Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas

Current Opinion in Biotechnology

Volumn 47, Issue , 2017, Pages 120-132

  Martínez García, Esteban ^a   de Lorenzo, Víctor ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC ENGINEERING; PLANT LIFE EXTENSION; PLANTS (BOTANY);

BIOLOGICAL CONTROLS; CHEMICAL POLLUTANTS; ENVIRONMENTAL REMEDIATION; INTRINSIC PROPERTY; MEASUREMENT STANDARDS; SYNTHETIC BIOLOGY; TECHNOLOGICAL DEVELOPMENT; WHOLE-CELL BIOCATALYSIS;

BACTERIA;

PLASMID VECTOR;

BACTERIAL GENOME; BIOTECHNOLOGY; DNA RECOMBINATION; GENE EDITING; GENE EXPRESSION SYSTEM; GENE REPLICATION; GENE STRUCTURE; GENETIC ENGINEERING; NONHUMAN; PLASMID; PRIORITY JOURNAL; PSEUDOMONAS; PSEUDOMONAS PUTIDA; REVIEW; STANDARDIZATION; TRANSPOSON; GENE VECTOR; GENETIC RECOMBINATION; GENETICS; GENOMICS; METABOLISM; PROCEDURES;

GENE EDITING; GENETIC ENGINEERING; GENETIC VECTORS; GENOMICS; PSEUDOMONAS; RECOMBINATION, GENETIC;

EID: 85025135321     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2017.06.013     Document Type: Review

References (127)

1. 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., et al. Design and synthesis of a minimal bacterial genome. Science, 351, 2016, aad6253.
2. Richardson, S.M., Mitchell, L.A., Stracquadanio, G., Yang, K., Dymond, J.S., DiCarlo, J.E., Lee, D., Huang, C.L.V., Chandrasegaran, S., Cai, Y., Design of a synthetic yeast genome. Science 355 (2017), 1040–1044.
3. Venter, J.C., Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life. 2013, Penguin.
4. Ginsberg, A.D., Calvert, J., Schyfter, P., Elfick, A., Endy, D., Synthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature. 2014, MIT Press.
5. de Lorenzo, V., Beware of metaphors: chasses and orthogonality in synthetic biology. Bioeng Bugs 2 (2011), 3–7.
6. Nikel, P.I., Martinez-Garcia, E., de Lorenzo, V., Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12 (2014), 368–379.
7. Nikel, P.I., Chavarria, M., Danchin, A., de Lorenzo, V., From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions. Curr Opin Chem Biol 34 (2016), 20–29.
8. Chavarria, M., Nikel, P.I., Perez-Pantoja, D., de Lorenzo, V., The Entner–Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol 15 (2013), 1772–1785 Article on the conspicuous lack of phosphofructokinase in Pseudomonas putida and its consequences.
9. Nikel, P.I., Chavarria, M., Fuhrer, T., Sauer, U., de Lorenzo, V., Pseudomonas putida KT2440 Strain metabolizes glucose through a cycle formed by enzymes of the Entner–Doudoroff, Embden–Meyerhof–Parnas, and pentose phosphate pathways. J Biol Chem 290 (2015), 25920–25932 Evidence of distinct organization of the central metabolism of P. putida that makes this species particularly suited to manage oxidative stress.
10. Bagdasarian, M., Lurz, R., Ruckert, B., Franklin, F.C., Bagdasarian, M.M., Frey, J., Timmis, K.N., Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host–vector system for gene cloning in Pseudomonas. Gene 16 (1981), 237–247.
11. Martinez-Garcia, E., Benedetti, I., Hueso, A., De Lorenzo, V., Mining environmental plasmids for synthetic biology parts and devices. Microbiol Spectr, 3, 2015 PLAS-0033-2014.
12. de Lorenzo, V., Schmidt, M., Biological standards for the Knowledge-Based BioEconomy: what is at stake. N Biotechnol, 2017, 10.1016/j.nbt.2017.05.001.
13. Regenhardt, D., Heuer, H., Heim, S., Fernandez, D.U., Strompl, C., Moore, E.R., Timmis, K.N., Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ Microbiol 4 (2002), 912–915.
