function and base pair binding probabilities for RNA secondary structure Biopolymers 29 1990 1105 1119 (Pubitemid 20145703)
49. J. Messing New M13 vectors for cloning Methods Enzymol. 101 1983 20 78 (Pubitemid 13071037)
50. O.V. Moskvin, S. Kaplan, M.A. Gilles-Gonzalez, and M. Gomelsky Novel heme-based oxygen sensor with a revealing evolutionary history J. Biol. Chem. 282 2007 28740 28748 (Pubitemid 47606067)
51. T. Nakamoto Evolution and the universality of the mechanism of initiation of protein synthesis Gene 432 2009 1 6
52. K.B. Narayanan, and N. Sakthivel Biological synthesis of metal nanoparticles by microbes Adv. Coll. Interface Sci. 156 2010 1 13
53. S. Noll, G. Hampp, H. Bausbacher, N.S. Pellegata, and H. Kranz Site-directed mutagenesis of multi-copy-number plasmids: Red/ET recombination and unique restriction site elimination Biotechniques 46 2009 527 533
54. J.I. Oh, and S. Kaplan Redox signaling: Globalization of gene expression EMBO J. 19 2000 4237 4247 (Pubitemid 30623734)
55. P. Prentki, and H.M. Krisch In vitro insertional mutagenesis with a selectable DNA fragment Gene 29 1984 303 313 (Pubitemid 14038235)
56. P. Qian, C.N. Hunter, and P.A. Bullough The 8.5 angstrom projection structure of the core RC-LH1-PufX dimer of Rhodobacter sphaeroides J. Mol. Biol. 349 2005 948 960 (Pubitemid 40779618)
57. N. Rajasekhar, C. Sasikala, and C.V. Ramana Photoproduction of indole 3-acetic acid by Rhodobacter sphaeroides from indole and glycine Biotech. Lett. 21 1999 543 545 (Pubitemid 29349163)
58. N. Rajasekhar, C. Sasikala, and C.V. Ramana Photoproduction of l-tryptophan from indole and glycine by Rhodobacter sphaeroides OU5 Biotech. Appl. Biochem. 30 1999 209 212
59. J.H. Roh, W.E. Smith, and S. Kaplan Effects of oxygen and light intensity on transcriptome expression in Rhodobacter sphaeroides 2.4.1 J. Biol. Chem. 279 2004 9146 9155 (Pubitemid 38295978)
60. S. Romagnoli, and F.R. Tabita Carbon dioxide metabolism and its regulation in nonsulfur purple photosynthetic bacteria C.N. Hunter, F. Daldal, M.C. Thurnauer, J.T. Beatty, The Purple Phototrophic Bacteria 2009 Springer Science Dordrecht, The Netherlands 563 576
61. P.D. Sadowski The Flp Recombinase of the 2-Mu-M Plasmid of Saccharomyces cerevisiae Prog. Nucleic Acid Res. Mol. Biol. 51 51 1995 53 91
62. H.M. Salis, E.A. Mirsky, and C.A. Voigt Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotech. 27 2009 946 950
63. J.A. Sawitzke, L.C. Thomason, N. Costantino, M. Bubunenko, S. Datta, and D.L. Court Recombineering: In vivo genetic engineering in E. coli, S. enterica, and beyond Methods Enzymol. 421 2007 171 199 (Pubitemid 46367194)
64. S. Scheuring, F. Francia, J. Busselez, B.A. Melandri, J.L. Rigaud, and D. Levy Structural role of PufX in the dimerization of the photosynthetic core complex of Rhodobacter sphaeroides J. Biol. Chem. 279 2004 3620 3626 (Pubitemid 38140603)
65. S. Scheuring, J. Busselez, and D. Levy Structure of the dimeric PufX-containing core complex of Rhodobacter blasticus by in situ atomic force microscopy J. Biol. Chem. 280 2005 1426 1431
66. A. Schuck, A. Diwa, and J.G. Belasco RNase E autoregulates its synthesis in Escherichia coli by binding directly to a stem-loop in the rne 5′ untranslated region Mol. Microbiol. 72 2009 470 478
67. H.P. Schweizer Applications of the Saccharomyces cerevisiae Flp-FRT system in bacterial genetics J. Mol. Microbiol. Biotech. 5 2003 67 77 (Pubitemid 37475749)
68. S. Shuman Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase J. Biol. Chem. 269 1994 32678 32684
69. R. Simon, U. Priefer, and A. Puhler A broad host range mobilization system for in vivo genetic engineering transposon mutagenesis in gram-negative bacteria Bio/Technology 1 1983 784 791 (Pubitemid 14239484)
