Genetic tools for reliable gene expression and recombineering in Pseudomonas putida

Journal of Industrial Microbiology and Biotechnology

Volumn 45, Issue 7, 2018, Pages 517-527

  Cook, Taylor B ^a   Rand, Jacqueline M ^a   Nurani, Wasti ^a   Courtney, Dylan K ^a   Liu, Sophia A ^a,c   Pfleger, Brian F ^a,b  

^a University of Wisconsin Madison   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c Chemistry Department   (United States)

Author keywords

Cas9 recombineering; Copy number; LacI; Promoter; Pseudomonas putida; Synthetic biology

Indexed keywords

ARTICLE; BACTERIAL GROWTH; BACTERIAL MUTATION; BACTERIAL STRAIN; CONTROLLED STUDY; ELECTROPORATION; ESCHERICHIA COLI; FLOW CYTOMETRY; GENE EDITING; GENE EXPRESSION; GENETIC ENGINEERING; HOMOLOGOUS RECOMBINATION; HOST RANGE; NONHUMAN; PH; PROMOTER REGION; PSEUDOMONAS PUTIDA; START CODON; STOP CODON; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PLASMID; PROCEDURES; SYNTHETIC BIOLOGY;

BACTERIAL PROTEIN;

BACTERIAL PROTEINS; ESCHERICHIA COLI; GENE EDITING; GENE EXPRESSION REGULATION, BACTERIAL; PLASMIDS; PROMOTER REGIONS, GENETIC; PSEUDOMONAS PUTIDA; SYNTHETIC BIOLOGY;

EID: 85039981962     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-017-2001-5     Document Type: Article

References (69)