14. Belda, E., van Heck, R.G., Jose Lopez-Sanchez, M., Cruveiller, S., Barbe, V., Fraser, C., Klenk, H.P., Petersen, J., Morgat, A., Nikel, P.I., et al. The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis. Environ Microbiol 18 (2016), 3403–3424.
15. Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V.A., Fouts, D.E., Gill, S.R., Pop, M., Holmes, M., et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4 (2002), 799–808.
16. Cases, I., de Lorenzo, V., Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int Microbiol 8 (2005), 213–222.
17. Poblete-Castro, I., Becker, J., Dohnt, K., dos Santos, V.M., Wittmann, C., Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol 93 (2012), 2279–2290.
18. Kim, J., Salvador, M., Saunders, E., Gonzalez, J., Avignone-Rossa, C., Jimenez, J.I., Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis. Essays Biochem 60 (2016), 303–313.
19. Loeschcke, A., Thies, S., Pseudomonas putida — a versatile host for the production of natural products. Appl Microbiol Biotechnol 99 (2015), 6197–6214.
20. Hintermayer, S.B., Weuster-Botz, D., Experimental validation of in silico estimated biomass yields of Pseudomonas putida KT2440. Biotechnol J, 2017, 10.1002/biot.201600720.
21. Sohn, S.B., Kim, T.Y., Park, J.M., Lee, S.Y., In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol J 5 (2010), 739–750.
22. Puchalka, J., Oberhardt, M.A., Godinho, M., Bielecka, A., Regenhardt, D., Timmis, K.N., Papin, J.A., Martins dos Santos, V.A., Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol, 4, 2008, e1000210.
23. Nogales, J., Palsson, B.O., Thiele, I., A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol, 2, 2008, 79 The best metabolic model available thus far for Pseudomonas putida, although it surely needs to be updated.
24. Dos Santos, V.A., Heim, S., Moore, E.R., Stratz, M., Timmis, K.N., Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6 (2004), 1264–1286.
25. Wu, X., Monchy, S., Taghavi, S., Zhu, W., Ramos, J., van der Lelie, D., Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida. FEMS Microbiol Rev 35 (2011), 299–323.
26. Martinez-Garcia, E., Nikel, P.I., Aparicio, T., de Lorenzo, V., Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb Cell Fact, 13, 2014, 159 Evidence that deleting parasitic genes (e.g. from prophages) and elimination of flagellum of P. putida originates strains that tolerate oxidative stress much better than the wild-type.
27. Lieder, S., Nikel, P.I., de Lorenzo, V., Takors, R., Genome reduction boosts heterologous gene expression in Pseudomonas putida. Microb Cell Fact, 14, 2015, 23 Eliminating a few dispensable segments of the P. putida's genome increases intracellular NAD(P)H and ATP.
28. Leprince, A., de Lorenzo, V., Voller, P., van Passel, M.W., Martins dos Santos, V.A., Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol 14 (2012), 1444–1453 Astute strategy to delete non-essential genomic segments of P. putida.
29. Leprince, A., Janus, D., de Lorenzo, V., Santos, V.M., Streamlining of a Pseudomonas putida genome using a combinatorial deletion method based on minitransposon insertion and the Flp-FRT recombination system. Methods Mol Biol 813 (2012), 249–266.
30. Martinez-Garcia, E., de Lorenzo, V., The quest for the minimal bacterial genome. Curr Opin Biotechnol 42 (2016), 216–224.
31. Umenhoffer, K., Draskovits, G., Nyerges, Á., Karcagi, I., Bogos, B., Tímár, E., Csörgő, B., Herczeg, R., Nagy, I., Fehér, T., Pál, C., Pósfai, G., Genome-wide abolishment of mobile genetic elements using genome shuffling and CRISPR/Cas-assisted MAGE allows the efficient stabilization of a bacterial chassis. ACS Synth Biol, 2017, 10.1021/acssynbio.6b00378.
32. Benedetti, I., de Lorenzo, V., Nikel, P.I., Genetic programming of catalytic Pseudomonas putida biofilms for boosting biodegradation of haloalkanes. Metab Eng 33 (2016), 109–118.
33. Bagdasarian, M., Timmis, K., Host: vector systems for gene cloning in Pseudomonas. Curr Top Microbiol Immunol, 96, 1982, 47.
