In-frame and unmarked gene deletions in Burkholderia cenocepacia via an allelic exchange system compatible with gateway technology

Applied and Environmental Microbiology

Volumn 81, Issue 11, 2015, Pages 3623-3630

  Fazli, Mustafa ^a   Harrison, Joe J ^b   Gambino, Michela ^c   Givskov, Michael ^d,e   Tolker Nielsen, Tim ^d  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF CALGARY   (Canada)

^c UNIVERSITY OF MILAN   (Italy)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

^e NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ENCODING (SYMBOLS); GENE ENCODING; MOLECULAR BIOLOGY;

BIOFILM FORMATION; CYSTIC FIBROSIS; DELETION MUTATIONS; GATEWAY TECHNOLOGIES; GENETIC BASIS; GENETIC MANIPULATIONS; LIFE-THREATENING INFECTIONS; PROOF OF CONCEPT;

GENES;

ALLELE; BIOFILM; CLONE; GENE EXPRESSION; GENETIC MARKER; INFECTIVITY; PATHOGEN; VIRULENCE;

BURKHOLDERIA CENOCEPACIA;

BURKHOLDERIA CENOCEPACIA; GENE DELETION; GENE INACTIVATION; GENETICS; HOMOLOGOUS RECOMBINATION; MICROBIAL GENETICS; PROCEDURES;

BURKHOLDERIA CENOCEPACIA; GENE DELETION; GENE KNOCKOUT TECHNIQUES; GENETICS, MICROBIAL; HOMOLOGOUS RECOMBINATION;

EID: 84930022952     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03909-14     Document Type: Article

References (29)

