Environmental Performance of Pseudomonas putida with a Uracylated Genome.
GMO escape
Pseudomonas putida
biocontainment
horizontal gene transfer
uracil
Journal
Chembiochem : a European journal of chemical biology
ISSN: 1439-7633
Titre abrégé: Chembiochem
Pays: Germany
ID NLM: 100937360
Informations de publication
Date de publication:
16 11 2020
16 11 2020
Historique:
received:
24
05
2020
revised:
27
06
2020
pubmed:
1
7
2020
medline:
7
7
2021
entrez:
30
6
2020
Statut:
ppublish
Résumé
A variant of the soil bacterium Pseudomonas putida with a genome containing a ∼20 % replacement of the whole of thymine (T) by uracil (U) was made by deleting genes ung (uracil DNA glycosylase) and dut (deoxyuridine 5'-triphosphate nucleotide hydrolase). Proteomic comparisons revealed that, of 281 up-regulated and 96 down-regulated proteins in the Δung Δdut cells, as compared to the wild-type, many were involved in nucleotide metabolism. Unexpectedly, genome uracylation did not greatly change the gross environmental endurance profile of P. putida, increased spontaneous mutagenesis by only twofold and supported expression of heterologous proteins well. As U-enriched DNA is potentially degraded by the base excision repair of recipients encoding a uracil DNA glycosylase, we then tested the spread potential of genetic material originating in the Δung Δdut cells either within the same species or in a commonly used Escherichia coli strain. Transformation and conjugation experiments revealed that horizontal gene transfer of U-containing plasmids fared worse than those made of standard DNA by two orders of magnitude. Although this figure does not guarantee the certainty of containment, it suggests a general strategy for curbing the dispersal of recombinant genetic constructs.
Identifiants
pubmed: 32597553
doi: 10.1002/cbic.202000330
doi:
Substances chimiques
DNA, Bacterial
0
Uracil
56HH86ZVCT
Hydrolases
EC 3.-
Uracil-DNA Glycosidase
EC 3.2.2.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3255-3265Informations de copyright
© 2020 Wiley-VCH GmbH.
Références
V. de Lorenzo, M. Schmidt, Nat. Biotechnol. 2018, 40, 170-180.
M. Schmidt, V. de Lorenzo, FEBS Lett. 2012, 586, 2199-2206;
M. Schmidt, V. de Lorenzo, Curr. Opin. Biotechnol. 2016, 38, 90-96;
J. W. Lee, C. T. Y. Chan, S. Slomovic, J. J. Collins, Nat. Chem. Biol. 2018, 1-8.
L. F. C. Kampers, R. J. M. Volkers, V. A. P. Martins dos Santos, Microb. Biotechnol. 2019, 13, 1700161-1700164.
P. I. Nikel, M. Chavarria, A. Danchin, V. de Lorenzo, Curr. Opin. Chem. Biol. 2016, 34, 20-29;
P. I. Nikel, E. Martinez-Garcia, V. de Lorenzo, Nat. Rev. Microbiol. 2014, 12, 368-379.
H. H. el-Hajj, H. Zhang, B. Weiss, J. Bacteriol. 1988, 170, 1069-1075.
P. Brotherton, P. Endicott, J. J. Sanchez, M. Beaumont, R. Barnett, J. Austin, A. Cooper, Nucleic Acids Res. 2007, 35, 5717-5728.
B. t G Vértessy, J. Tóth, Acc. Chem. Res. 2009, 42, 97-106.
H. R. Warner, B. K. Duncan, C. Garrett, J. Neuhard, J. Bacteriol. 1981, 145, 687-695.
G. L. Winsor, D. K. W. Lam, L. Fleming, R. Lo, M. D. Whiteside, N. Y. Yu, R. E. W. Hancock, F. S. L. Brinkman, Nucleic Acids Res. 2010, 39, D596-D600.
E. Martínez-García, V. de Lorenzo, Methods Mol. Biol. 2012, 813, 267-283.
S.-U. Lari, C.-Y. Chen, B. t G Vértessy, J. Morré, S. E. Bennett, DNA Repair 2006, 5, 1407-1420.
H. H. el-Hajj, L. Wang, B. Weiss, J. Bacteriol. 1992, 174, 4450-4456.
T. A. Kunkel, Proc. Natl. Acad. Sci. USA 1985, 82, 488-492.
P. E. Nisson, A. Rashtchian, P. C. Watkins, PCR Methods Appl. 1991, 1, 120-123;
C. Smith, P. J. Day, M. R. Walker, Genome Res. 1993, 2, 328-332;
H. H. Nour-Eldin, B. G. Hansen, M. H. H. Norholm, J. K. Jensen, B. A. Halkier, Nucleic Acids Res. 2006, 34, e122-e122.
A. F. Taylor, B. Weiss, J. Bacteriol. 1982, 151, 351-357.
O. V. Moroz, A. G. Murzin, K. S. Makarova, E. V. Koonin, K. S. Wilson, M. Y. Galperin, J. Mol. Biol. 2005, 347, 243-255.
C. J. Jeffery, Trends Biochem. Sci. 1999, 24, 8-11.
S. C. Williams, Y. Hong, D. C. A. Danavall, M. H. Howard-Jones, D. Gibson, M. E. Frischer, P. G. Verity, J. Microbiol. Methods 1998, 32, 225-236.