34. Nieto, C., Fernandez-Tresguerres, E., Sanchez, N., Vicente, M., Diaz, R., Cloning vectors, derived from a naturally occurring plasmid of Pseudomonas savastanoi, specifically tailored for genetic manipulations in Pseudomonas. Gene 87 (1990), 145–149.
35. Simon, R., O'Connell, M., Labes, M., Puhler, A., Plasmid vectors for the genetic analysis and manipulation of rhizobia and other Gram-negative bacteria. Methods Enzymol 118 (1986), 640–659.
36. Priefer, U.B., Simon, R., Puhler, A., Extension of the host range of Escherichia coli vectors by incorporation of RSF1010 replication and mobilization functions. J Bacteriol 163 (1985), 324–330.
37. Choi, K.H., Kumar, A., Schweizer, H.P., A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J Microbiol Methods 64 (2006), 391–397 This method, simple as it is, made a considerable difference in the ease to handle Pseudomonas putida in the Laboratory.
38. Ferrieres, L., Hemery, G., Nham, T., Guerout, A.M., Mazel, D., Beloin, C., Ghigo, J.M., Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery. J Bacteriol 192 (2010), 6418–6427.
39. Yamaguchi, Y., Park, J-H., Inouye, M., Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet 45 (2011), 61–79.
40. Katzke, N., Knapp, A., Loeschcke, A., Drepper, T., Jaeger, K.E., Novel tools for the functional expression of metagenomic DNA. Methods Mol Biol 1539 (2017), 159–196.
41. Terron-Gonzalez, L., Medina, C., Limon-Mortes, M.C., Santero, E., Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries. Sci Rep, 3, 2013, 1107.
42. Kelly, J.R., Rubin, A.J., Davis, J.H., Ajo-Franklin, C.M., Cumbers, J., Czar, M.J., de Mora, K., Glieberman, A.L., Monie, D.D., Endy, D., Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng, 3, 2009, 4.
43. Endy, D., Foundations for engineering biology. Nature 438 (2005), 449–453.
44. Silva-Rocha, R., Martinez-Garcia, E., Calles, B., Chavarria, M., Arce-Rodriguez, A., de Las Heras, A., Paez-Espino, A.D., Durante-Rodriguez, G., Kim, J., Nikel, P.I., et al. The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res 41 (2013), D666–D675.
45. Martinez-Garcia, E., Aparicio, T., Goni-Moreno, A., Fraile, S., de Lorenzo, V., SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities. Nucleic Acids Res 43 (2015), D1183–D1189 This database and physical repository of formatted vectors is the only attempt thus far to standardize genetic tools for engineering Pseudomonas (http://seva.cnb.csic.es).
46. de Lorenzo, V., Herrero, M., Sánchez, J.M., Timmis, K.N., Mini-transposons in microbial ecology and environmental biotechnology. FEMS Microbiol Ecol 27 (1998), 211–224.
47. Mi, J., Sydow, A., Schempp, F., Becher, D., Schewe, H., Schrader, J., Buchhaupt, M., Investigation of plasmid-induced growth defect in Pseudomonas putida. J Biotechnol 231 (2016), 167–173.
48. Herrero, M., de Lorenzo, V., Timmis, K.N., Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in Gram-negative bacteria. J Bacteriol 172 (1990), 6557–6567.
49. de Lorenzo, V., Herrero, M., Jakubzik, U., Timmis, K.N., Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in Gram-negative eubacteria. J Bacteriol 172 (1990), 6568–6572.
50. Choi, K.H., Gaynor, J.B., White, K.G., Lopez, C., Bosio, C.M., Karkhoff-Schweizer, R.R., Schweizer, H.P., A Tn7-based broad-range bacterial cloning and expression system. Nat Methods 2 (2005), 443–448.
51. Martinez-Garcia, E., Calles, B., Arevalo-Rodriguez, M., de Lorenzo, V., pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol, 11, 2011, 38.
52. Martinez-Garcia, E., de Lorenzo, V., Transposon-based and plasmid-based genetic tools for editing genomes of Gram-negative bacteria. Methods Mol Biol 813 (2012), 267–283.
