Sequence analysis of plasmid pIR52-1 from Lactobacillus helveticus R0052 and investigation of its origin of replication

Plasmid

Volumn 63, Issue 2, 2010, Pages 108-117

  Hagen, Karen E ^a   Tramp, Cody A ^b   Altermann, Eric ^c   Welker, Dennis L ^b   Tompkins, Thomas A ^a  

^a INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

^b UTAH STATE UNIVERSITY   (United States)

^c AGRESEARCH GRASSLANDS   (New Zealand)

Author keywords

Cloning vector; Copy number control; Origin of replication; Plasmid; RepA_N; Toxin antitoxin

Indexed keywords

BACTERIAL PROTEIN; PLASMID VECTOR; PROTEIN REPA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENETICS; BACTERIUM TRANSFORMATION; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA REPLICATION ORIGIN; DNA SEQUENCE; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC CONSERVATION; LACTOBACILLUS HELVETICUS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; PLASMID PIR52 1; SEQUENCE ANALYSIS;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA REPLICATION; GENE DOSAGE; GENETIC VECTORS; LACTOBACILLUS HELVETICUS; LACTOBACILLUS PLANTARUM; MOLECULAR SEQUENCE DATA; PLASMIDS; REPLICATION ORIGIN; SEQUENCE ANALYSIS, DNA; TRANSFORMATION, GENETIC;

BACTERIA (MICROORGANISMS); LACTOBACILLUS; LACTOBACILLUS HELVETICUS; POSIBACTERIA;

EID: 75549083582     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2009.12.004     Document Type: Article

References (45)

