The ClosTron: A universal gene knock-out system for the genus Clostridium

Journal of Microbiological Methods

Volumn 70, Issue 3, 2007, Pages 452-464

  Heap, John T ^a   Pennington, Oliver J ^a   Cartman, Stephen T ^a   Carter, Glen P ^a   Minton, Nigel P ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Clostridia; Clostridium; Integration; Intron; Mutant; pMTL007

Indexed keywords

ERYTHROMYCIN;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; CLOSTRIDIUM; CLOSTRIDIUM ACETOBUTYLICUM; CLOSTRIDIUM BOTULINUM; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM SPOROGENES; FUNCTIONAL GENOMICS; GENE FUNCTION; GENE INACTIVATION; INTRON; KNOCKOUT GENE; LACTOCOCCUS LACTIS; MUTAGENESIS; NONHUMAN; PLASMID; PRIORITY JOURNAL;

BACTERIAL PROTEINS; BASE SEQUENCE; CLOSTRIDIUM; CONJUGATION, GENETIC; GENE DELETION; INTRONS; ISOPROPYL THIOGALACTOSIDE; LACTOCOCCUS LACTIS; MUTAGENESIS, INSERTIONAL; PLASMIDS; PROMOTER REGIONS (GENETICS); RECOMBINATION, GENETIC; RETROELEMENTS; RNA-DIRECTED DNA POLYMERASE;

CLOSTRIDIA; CLOSTRIDIUM; CLOSTRIDIUM ACETOBUTYLICUM; CLOSTRIDIUM BOTULINUM; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM SPOROGENES; LACTOCOCCUS LACTIS;

EID: 34548124567     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2007.05.021     Document Type: Article

References (39)