53. Martinez-Garcia, E., Aparicio, T., de Lorenzo, V., Nikel, P.I., New transposon tools tailored for metabolic engineering of Gram-negative microbial cell factories. Front Bioeng Biotechnol, 2, 2014, 46.
54. Martinez-Garcia, E., Aparicio, T., de Lorenzo, V., Nikel, P.I., Engineering Gram-negative microbial cell factories using transposon vectors. Methods Mol Biol 1498 (2017), 273–293.
55. Nikel, P.I., de Lorenzo, V., Implantation of unmarked regulatory and metabolic modules in Gram-negative bacteria with specialised mini-transposon delivery vectors. J Biotechnol 163 (2013), 143–154.
56. Hoffman, L.M., Jendrisak, J.J., Meis, R.J., Goryshin, I.Y., Reznikof, S.W., Transposome insertional mutagenesis and direct sequencing of microbial genomes. Genetica 108 (2000), 19–24.
57. Kirby, J.R., In vivo mutagenesis using EZ-Tn5. Methods Enzymol 421 (2007), 17–21.
58. Calles, B., de Lorenzo, V., Expanding the Boolean logic of the prokaryotic transcription factor XylR by functionalization of permissive sites with a protease-target sequence. ACS Synth Biol 2 (2013), 594–603.
59. Englaender, J.A., Jones, J.A., Cress, B.F., Kuhlman, T.E., Linhardt, R.J., Koffas, M.A.G., Effect of genomic integration location on heterologous protein expression and metabolic engineering in E. coli. ACS Synth Biol 6 (2017), 710–720.
60. Kulasekara, H.D., Transposon mutagenesis. Methods Mol Biol 1149 (2014), 501–519.
61. Withers, T.R., Yin, Y., Yu, H.D., Identification of novel genes associated with alginate production in Pseudomonas aeruginosa using mini-himar1 mariner transposon-mediated mutagenesis. J Vis Exp, 2014, 10.3791/51346.
62. Wong, S.M., Mekalanos, J.J., Genetic footprinting with mariner-based transposition in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 97 (2000), 10191–10196.
63. Schweizer, H.P., Choi, K.H., Characterization of molecular mechanisms controlling fabAB transcription in Pseudomonas aeruginosa. PLoS ONE, 7, 2012, e45646.
64. Skurnik, D., Roux, D., Aschard, H., Cattoir, V., Yoder-Himes, D., Lory, S., Pier, G.B., A comprehensive analysis of in vitro and in vivo genetic fitness of Pseudomonas aeruginosa using high-throughput sequencing of transposon libraries. PLoS Pathog, 9, 2013, e1003582.
65. Bruckbauer, S.T., Kvitko, B.H., Karkhoff-Schweizer, R.R., Schweizer, H.P., Tn5/7-lux: a versatile tool for the identification and capture of promoters in Gram-negative bacteria. BMC Microbiol, 15, 2015, 17.
66. Choi, K.H., Schweizer, H.P., mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat Protoc 1 (2006), 153–161.
67. Damron, F.H., McKenney, E.S., Barbier, M., Liechti, G.W., Schweizer, H.P., Goldberg, J.B., Construction of mobilizable mini-Tn7 vectors for bioluminescent detection of Gram-negative bacteria and single-copy promoter lux reporter analysis. Appl Environ Microbiol 79 (2013), 4149–4153.
68. Damron, F.H., McKenney, E.S., Schweizer, H.P., Goldberg, J.B., Construction of a broad-host-range Tn7-based vector for single-copy P(BAD)-controlled gene expression in Gram-negative bacteria. Appl Environ Microbiol 79 (2013), 718–721.
69. Koch, B., Jensen, L.E., Nybroe, O., A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. J Microbiol Methods 45 (2001), 187–195.
70. Lambertsen, L., Sternberg, C., Molin, S., Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins. Environ Microbiol 6 (2004), 726–732.
71. Hoang, T.T., Karkhoff-Schweizer, R.R., Kutchma, A.J., Schweizer, H.P., A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212 (1998), 77–86.