1. Altermann E., Klaenhammer T.R. GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes. Omics 2003, 7:161-169.
2. Bhowmik T., Steele J.L. Cloning, characterization and insertional inactivation of the Lactobacillus helveticus d(̄) lactate dehydrogenase gene. Appl. Microbiol. Biotechnol. 1994, 41:432-439.
3. Chassy B.M., Gibson E., Giuffrida A. Evidence for extrachromosomal elements in Lactobacillus. J. Bacteriol. 1976, 127:1576-1578.
4. Christensen S.K., Mikkelsen M., Pedersen K., Gerdes K. RelE, a global inhibitor of translation, is activated during nutritional stress. Proc. Natl. Acad. Sci. USA 2001, 98:14328-14333.
5. Claesson M.J., Li Y., Leahy S., Canchaya C., van Pijkeren J.P., Cerdeno-Tarraga A.M., Parkhill J., Flynn S., O'Sullivan G.C., Collins J.K., Higgins D., Shanahan F., Fitzgerald G.F., van Sinderen D., O'Toole P.W. From the cover: multireplicon genome architecture of Lactobacillus salivarius. Proc. Natl. Acad. Sci. USA 2006, 103:6718-6723.
6. Dao M.L., Ferretti J.J. Streptococcus-Escherichia coli shuttle vector pSA3 and its use in the cloning of streptococcal genes. Appl. Environ. Microbiol. 1985, 49:115-119.
7. de Los Reyes-Gavilan C.G., Limsowtin G.K., Sechaud L., Veaux M., Accolas J.P. Evidence for a plasmid-linked restriction-modification system in Lactobacillus helveticus. Appl. Environ. Microbiol. 1990, 56:3412-3419.
8. de Rossi E., Brigidi P., Riccardi G., Milano A., Matteuzzi D. Preliminary studies on the correlation between the plasmid pLHJ1 and its proteolytic activity in Lactobacillus helveticus S 36.2. Physical mapping and molecular cloning of the plasmid in Escherichia coli. Microbiologica 1989, 12:273-276.
9. Desmond C., Ross R.P., Fitzgerald G., Stanton C. Sequence analysis of the plasmid genome of the probiotic strain Lactobacillus paracasei NFBC338 which includes the plasmids pCD01 and pCD02. Plasmid 2005, 54:160-175.
10. Diaz-Lopez T., Lages-Gonzalo M., Serrano-Lopez A., Alfonso C., Rivas G., Diaz-Orejas R., Giraldo R. Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. J. Biol. Chem. 2003, 278:18606-18616.
11. Fang F., Flynn S., Li Y., Claesson M.J., van Pijkeren J.P., Collins J.K., van Sinderen D., O'Toole P.W. Characterization of endogenous plasmids from Lactobacillus salivarius UCC118. Appl. Environ. Microbiol. 2008, 74:3216-3228.
12. Ferreira I.D., Rosario V.E., Cravo P.V. Real-time quantitative PCR with SYBR Green I detection for estimating copy numbers of nine drug resistance candidate genes in Plasmodium falciparum. Malar. J. 2006, 5:1.
13. Fortina M.G., Silva M. Mapping of two plasmids from Lactobacillus helveticus ILC 54, plasmid curing and preliminary studies on their involvement in lactose metabolism and peptidase activity. Biotechnol. Lett. 1996, 18:1003-1006.
14. Fortina M.G., Parini C., Rossi P., Manachini P.L. Mapping of three plasmids from Lactobacillus helveticus ATCC 15009. Lett. Appl. Microbiol. 1993, 17:303-306.
15. Francia M.V., Fujimoto S., Tille P., Weaver K.E., Clewell D.B. Replication of Enterococcus faecalis pheromone-responding plasmid pAD1: location of the minimal replicon and oriV site and RepA involvement in initiation of replication. J. Bacteriol. 2004, 186:5003-5016.
16. Galvani C., Terry J., Ishiguro E.E. Purification of the RelB and RelE proteins of Escherichia coli: RelE binds to RelB and to ribosomes. J. Bacteriol. 2001, 183:2700-2703.
17. Gering M., Gotz F., Bruckner R. Sequence and analysis of the replication region of the Staphylococcus xylosus plasmid pSX267. Gene 1996, 182:117-122.
18. Gotfredsen M., Gerdes K. The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family. Mol. Microbiol. 1998, 29:1065-1076.
19. Hashiba H., Takiguchi R., Jyoho K., Aoyama K. Establishment of a host-vector system in Lactobacillus helveticus with beta-galactosidase activity as a selection marker. Biosci. Biotechnol. Biochem. 1992, 56:190-194.
20. Ito Y., Kawai Y., Arakawa K., Honme Y., Sasaki T., Saito T. A conjugative plasmid from Lactobacillus gasseri LA39 that carries genes for the circular bacteriocin gassericin A-production and immunity. Appl. Environ. Microbiol. 2009, 75:6340-6351.
21. Jeong S.J., Park J.Y., Lee H.J., Kim J.H. Characterization of pFMBL1, a small cryptic plasmid isolated from Leuconostoc mesenteroides SY2. Plasmid 2007, 57:314-323.
22. Kleerebezem M., Boekhorst J., van Kranenburg R., Molenaar D., Kuipers O.P., Leer R., Tarchini R., Peters S.A., Sandbrink H.M., Fiers M.W., Stiekema W., Lankhorst R.M., Bron P.A., Hoffer S.M., Groot M.N., Kerkhoven R., de Vries M., Ursing B., de Vos W.M., Siezen R.J. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. USA 2003, 100:1990-1995.