1. Awad M.M., Bryant A.E., Stevens D.L., and Rood J.L. Virulence studies on chromosomal α-toxin and θ-toxin mutants constructed by allelic exchange provide genetic evidence for the essential role of α-toxin in Clostridium perfringens-mediated gas gangrene. Mol. Microbiol. 15 (1995) 191-202
2. Bannam T.L., Crellin P.K., and Rood J.I. Molecular genetics of the chlorophenicol-resistance transposon Tn4451 from Clostridium perfringens: the TnpX site-specific recombinase excises a circular transposon molecule. Mol. Microbiol. 16 (1995) 535-551
3. Brehm J.K., Chambers S.P., Brown K.J., Atkinson T., and Minton N.P. Molecular cloning and nucleotide sequence determination of the Bacillus stearothermophilus NCA 1503 superoxide dismutase gene and its overexpression in Escherichia coli. Appl. Microbiol. Biotechnol. 36 (1991) 358-363
4. - cloning vectors: I. Improved pUC polylinker regions to facilitate the use of sonicated DNA for nucleotide sequencing. Gene 68 (1988) 139-149
5. Chang A.C.Y., and Cohen S.N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134 (1978) 1141-1156
6. Chen Y., McClane B.A., Fisher D.J., Rood J.I., and Gupta P. Construction of an alpha toxin gene knockout mutant of Clostridium perfringens type A by use of a mobile group II intron. Appl. Environ. Microbiol. 71 (2005) 7542-7547
7. Cousineau B., Smith D., Lawrence-Cavanagh S., Mueller J.E., Yang J., Mills D., Manias D., Dunny G., Lambowitz A.M., and Belfort M. Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination. Cell 94 (1998) 451-462
8. Dürre, P. Handbook on Clostridia. 2005. Taylor and Francis, CRC Press.
9. Fox M.E., Lemmon M.J., Mauchline M.L., Davis T.O., Giaccia A.J., Minton N.P., and Brown J.M. Anaerobic bacteria as a delivery system for cancer gene therapy: in vitro activation of 5-fluorocytosine by genetically engineered clostridia. Gene Ther. 3 (1996) 173-178
10. Frazier C.L., San Filippo J., Lambowitz A.M., and Mills D.A. Genetic manipulation of Lactococcus lactis by using targeted group II introns: generation of stable insertions without selection. Appl. Environ. Microbiol. 69 (2003) 1121-1128
11. Gilbert H.J., Blazek R., Bullman H.M., and Minton N.P. Cloning and expression of the Erwinia chrysanthemi asparaginase gene in Escherichia coli and Erwinia carotovora. J. Gen. Microbiol. 132 (1986) 151-160
12. Girbal L., Mortier-Barriere I., Raynaud F., Rouanet C., Croux C., and Soucaille P. Development of a sensitive gene expression reporter system and an inducible promoter-repressor system for Clostridium acetobutylicum. Appl. Environ. Microbiol. 69 (2003) 4985-4988
13. Green E.M., and Bennett G.N. Inactivation of an aldehyde/alcohol dehydrogenase gene from Clostridium acetobutylicum ATCC 824. Appl. Biochem. Biotechnol. 213 (1996) 57-58
14. Green E.M., Boynton Z.L., Harris L.M., Rudolph F.B., Papoutsakis E.T., and Bennett G.N. Genetic manipulation of acid and solvent formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824. Microbiology 142 (1996) 2079-2086
15. Guo H., Karberg M., Long M., Jones III J.P., Sullenger B., and Lambowitz A.M. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science 289 (2000) 452-457
16. Harris L.M., Welker N.E., and Papoutsakis E.T. Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824. J. Bacteriol. 184 (2002) 3586-3597
17. Hartmanis M.G.N., and Gatenbeck S. Intermediary metabolism in C. acetobutylicum: levels of enzymes involved in the formation of acetate and butyrate. Appl. Environ. Microbiol. 47 (1984) 1277-1283
18. Hussain H.A., Roberts A.P., and Mullany P. Generation of an erythromycin-sensitive derivative of Clostridium difficile strain 630 (630Deltaerm) and demonstration that the conjugative transposon Tn916DeltaE enters the genome of this strain at multiple sites. J. Med. Microbiol. 54 (2005) 137-141
19. Karberg M., Guo H., Zhong J., Coon R., Perutka J., and Lambowitz A.M. Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nat. Biotechnol. 19 (2001) 1162-1167
20. Liyanage H., Kashket S., Young M., and Kashket E.R. Clostridium beijerinckii and Clostridium difficile detoxify methylglyoxal by a novel mechanism involving glycerol dehydrogenase. Appl. Environ. Microbiol. 67 (2001) 2004-2010
21. Matsuura M., Saldanha R., Ma H., Wank H., Yang J., Mohr G., Cavanagh S., Dunny G.M., Belfort M., and Lambowitz A.M. A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. Genes Dev. 11 (1997) 2910-2924
22. Mermelstein L.D., and Papoutsakis E.T. In vivo methylation in Escherichia coli by the Bacillus subtilis phage φ{symbol}3T I methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 59 (1993) 1077-1081
23. Minton N.P. Clostridia in cancer therapy. Nat. Microbiol. Rev. 1 (2003) 237-242
24. Minton N.P., and Morris J.G. Isolation and partial characterisation of three cryptic plasmids from strains of Clostridium butyricum. J. Gen. Microbiol. 127 (1981) 325-331
25. Minton N.P., Brehm J.K., Oultram J.D., Thompson D.E., Swinfield T.J., Pennock A., Schimming S., Whelan S.E., Vetter U., Young M., and Staudenbauer W.L. Vector systems for the genetic analysis of Clostridium acetobutylicum. In: Boriello P., and Hardie J. (Eds). Anaerobes in Human Medicine and Industry (1990), Wrightson Publishing, Petersfield, UK 187-206
26. Mohr G., Smith D., Belfort M., and Lambowitz A.M. Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes Dev. 14 (2000) 559-573
27. Nair R.V., Green E.M., Watson D.E., Bennett G.N., and Papoutsakis E.T. Regulation of the sol locus genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 by a putative transcriptional repressor. J. Bacteriol. 181 (1999) 319-330
28. O'Connor J.R., Lyras D., Farrow K.A., Adams V., Powell D.R., Hinds J., Cheung J.K., and Rood J.I. Construction and analysis of chromosomal Clostridium difficile mutants. Mol. Microbiol. 61 (2006) 1335-1351
29. Perutka J., Wang W., Goerlitz D., and Lambowitz A.M. Use of computer-designed group II introns to disrupt Escherichia coli DExH/D-box protein and DNA helicase genes. J. Mol. Biol. 336 (2004) 421-439
30. Purdy D., O'Keeffe T.A., Elmore M., Herbert M., McLeod A., Bokori-Brown M., Ostrowski A., and Minton N.P. Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction barrier. Mol. Microbiol. 46 (2002) 439-452
31. Shaw W.V. Chloramphenicol acetyltransferase from chloramphenicol-resistant bacteria. Methods Enzymol. 43 (1975) 737-755
32. Shimizu T., Ba-Thein W., Tamaki M., and Hayashi H. The virR gene, a member of a class of two-component response regulators, regulates the production of perfringolysin O, collagenase, and hemagglutinin in Clostridium perfringens. J. Bacteriol. 176 (1994) 1616-1623
33. Sloan J., Warner T.A., Scott P.T., Bannam T.L., Berryman D.I., and Rood J.I. Construction of a sequenced Clostridium perfringens-Escherichia coli shuttle plasmid. Plasmid 27 (1992) 207-219
34. Swinfield T.J., Oultram J.D., Thompson D.E., Brehm J.K., and Minton N.P. Physical characterisation of the replication region of the Streptococcus faecalis plasmid pAM β1. Gene 87 (1990) 79-90
35. Thomas C.A., Tummala S.B., and Paoutsakis E.T. Metabolic engineering of soventogenic clostridia. In: Dürre P. (Ed). Handbook on Clostridia (2005), CRC Press 813-830
36. Tummala S.B., Welker N.E., and Papoutsakis E.T. Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J. Bacteriol. 185 (2003) 1923-1934
37. Wilkinson S.R., and Young M. Targeted integration of genes into the Clostridium acetobutylicum chromosome. Microbiology 140 (1994) 89-95
38. Yao J., Zhong J., Fang Y., Geisinger E., Novick R.P., and Lambowitz A.M. Use of targetrons to disrupt essential and nonessential genes in Staphylococcus aureus reveals temperature sensitivity of Ll.LtrB group II intron splicing. RNA 12 (2006) 1271-1281
39. Zhong J., Karberg M., and Lambowitz A.M. Targeted and random bacterial gene disruption using a group II intron (targetron) vector containing a retrotransposition-activated selectable marker. Nucleic Acids Res. 31 (2003) 1656-1664