72. Zobel, S., Benedetti, I., Eisenbach, L., de Lorenzo, V., Wierckx, N., Blank, L.M., Tn7-based device for calibrated heterologous gene expression in Pseudomonas putida. ACS Synth Biol 4 (2015), 1341–1351 Useful collection of promoters coupled to translational enhancers for predictable genetic engineering of P. putida.
73. de las Heras, A., Carreno, C.A., de Lorenzo, V., Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ Microbiol 10 (2008), 3305–3316.
74. Kosuri, S., Goodman, D.B., Cambray, G., Mutalik, V.K., Gao, Y., Arkin, A.P., Endy, D., Church, G.M., Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A 110 (2013), 14024–14029.
75. Pfleger, B.F., Pitera, D.J., Smolke, C.D., Keasling, J.D., Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24 (2006), 1027–1032.
76. Cameron, D.E., Collins, J.J., Tunable protein degradation in bacteria. Nat Biotechnol 32 (2014), 1276–1281.
77. Venturelli, O.S., Tei, M., Bauer, S., Chan, L.J.G., Petzold, C.J., Arkin, A.P., Programming mRNA decay to modulate synthetic circuit resource allocation. Nat Commun, 8, 2017, 15128.
78. Kushwaha, M., Rostain, W., Prakash, S., Duncan, J.N., Jaramillo, A., Using RNA as molecular code for programming cellular function. ACS Synth Biol 5 (2016), 795–809.
79. Chappell, J., Takahashi, M.K., Lucks, J.B., Creating small transcription activating RNAs. Nat Chem Biol 11 (2015), 214–220.
80. Meyer, S., Chappell, J., Sankar, S., Chew, R., Lucks, J.B., Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies. Biotechnol Bioeng 113 (2016), 216–225.
81. Nikel, P.I., Silva-Rocha, R., Benedetti, I., de Lorenzo, V., The private life of environmental bacteria: pollutant biodegradation at the single cell level. Environ Microbiol 16 (2014), 628–642.
82. Goni-Moreno, A., Benedetti, I., Kim, J., de Lorenzo, V., Deconvolution of gene expression noise into spatial dynamics of transcription factor-promoter interplay. ACS Synth Biol, 2017, 10.1021/acssynbio.6b00397 Evidence that transcriptional noise in Pseudomonas can be modulated by the intracellular distance between the gene encoding a transcription factor and its target promoter.
83. Scott, S.R., Hasty, J., Quorum sensing communication modules for microbial consortia. ACS Synth Biol 5 (2016), 969–977.
84. Prindle, A., Samayoa, P., Razinkov, I., Danino, T., Tsimring, L.S., Hasty, J., A sensing array of radically coupled genetic ‘biopixels’. Nature 481 (2011), 39–44.
85. Pawar, S.V., Messina, M., Rinaldo, S., Cutruzzola, F., Kaever, V., Rampioni, G., Leoni, L., Novel genetic tools to tackle c-di-GMP-dependent signalling in Pseudomonas aeruginosa. J Appl Microbiol 120 (2016), 205–217.
86. Dvorak, P., Chrast, L., Nikel, P.I., Fedr, R., Soucek, K., Sedlackova, M., Chaloupkova, R., de Lorenzo, V., Prokop, Z., Damborsky, J., Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway. Microb Cell Fact, 14, 2015, 201.
87. Elmore, J.R., Furches, A., Wolff, G.N., Gorday, K., Guss, A.M., Development of a high efficiency integration system and promoter library for rapid modification of Pseudomonas putida KT2440. Metab Eng Commun 5 (2017), 1–8.
88. Xu, Y., Tao, F., Ma, C., Xu, P., New constitutive vectors: useful genetic engineering tools for biocatalysis. Appl Environ Microbiol 79 (2013), 2836–2840.
89. Sendy, B., Lee, D.J., Busby, S.J., Bryant, J.A., RNA polymerase supply and flux through the lac operon in Escherichia coli. Philos Trans R Soc Lond B: Biol Sci, 371, 2016 pii:20160080.
90. Schweizer, H.P., Bacterial genetics: past achievements, present state of the field, and future challenges. Biotechniques, 44, 2008, 633.
91. Hmelo, L.R., Borlee, B.R., Almblad, H., Love, M.E., Randall, T.E., Tseng, B.S., Lin, C., Irie, Y., Storek, K.M., Yang, J.J., et al. Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange. Nat Protoc 10 (2015), 1820–1841.