1. Coenye T, Vandamme P. 2003. Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719-729. http://dx.doi.org/10.1046/j.1462-2920.2003.00471.x.
2. Mahenthiralingam E, Baldwin A, Dowson CG. 2008. Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J Appl Microbiol 104:1539-1551. http://dx.doi.org/10.1111/j .1365-2672.2007.03706.x.
3. Chiarini L, Bevivino A, Dalmastri C, Tabacchioni S, Visca P. 2006. Burkholderia cepacia complex species: health hazards and biotechnological potential. Trends Microbiol 14:277-286. http://dx.doi.org/10.1016/j .tim.2006.04.006.
4. Drevinek P, Mahenthiralingam E. 2010. Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence. Clin Microbiol Infect 16:821- 830. http://dx.doi.org/10.1111/j.1469-0691.2010.03237.x.
5. Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J. 2009. The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol 191:261-277. http://dx.doi.org/10.1128/JB .01230-08.
6. Varga JJ, Losada L, Zelazny AM, Kim M, McCorrison J, Brinkac L, Sampaio EP, Greenberg DE, Singh I, Heiner C, Ashby M, Nierman WC, Holland SM, Goldberg JB. 2013. Draft genome sequences of Burkholderia cenocepacia ET12 lineage strains K56-2 and BC7. Genome Announc 1(5):e00841-13. http://dx.doi.org/10.1128/genomeA.00841-13.
7. Carlier A, Agnoli K, Pessi G, Suppiger A, Jenul C, Schmid N, Tümmler B, Pinto-Carbo M, Eberl L. 2014. Genome sequence of Burkholderia cenocepacia H111, a cystic fibrosis airway isolate. Genome Announc 2(2): e00298-14. http://dx.doi.org/10.1128/genomeA.00298-14.
8. Suppiger A, Schmid N, Aguilar C, Pessi G, Eberl L. 2013. Two quorum sensing systems control biofilm formation and virulence in members of Burkholderia cepacia complex. Virulence 4:400-409. http://dx.doi.org /10.4161/viru.25338.
9. Fazli M, Almblad H, Rybtke ML, Givskov M, Eberl L, Tolker-Nielsen T. 2014. Regulation of biofilm formation in Pseudomonas and Burkholderia species. Environ Microbiol 16:1961-1981. http://dx.doi.org/10.1111/1462-2920.12448.
10. Uehlinger S, Schwager S, Bernier SP, Riedel K, Nguyen DT, Sokol PA, Eberl L. 2009. Identification of specific and universal virulence factors in Burkholderia cenocepacia strains by using multiple infection hosts. Infect Immun 77:4102-4110. http://dx.doi.org/10.1128/IAI.00398-09.
11. Schwager S, Agnoli K, Köthe M, Feldmann F, Givskov M, Carlier A, Eberl L. 2013. Identification of Burkholderia cenocepacia strain H111 virulence factors using nonmammalian infection hosts. Infect Immun 81: 143-153. http://dx.doi.org/10.1128/IAI.00768-12.
12. Flannagan RS, Linn T, Valvano MA. 2008. A system for construction of targeted unmarked gene deletions in the genus Burkholderia. Environ Microbiol 10:1652-1660. http://dx.doi.org/10.1111/j.1462-2920.2008.01576.x.
13. Aubert DF, Hamad MA, Valvano MA. 2014. A markerless deletion method for genetic manipulation of Burkholderia cenocepacia and other multidrug-resistant gram-negative bacteria. Methods Mol Biol 1197:311-327. http://dx.doi.org/10.1007/978-1-4939-1261-2_18.
14. Barrett AR, Kang Y, Inamasu KS, Son MS, Vukovich JM, Hoang TT. 2008. Genetic tools for allelic replacement in Burkholderia species. Appl Environ Microbiol 74:4498- 4508. http://dx.doi.org/10.1128/AEM.00531-08.
15. López CM, Rholl DA, Trunck LA, Schweizer HP. 2009. Versatile dualtechnology system for markerless allele replacement in Burkholderia pseudomallei. Appl Environ Microbiol 75:6496-6503. http://dx.doi.org /10.1128/AEM.01669-09.
16. Hamad MA, Zajdowicz SL, Holmes RK, Voskuil MI. 2009. An allelic exchange system for compliant genetic manipulation of the select agents Burkholderia pseudomallei and Burkholderia mallei. Gene 430:123-131. http://dx.doi.org/10.1016/j.gene.2008.10.011.
17. Logue CA, Peak IR, Beacham IR. 2009. Facile construction of unmarked gene deletion mutants in Burkholderia pseudomallei using sacB counterselection in sucrose-resistant and sucrose-sensitive isolates. J Microbiol Methods 76:320-323. http://dx.doi.org/10.1016/j.mimet.2008.12.007.
18. Katzen F. 2007. Gateway recombinational cloning: a biological operating system. Expert Opin Drug Dicov 2:571-589. http://dx.doi.org/10.1517/17460441.2.4.571.
19. Clark DJ, Maaløe O. 1967. DNA replication and division cycle in Escherichia coli. J Mol Biol 23:99-112. http://dx.doi.org/10.1016/S0022-2836(67)80070-6.
20. Horton RM, Hunt HD, Ho SN, Pullen JK, Pease LR. 1989. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77:61-68. http://dx.doi.org/10.1016/0378-1119(89)90359-4.
21. Ausmees N, Mayer R, Weinhouse H, Volman G, Amikam D, Benziman M, Lindberg M. 2001. Genetic data indicate that proteins containing GGDEF domain possess diguanylate cyclase activity. FEMS Microbiol Lett 204:163-167. http://dx.doi.org/10.1111/j.1574-6968.2001.tb10880.x.
22. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM, II, Peterson KM. 1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175-176. http://dx.doi.org/10.1016/0378-1119(95)00584-1.
23. Fazli M, O'Connell A, Nilsson M, Niehaus K, Dow JM, Givskov M, Ryan RP, Tolker-Nielsen T. 2011. The CRP/FNR family protein Bcam1349 is a c-di-GMP effector that regulates biofilm formation in the respiratory pathogen Burkholderia cenocepacia. Mol Microbiol 82:327-341. http://dx.doi.org/10.1111/j.1365-2958.2011.07814.x.
24. Fazli M, McCarthy Y, Givskov M, Ryan RP, Tolker-Nielsen T. 2013. The exopolysaccharide gene cluster Bcam1330-Bcam1341 is involved in Burkholderia cenocepacia biofilm formation, and its expression is regulated by c-di-GMP and Bcam1349. Microbiologyopen 2:105-122. http: //dx.doi.org/10.1002/mbo3.61.
25. 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. http: //dx.doi.org/10.1016/S0378-1119(98)00130-9.
26. Yu M, Tsang JS. 2006. Use of ribosomal promoters from Burkholderia cenocepacia and Burkholderia cepacia for improved expression of transporter protein in Escherichia coli. Protein Expr Purif 49:219-227. http: //dx.doi.org/10.1016/j.pep.2006.04.004.
27. Peano C, Chiaramonte F, Motta S, Pietrelli A, Jaillon S, Rossi E, Consolandi C, Champion OL, Michell SL, Freddin L, Falciola L, Basilico F, Garlanda C, Mauri P, De Bellis G, Landini P. 2014. Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis. PLoS One 9:e93009. http: //dx.doi.org/10.1371/journal.pone.0093009.
28. Kessler B, de Lorenzo V, Timmis KN. 1992. A general system to integrate lacZ fusions into the chromosomes of gram-negative eubacteria: regulation of Pm promoter in the TOL plasmid studied with all controlling elements in monocopy. Mol Gen Genet 233:293-301. http://dx.doi.org/10.1007/BF00587591.
29. Choi KH, Schweizer HP. 2005. An improved method for rapid generation of unmarked Pseudomonas aeruginosa deletion mutants. BMC Microbiol 5:30. http://dx.doi.org/10.1186/1471-2180-5-30.