70. M. Steinmetz, D. Le Coq, H.B. Djemia, and P. Gay Genetic analysis of sacB, the structural gene of a secreted enzyme, levansucrase of Bacillus subtilis Marburg Mol. Gen. Genet. 191 1983 138 144 (Pubitemid 13016131)
71. N. Sternberg, B. Sauer, R. Hoess, and K. Abremski Bacteriophage P1 cre gene and its regulatory regionEvidence for multiple promoters and for regulation by DNA methylation J. Mol. Biol. 187 1986 197 212 (Pubitemid 16046660)
72. L.R. Swem, S. Elsen, T.H. Bird, D.L. Swem, H. Koch, H. Myllykallio, F. Daldal, and C.E. Bauer The RegB/RegA two-component regulatory system controls synthesis of photosynthesis and respiratory electron transfer components in Rhodobacter capsulatus J. Mol. Biol. 309 2001 121 138 (Pubitemid 32553512)
73. B. Swingle, Z.M. Bao, E. Markel, A. Chambers, and S. Cartinhour Recombineering Using RecTE from Pseudomonas syringae Appl. Environ. Microbiol. 76 2010 4960 4968
74. A. Takshi, J.D. Madden, and J.T. Beatty Diffusion model for charge transfer from a photosynthetic reaction center to an electrode in a photovoltaic device Electrochim. Acta 54 2009 3806 3811
75. A. Tehrani, and J.T. Beatty Effects of precise deletions in Rhodobacter sphaeroides reaction center genes on steady-state levels of reaction center proteins: A revised model for reaction center assembly Photosynth. Res. 79 2004 101 108 (Pubitemid 38184779)
76. L.C. Thomason, N. Costantino, D.V. Shaw, and D.L. Court Multicopy plasmid modification with phage lambda Red recombineering Plasmid 58 2007 148 158 (Pubitemid 47238182)
77. T. Tuller, A. Carmi, K. Vestsigian, S. Navon, Y. Dorfan, J. Zaborske, T. Pan, O. Dahan, I. Furman, and Y. Pilpel An evolutionarily conserved mechanism for controlling the efficiency of protein translation Cell 141 2010 344 354
78. V. Van Fleet-Stalder, T.G. Chasteen, I.J. Pickering, G.N. George, and R.C. Prince Fate of selenate and selenite metabolized by Rhodobacter sphaeroides Appl. Environ. Microbiol. 66 2000 4849 4853
79. J.C. van Kessel, and G.F. Hatfull Recombineering in Mycobacterium tuberculosis Nat. Methods 4 2007 147 152 (Pubitemid 46454684)
80. A. Villalobos, J.E. Ness, C. Gustafsson, J. Minshull, and S. Govindarajan Gene designer: A synthetic biology tool for constructing artificial DNA segments BMC Bioinform. 7 2006 285
81. D.M. Widmaier, D. Tullman-Ercek, E.A. Mirsky, R. Hill, S. Govindarajan, J. Minshull, and C.A. Voigt Engineering the Salmonella type III secretion system to export spider silk monomers Mol. Syst. Biol. 5 2009 1 9
82. J. Xiong, and C.E. Bauer Complex evolution of photosynthesis Annu. Rev. Plant Biol. 53 2002 503 521 (Pubitemid 36257505)
83. D. Yang, Y. Oyaizu, H. Oyaizu, G.J. Olsen, and C.R. Woese Mitochondrial origins Proc. Natl. Acad. Sci. USA 82 1985 4443 4447 (Pubitemid 15234250)
84. T.O. Yeates, H. Komiya, A. Chirino, D.C. Rees, J.P. Allen, and G. Feher Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: Proteincofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions Proc. Natl. Acad. Sci. USA 85 1988 7993 7997
85. D. Zannoni, B. Schoepp-Cothenet, and J. Hosler Respiration and respiratory complexes C.N. Hunter, F. Daldal, M.C. Thurnauer, J.T. Beatty, The Purple Phototrophic Bacteria 2009 Springer Science Dordrecht, The Netherlands 537 561
86. X. Zeng, J.H. Roh, S.J. Callister, C.L. Tavano, T.J. Donohue, M.S. Lipton, and S. Kaplan Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: Identification of new proteins J. Bacteriol. 189 2007 7464 7474 (Pubitemid 47557363)
87. M.Y. Zhou, S.E. Clark, and C.E. Gomezsanchez Universal cloning method by TA strategy Biotechniques 19 1995 34 35
88. M. Zuker, and P. Stiegler Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Res. 9 1981 133 148