92. Galvao, T.C., de Lorenzo, V., Adaptation of the yeast URA3 selection system to Gram-negative bacteria and generation of a ΔbetCDE Pseudomonas putida strain. Appl Environ Microbiol 71 (2005), 883–892.
93. Graf, N., Altenbuchner, J., Development of a method for markerless gene deletion in Pseudomonas putida. Appl Environ Microbiol 77 (2011), 5549–5552 Useful alternative to sacB as a counterselection marker for genetic manipulations of P. putida.
94. Pósfai, G., Kolisnychenko, V., Bereczki, Z., Blattner, F.R., Markerless gene replacement in Escherichia coli stimulated by a double-strand break in the chromosome. Nucleic Acids Res 27 (1999), 4409–4415.
95. Martinez-Garcia, E., de Lorenzo, V., Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environ Microbiol 13 (2011), 2702–2716 This method left behind the many inconveniences of using sacB as a counterselection marker for genomic editing of P. putida.
96. Luo, X., Yang, Y., Ling, W., Zhuang, H., Li, Q., Shang, G., Pseudomonas putida KT2440 markerless gene deletion using a combination of lambda Red recombineering and Cre/loxP site-specific recombination. FEMS Microbiol Lett, 363, 2016.
97. Datsenko, K.A., Wanner, B.L., One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97 (2000), 6640–6645.
98. Ellis, H.M., Yu, D., DiTizio, T., Court, D.L., High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci U S A 98 (2001), 6742–6746.
99. Nyerges, A., Csorgo, B., Nagy, I., Balint, B., Bihari, P., Lazar, V., Apjok, G., Umenhoffer, K., Bogos, B., Posfai, G., et al. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species. Proc Natl Acad Sci U S A 113 (2016), 2502–2507.
100. Ronda, C., Pedersen, L.E., Sommer, M.O.A., Nielsen, A.T., CRMAGE: CRISPR Optimized MAGE Recombineering. Sci Rep, 6, 2016, 19452 This work reports the use of CRISPR/Cas9 as a strategy to counterselect wild-type genomic sequences after mutagenesis.
101. Jiang, W., Bikard, D., Cox, D., Zhang, F., Marraffini, L.A., RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31 (2013), 233–239.
102. Wang, H.H., Isaacs, F.J., Carr, P.A., Sun, Z.Z., Xu, G., Forest, C.R., Church, G.M., Programming cells by multiplex genome engineering and accelerated evolution. Nature 460 (2009), 894–898.
103. Liang, R., Liu, J., Scarless and sequential gene modification in Pseudomonas using PCR product flanked by short homology regions. BMC Microbiol, 10, 2010, 209.
104. Lesic, B., Rahme, L.G., Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa. BMC Mol Biol, 9, 2008, 20.
105. Chen, Z., Ling, W., Shang, G., Recombineering and I-SceI-mediated Pseudomonas putida KT2440 scarless gene deletion. FEMS Microbiol Lett, 2016, 10.1093/femsle/fnw231.
106. Swingle, B., Bao, Z., Markel, E., Chambers, A., Cartinhour, S., Recombineering using RecTE from Pseudomonas syringae. Appl Environ Microbiol 76 (2010), 4960–4968 First efficient platform to implement recombineering in a Pseudomonas species. Alas, it many not be transplanted to other species with the same efficacy.
107. Swingle, B., RecTE(Psy)-mediated recombineering in Pseudomonas syringae. Methods Mol Biol 1114 (2014), 3–10.
108. Swingle, B.M., Oligonucleotide recombination enabled site-specific mutagenesis in bacteria. Methods Mol Biol 978 (2013), 127–132 One of the first protocols for recombineering in Pseudomonas.
109. Bao, Z., Cartinhour, S., Swingle, B., Substrate and target sequence length influence RecTE(Psy) recombineering efficiency in Pseudomonas syringae. PLoS ONE, 7, 2012, e50617.
110. Aparicio, T., Jensen, S.I., Nielsen, A.T., de Lorenzo, V., Martinez-Garcia, E., The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42. Biotechnol J 11 (2016), 1309–1319 ssDNA recombineering shown in P. putida with a functional homologue of the β protein found in a prophage of strain DOT-T1E.