1. Anderson J (2006) Anderson promoter library registry of standard biological parts. http://partsregistry.org/Promoters/Catalog/Anderson. Accessed 1 Sept 2017
2. Antoine R, Locht C (1992) Isolation and molecular characterization of a novel broad-host-range plasmid from Bordetella bronchiseptica with sequence similarities to plasmids from gram-positive organisms. Mol Microbiol 6:1785–1799. 10.1111/j.1365-2958.1992.tb01351.x
3. Aparicio T, Jensen SI, Nielsen AT et al (2016) The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42. Biotechnol J 11:1309–1319. 10.1002/biot.201600317
4. Aparicio T, de Lorenzo V, Martínez-García E (2017) CRISPR/Cas9-based counterselection boosts recombineering efficiency in Pseudomonas putida. Biotechnol J. 10.1002/biot.201700161
5. Bagdasarian MM, Lurz R, Rückert B et al (1981) 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 16:237–247. 10.1016/0378-1119(81)90080-9
6. Bassalo MC, Garst AD, Halweg-Edwards AL et al (2016) Rapid and efficient one-step metabolic pathway integration in E. coli. ACS Synth Biol. 10.1021/acssynbio.5b00187
7. Beckwith JR, Zipser D (1970) The lactose operon. Cold Spring Harbor, New York
8. Bentley WE, Mirjalili N, Andersen DC et al (1990) Plasmid-encoded protein: the principal factor in the “metabolic burden” associated with recombinant bacteria. Biotechnol Bioeng 35:668–681. 10.1002/bit.260350704
9. De Bernardez ER, Dhurjati PS (1987) Effect of a broad-host range plasmid on growth dynamics of Escherichia coli and Pseudomonas putida. Biotechnol Bioeng 29:558–565. 10.1002/bit.260290504
10. Brendel N, Partida-Martinez LP, Scherlach K, Hertweck C (2007) A cryptic PKS–NRPS gene locus in the plant commensal Pseudomonas fluorescens Pf-5 codes for the biosynthesis of an antimitotic rhizoxin complex. Org Biomol Chem 5:2211–2213. 10.1039/b707762a
11. Calero P, Jensen SI, Nielsen AT (2016) 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 5:741–753. 10.1021/acssynbio.6b00081
12. Chai Y, Shan S, Weissman KJ et al (2012) Heterologous expression and genetic engineering of the tubulysin biosynthetic gene cluster using red/ET recombineering and inactivation mutagenesis. Chem Biol 19:361–371. 10.1016/j.chembiol.2012.01.007
13. Chiang YM, Chang SL, Oakley BR, Wang CCC (2011) Recent advances in awakening silent biosynthetic gene clusters and linking orphan clusters to natural products in microorganisms. Curr Opin Chem Biol 15:137–143. 10.1016/j.cbpa.2010.10.011
14. Cobb RE, Wang Y, Zhao H (2015) High-efficiency multiplex genome editing of streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 4:723–728. 10.1021/sb500351f
15. Davison J (2002) Genetic tools for pseudomonads, rhizobia, and other gram-negative bacteria. Biotechniques 32:386–401
16. Durland RH, Helinski DR (1990) Replication of the broad-host-range plasmid RK2: direct measurement of intracellular concentrations of the essential TrfA replication proteins and their effect on plasmid copy number. J Bacteriol 172:3849–3858. 10.1016/j.mimet.2011.10.007
17. Durland RH, Toukdarian A, Fang F, Helinski DR (1990) Mutations in the trfA replication gene of the broad-host-range plasmid RK2 result in elevated plasmid copy numbers. J Bacteriol 172:3859–3867
18. Elmore JR, Furches A, Wolff GN et al (2017) Development of a high efficiency integration system and promoter library for rapid modification of Pseudomonas putida KT2440. Metab Eng Commun 5:1–8. 10.1016/j.meteno.2017.04.001
19. Graf N, Altenbuchner J (2013) Functional characterization and application of a tightly regulated MekR/P mekA expression system in Escherichia coli and Pseudomonas putida. Appl Microbiol Biotechnol 97:8239–8251. 10.1007/s00253-013-5030-7
20. Graf N, Altenbuchner J (2011) Development of a method for markerless gene deletion in Pseudomonas putida. Appl Environ Microbiol 77:5549–5552. 10.1128/AEM.05055-11
21. Graf N, Altenbuchner J (2014) Genetic engineering of Pseudomonas putida KT2440 for rapid and high-yield production of vanillin from ferulic acid. Appl Microbiol Biotechnol 98:137–149. 10.1007/s00253-013-5303-1
22. Hansen LH, Sørensen SJ, Jensen LB (1997) Chromosomal insertion of the entire Escherichia coli lactose operon, into two strains of Pseudomonas, using a modified mini-Tn5 delivery system. Gene 186:167–173. 10.1016/S0378-1119(96)00688-9
23. Hashimoto J, Stevenson B, Schmidt TM (2002) Rates and consequences of recombination between ribosomal RNA operons. J Bacteriol 185:966–972. 10.1128/JB.185.3.966
24. Hoang TT, Karkhoff-Schweizer RR, Kutchma AJ, Schweizer HP (1998) 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 212:77–86. 10.1016/S0378-1119(98)00130-9
25. Hoffmann J, Altenbuchner J (2015) 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 10:1–22. 10.1371/journal.pone.0133248
26. Itoh N, Kawanami T, Nitta C et al (2003) Characterization of pNI10 plasmid in Pseudomonas, and the construction of an improved Escherichia and Pseudomonas shuttle vector, pNUK73. Appl Microbiol Biotechnol 61:240–246. 10.1007/s00253-002-1195-1
27. Itoh Y, Soldati L, Leisinger T, Haas D (1988) Low- and intermediate-copy-number cloning vectors based on the Pseudomonas plasmid pVS1. Antonie Van Leeuwenhoek 54:567–573. 10.1007/BF00588392
28. Jain A, Srivastava P (2013) Broad host range plasmids. FEMS Microbiol Lett 348:87–96. 10.1111/1574-6968.12241
29. Jeffrey V, Joachim M (1991) New pUC-derived cloning vectors with different selectable markers and DNA replication origins. Gene 100:189–194. 10.1016/0378-1119(91)90365-I
30. Jeske M, Altenbuchner J (2010) The Escherichia coli rhamnose promoter rhaPBAD is in Pseudomonas putida KT2440 independent of Crp-cAMP activation. Appl Microbiol Biotechnol 85:1923–1933. 10.1007/s00253-009-2245-8
31. Jiang W, Bikard D, Cox D et al (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–239. 10.1038/nbt.2508
32. Jinek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA—guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–822
33. Khlebnikov A, Datsenko KA, Skaug T et al (2001) Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity araE transporter. Microbiology 147:3241–3247. 10.1099/00221287-147-12-3241