H. Fuller, G. Morris, in Integrative Proteomics (Ed.: H.-C. Leung), InTech, 2012, 347-362.
D. Szklarczyk, A. L. Gable, D. Lyon, A. Junge, S. Wyder, J. Huerta-Cepas, M. Simonovic, N. T. Doncheva, J. H. Morris, P. Bork, L. J. Jensen, Christian v. Mering, Nucleic Acids Res. 2018, 47, D607-D613.
D. W. Huang, B. T. Sherman, R. A. Lempicki, Nucleic Acids Res. 2008, 37, 1-13;
D. W. Huang, B. T. Sherman, R. A. Lempicki, Nat. Protoc. 2009, 4, 44-57.
M. Chavarría, P. I. Nikel, D. Pérez-Pantoja, V. de Lorenzo, Environ. Microbiol. 2013, 15, 1772-1785.
T. Lindahl in Progress in Nucleic Acid Research and Molecular Biology, Vol. 22 (Ed.: W. E. Cohn), Academic Press, 1979, pp. 135-192.
B. K. Tye, P. O. Nyman, I. R. Lehmann, S. Hochhauser, B. Weiss, Proc. Natl. Acad. Sci. USA 1977, 74, 154-157.
B. K. Duncan, B. Weiss, J. Bacteriol. 1982, 151, 750-755.
E. A. Campbell, N. Korzheva, A. Mustaev, K. Murakami, S. Nair, A. Goldfarb, S. A. Darst, Cell 2001, 104, 901-912.
T. Jatsenko, A. Tover, R. Tegova, M. Kivisaar, Mutat. Res. 2010, 683, 106-114.
M. Mergeay, P. Lejeune, A. Sadouk, J. Gerits, L. Fabry, Mol. Gen. Genet. 1987, 209, 61-70;
J. A. Heinemann, R. G. Ankenbauer, J. Bacteriol. 1993, 175, 583-588;
E. A. Sia, D. M. Kuehner, D. H. Figurski, J. Bacteriol. 1996, 178, 1457-1464.
S. A. Koser, J. Bacteriol. 1924, 9, 59-77;
B. G. Hall, J. Bacteriol. 1982, 151, 269-273.
E. B. Konrad, J. Bacteriol. 1977, 130, 167-172;
E. A. Kouzminova, A. Kuzminov, Mol. Microbiol. 2004, 51, 1279-1295.
F. T. Gates III, S. Linn, J. Biol. Chem. 1977, 252, 1647-1653.
P. Marlière, J. Patrouix, V. Döring, P. Herdewijn, S. Tricot, S. Cruveiller, M. Bouzon, R. Mutzel, Angew. Chem. Int. Ed. 2011, 50, 7109-7114;
Angew. Chem. 2011, 123, 7247-7252.
J. Sambrook, T. Maniatis, E. F. Fritsch, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York, 1989.
K.-H. Choi, H. P. Schweizer, Nat. Protoc. 2006, 1, 153-161;
B. Koch, L. E. Jensen, O. Nybroe, J. Microbiol. Methods 2001, 45, 187-195.
E. Martínez-García, V. de Lorenzo, Environ. Microbiol. 2011, 13, 2702-2716.
R. M. Horton, H. D. Hunt, S. N. Ho, J. K. Pullen, L. R. Pease, Gene 1989, 77, 61-68.
L. Garibyan, DNA Repair 2003, 2, 593-608.
K. Wilson, Curr. Protoc. Mol. Biol. 2001, 56, 2.4.1-2.4.5.
C. Manoil, J. Beckwith, Proc. Natl. Acad. Sci. USA 1985, 82, 8129-8133.
M. Herrero, V. de Lorenzo, K. N. Timmis, J. Bacteriol. 1990, 172, 6557-6567.
H. W. Boyer, D. Roulland-Dussoix, J. Mol. Biol. 1969, 41, 459-472.
T. A. Kunkel, J. D. Roberts, R. A. Zakour in Methods in Enzymology, Vol. 154, Academic Press, 1987, pp. 367-382.
K. Murray, C. J. Duggleby, P. A. Williams, J. M. Sala-Trepat, Eur. J. Biochem. 1972, 28, 301-310.
M. Bagdasarian, R. Lurz, B. Ruckert, F. C. Franklin, M. M. Bagdasarian, J. Frey, K. N. Timmis, Gene 1981, 16, 237-247.
F. C. Franklin, M. Bagdasarian, M. M. Bagdasarian, K. N. Timmis, Proc. Natl. Acad. Sci. USA 1981, 78, 7458-7462.
D. R. Espeso, E. Martínez-García, V. de Lorenzo, A. Goñi-Moreno, Front. Matrix Biol. 2016, 7, 1437.
I. M. Benedetti, V. de Lorenzo, R. Silva-Rocha, PLoS One 2012, 7, e52000.
R. Silva-Rocha, E. Martinez-Garcia, B. Calles, M. Chavarria, A. Arce-Rodriguez, A. de Las Heras, A. D. Paez-Espino, G. Durante-Rodriguez, J. Kim, P. I. Nikel, R. Platero, V. de Lorenzo, Nucleic Acids Res. 2013, 41, D666-675.
B. Kessler, V. de Lorenzo, K. N. Timmis, Mol. Gen. Genet. 1992, 233, 293-301.
S. M. Wong, J. J. Mekalanos, Proc. Natl. Acad. Sci. USA 2000, 97, 10191-10196.