111. de Lorenzo, V., Eltis, L., Kessler, B., Timmis, K.N., Analysis of Pseudomonas gene products using lacIq/Ptrp-lac plasmids and transposons that confer conditional phenotypes. Gene 123 (1993), 17–24.
112. de Lorenzo, V., Fernandez, S., Herrero, M., Jakubzik, U., Timmis, K.N., Engineering of alkyl- and haloaromatic-responsive gene expression with mini-transposons containing regulated promoters of biodegradative pathways of Pseudomonas. Gene 130 (1993), 41–46.
113. Winther-Larsen, H.C., Blatny, J.M., Valand, B., Brautaset, T., Valla, S., Pm promoter expression mutants and their use in broad-host-range RK2 plasmid vectors. Metab Eng 2 (2000), 92–103.
114. Blatny, J.M., Brautaset, T., Winther-Larsen, H.C., Karunakaran, P., Valla, S., Improved broad-host-range RK2 vectors useful for high and low regulated gene expression levels in Gram-negative bacteria. Plasmid 38 (1997), 35–51.
115. Blatny, J.M., Brautaset, T., Winther-Larsen, H.C., Haugan, K., Valla, S., Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl Environ Microbiol 63 (1997), 370–379.
116. Calero, P., Jensen, S.I., Nielsen, A.T., Broad-host-range ProUSER vectors enable fast characterization of inducible promoters and optimization of p-coumaric acid production in Pseudomonas putida KT2440. ACS Synth Biol 5 (2016), 741–753 Useful collection of formatted expression vectors for use in Pseudomonas. The mechanism of entry of the inducers in the cells is uncertain in some cases.
117. Steigedal, M., Valla, S., The Acinetobacter sp. chnB promoter together with its cognate positive regulator ChnR is an attractive new candidate for metabolic engineering applications in bacteria. Metab Eng 10 (2008), 121–129.
118. Benedetti, I., Nikel, P.I., de Lorenzo, V., Data on the standardization of a cyclohexanone-responsive expression system for Gram-negative bacteria. Data Brief 6 (2016), 738–744.
119. Levy, C., Pike, K., Heyes, D.J., Joyce, M.G., Gabor, K., Smidt, H., van der Oost, J., Leys, D., Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator. Mol Microbiol 70 (2008), 151–167.
120. Makart, S., Heinemann, M., Panke, S., Characterization of the AlkS/P(alkB)-expression system as an efficient tool for the production of recombinant proteins in Escherichia coli fed-batch fermentations. Biotechnol Bioeng 96 (2007), 326–336.
121. Panke, S., Meyer, A., Huber, C.M., Witholt, B., Wubbolts, M.G., An alkane-responsive expression system for the production of fine chemicals. Appl Environ Microbiol 65 (1999), 2324–2332.
122. Eaton, R.W., p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate. J Bacteriol 179 (1997), 3171–3180.
123. Graf, N., Altenbuchner, J., Functional characterization and application of a tightly regulated MekR/PmekA expression system in Escherichia coli and Pseudomonas putida. Appl Microbiol Biotechnol 97 (2013), 8239–8251.
124. Hanko, E.K.R., Minton, N.P., Malys, N., Characterisation of a 3-hydroxypropionic acid-inducible system from Pseudomonas putida for orthogonal gene expression control in Escherichia coli and Cupriavidus necator. Sci Rep, 7, 2017, 1724.
125. Hoffmann, J., Altenbuchner, J., Functional characterization of the mannitol promoter of Pseudomonas fluorescens DSM 50106 and its application for a mannitol-inducible expression system for Pseudomonas putida KT2440. PLOS ONE, 10, 2015, e0133248.
126. Suh, S.J., Silo-Suh, L.A., Ohman, D.E., Development of tools for the genetic manipulation of Pseudomonas aeruginosa. J Microbiol Methods 58 (2004), 203–212.
127. Herrero, M., de Lorenzo, V., Ensley, B., Timmis, K.N., A T7 RNA polymerase-based system for the construction of Pseudomonas strains with phenotypes dependent on TOL-meta pathway effectors. Gene 134 (1993), 103–106.