34. Kovach ME, Elzer PH, Hill DS et al (1995) Four new derivatives of the broad host range cloning vector PBBR1MCS, carrying different antibiotic resistance cassettes. Gene 166:175–176. 10.1089/152045500436104
35. Kües U, Stahl U (1989) Replication of plasmids in gram-negative bacteria. Microbiol Rev 53:491–516
36. Lee CL, Ow DSW, Oh SKW (2006) Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria. J Microbiol Methods 65:258–267. 10.1016/j.mimet.2005.07.019
37. Lee E-C, Yu D, Martinez de Velasco J et al (2001) A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73:56–65. 10.1006/geno.2000.6451
38. Lee T, Krupa RA, Zhang F et al (2011) BglBrick vectors and datasheets: a synthetic biology platform for gene expression. J Biol Eng 5:12. 10.1186/1754-1611-5-12
39. Lesic B, Rahme LG (2008) Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa. BMC Mol Biol 9:20. 10.1186/1471-2199-9-20
40. Lieder S, Nikel PI, de Lorenzo V, Takors R (2015) Genome reduction boosts heterologous gene expression in Pseudomonas putida. Microb Cell Fact 14:23. 10.1186/s12934-015-0207-7
41. Lin J, Helinski DR (1992) Analysis of mutations in trfA, the replication initiation gene of the broad-host-range plasmid RK2. J Bacteriol 174:4110–4119
42. Loeschcke A, Thies S (2015) Pseudomonas putida—a versatile host for the production of natural products. Appl Microbiol Biotechnol. 10.1007/s00253-015-6745-4
43. de Lorenzo V, Fernández S, Herrero M et al (1993) Engineering of alkyl- and haloaromatic-responsive gene expression with mini-transposons containing regulated promoters of biodegradative pathways of Pseudomonas. Gene 130:41–46. 10.1016/0378-1119(93)90344-3
44. Luo X, Yang Y, Ling W et al (2016) Pseudomonas putida KT2440 markerless gene deletion using a combination of λ Red recombineering and Cre/loxP site-specific recombination. FEMS Microbiol Lett. 10.1093/femsle/fnw014
45. Mali P, Esvelt KM, Church GM (2013) Cas9 as a versatile tool for engineering biology. Nat Methods 10:957–963. 10.1038/nmeth.2649
46. Martínez-García E, de Lorenzo V (2011) Engineering multiple genomic deletions in gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environ Microbiol 13:2702–2716. 10.1111/j.1462-2920.2011.02538.x
47. Marx CJ, Lidstrom ME (2002) Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 33:1062–1067
48. McMurry L, Petrucci RE, Levy SB (1980) Active efflux of tetracycline encoded by four genetically different tetracycline resistance determinants in Escherichia coli. Proc Natl Acad Sci USA 77:3974–3977. 10.1073/pnas.77.7.3974
49. Meijnen JP, De Winde JH, Ruijssenaars HJ (2008) Engineering Pseudomonas putida S12 for efficient utilization of d-xylose and l-arabinose. Appl Environ Microbiol 74:5031–5037. 10.1128/AEM.00924-08
50. Morgan-Kiss RM, Wadler C, Cronan JE (2002) Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity. Proc Natl Acad Sci USA 99:7373–7377. 10.1073/pnas.122227599
51. Nagahari K, Sakaguchi K (1978) RSF1010 plasmid as a potentially useful vector in Pseudomonas species. J Bacteriol 133:1527–1529
52. Nelson KE, Weinel C, Paulsen IT et al (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4:799–808. 10.1046/j.1462-2920.2002.00366.x
53. Nikel PI, Chavarría M, Danchin A, de Lorenzo V (2016) From dirt to industrial applications: Pseudomonas putida as a synthetic biology chassis for hosting harsh biochemical reactions. Curr Opin Chem Biol 34:20–29. 10.1016/j.cbpa.2016.05.011
54. Nikel PI, Martínez-García E, de Lorenzo V (2014) Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12:368–379. 10.1038/nrmicro3253
55. Oh J-H, van Pijkeren J-P (2014) CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res 42:1–11. 10.1093/nar/gku623
56. Panke S, De Lorenzo V, Kaiser A, Wubbolts MG (1999) Engineering of a stable whole-cell biocatalyst capable of (S)-styrene oxide formation for continuous two-liquid-phase applications. Appl Environ Microbiol 65:5619–5623
57. Persson C, Nordström K (1986) Control of replication of the broad host range plasmid RSF1010: the incompatibility determinant consists of directly repeated DNA sequences. Mol Gen Genet 203:189–192. 10.1007/BF00330402
58. Prior JE, Lynch MD, Gill RT (2010) Broad-host-range vectors for protein expression across gram negative hosts. Biotechnol Bioeng 106:326–332. 10.1002/bit.22695
59. Pyne ME, Moo-Young M, Chung DA, Chou CP (2015) Coupling the CRISPR/Cas9 system with lambda red recombineering enables simplified chromosomal gene replacement in Escherichia coli. Appl Environ Microbiol 81:5103–5114. 10.1128/AEM.01248-15
60. Rand JM, Pisithkul T, Clark RL et al (2017) A metabolic pathway for catabolizing levulinic acid in bacteria. Nat Microbiol. 10.1038/s41564-017-0028-z
61. Rvbetzt K (1981) Regulation of the l-arabinose transport operons in Escherichia coli. J Mol Biol 151:215–227
62. Schäfer A, Tauch A, Jäger W et al (1994) Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145:69–73. 10.1016/0378-1119(94)90324-7
63. Schweizer HP, Hoang TT (1995) An improved system for gene replacement and xylE fusion analysis in Pseudomonas aeruginosa. Gene 158:15–22. 10.1016/0378-1119(95)00055-B
64. Siegele DA, Hu JC (1997) Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations. Proc Natl Acad Sci USA 94:8168–8172. 10.1073/pnas.94.15.8168
65. Silva-Rocha R, Martínez-García E, Calles B et al (2013) The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res 41:666–675. 10.1093/nar/gks1119
66. Swingle B, Bao Z, Markel E et al (2010) Recombineering using RecTE from Pseudomonas syringae. Appl Environ Microbiol 76:4960–4968. 10.1128/AEM.00911-10
67. Tao L, Jackson RE, Cheng Q (2005) Directed evolution of copy number of a broad host range plasmid for metabolic engineering. Metab Eng 7:10–17. 10.1016/j.ymben.2004.05.006
68. Xiao A, Cheng Z, Kong L et al (2014) CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 30:1180–1182. 10.1093/bioinformatics/btt764
69. Zobel S, Benedetti I, Eisenbach L et al (2015) Tn7-based device for calibrated heterologous gene expression in Pseudomonas putida. ACS Synth Biol. 10.1021/acssynbio.5b00058