23. Kwong S.M., Skurray R.A., Firth N. Replication control of staphylococcal multiresistance plasmid pSK41: an antisense RNA mediates dual-level regulation of Rep expression. J. Bacteriol. 2006, 188:4404-4412.
24. Kwong S.M., Lim R., Lebard R.J., Skurray R.A., Firth N. Analysis of the pSK1 replicon, a prototype from the staphylococcal multiresistance plasmid family. Microbiology 2008, 154:3084-3094.
25. Le Chatelier E., Ehrlich S.D., Janniere L. Countertranscript-driven attenuation system of the pAM beta 1 repE gene. Mol. Microbiol. 1996, 20:1099-1112.
26. Maguin E., Prevost H., Ehrlich S.D., Gruss A. Efficient insertional mutagenesis in lactococci and other Gram-positive bacteria. J. Bacteriol. 1996, 178:931-935.
27. Makarova K., Slesarev A., Wolf Y., Sorokin A., Mirkin B., Koonin E., Pavlov A., Pavlova N., Karamychev V., Polouchine N., Shakhova V., Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K., Goodstein D.M., Hawkins T., Plengvidhya V., Welker D., Hughes J., Goh Y., Benson A., Baldwin K., Lee J.H., Diaz-Muniz I., Dosti B., Smeianov V., Wechter W., Barabote R., Lorca G., Altermann E., Barrangou R., Ganesan B., Xie Y., Rawsthorne H., Tamir D., Parker C., Breidt F., Broadbent J., Hutkins R., O'Sullivan D., Steele J., Unlu G., Saier M., Klaenhammer T., Richardson P., Kozyavkin S., Weimer B., Mills D. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. USA 2006, 103:15611-15616.
28. Nieto C., Pellicer T., Balsa D., Christensen S.K., Gerdes K., Espinosa M. The chromosomal relBE2 toxin-antitoxin locus of Streptococcus pneumoniae: characterization and use of a bioluminescence resonance energy transfer assay to detect toxin-antitoxin interaction. Mol. Microbiol. 2006, 59:1280-1296.
29. Pedersen K., Christensen S.K., Gerdes K. Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol. Microbiol. 2002, 45:501-510.
30. Pedersen K., Zavialov A.V., Pavlov M.Y., Elf J., Gerdes K., Ehrenberg M. The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell 2003, 112:131-140.
31. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29:e45.
32. Pridmore D., Stefanova T., Mollet B. Cryptic plasmids from Lactobacillus helveticus and their evolutionary relationship. FEMS Microbiol. Lett. 1994, 124:301-305.
33. Ricci G., Borgo F., Fortina M.G. Plasmids from Lactobacillus helveticus: distribution and diversity among natural isolates. Lett. Appl. Microbiol. 2006, 42:254-258.
34. Sambrook J., Fritsch E., Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor. second ed.
35. Skulj M., Okrslar V., Jalen S., Jevsevar S., Slanc P., Strukelj B., Menart V. Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes. Microb. Cell Fact. 2008, 7:6.
36. Smeianov V.V., Wechter P., Broadbent J.R., Hughes J.E., Rodriguez B.T., Christensen T.K., Ardo Y., Steele J.L. Comparative high-density microarray analysis of gene expression during growth of Lactobacillus helveticus in milk versus rich culture medium. Appl. Environ. Microbiol. 2007, 73:2661-2672.
37. Takiguchi R., Hashiba H., Aoyama K., Ishii S. Complete nucleotide sequence and characterization of a cryptic plasmid from Lactobacillus helveticus subsp. Jugurti. Appl. Environ. Microbiol. 1989, 55:1653-1655.
38. Tanaka T., Ogura M. A novel Bacillus natto plasmid pLS32 capable of replication in Bacillus subtilis. FEBS Lett. 1998, 422:243-246.
39. Thompson J.K., McConville K.J., Nicholson C., Collins M.A. DNA cloning in Lactobacillus helveticus by the exconjugation of recombinant mob-containing plasmid constructs from strains of transformable lactic acid bacteria. Plasmid 2001, 46:188-201.
40. van Kranenburg R., Golic N., Bongers R., Leer R.J., de Vos W.M., Siezen R.J., Kleerebezem M. Functional analysis of three plasmids from Lactobacillus plantarum. Appl. Environ. Microbiol. 2005, 71:1223-1230.
41. Walker D.C., Klaenhammer T.R. Isolation of a novel IS3 group insertion element and construction of an integration vector for Lactobacillus spp. J. Bacteriol. 1994, 176:5330-5340.
42. Weaver, K.E., Kwong, S.M., Firth, N., Francia, M.V., 2009. The RepA N replicons of Gram-positive bacteria: a family of broadly distributed but narrow host range plasmids. Plasmid. doi:10.1016/j.plasmid.2008.11.004.
43. Yamamoto N., Takano T. Isolation and characterization of a plasmid from Lactobacillus helveticus CP53. Biosci. Biotechnol. Biochem. 1996, 60:2069-2070.
44. Zhang W., Yu D., Sun Z., Chen X., Bao Q., Meng H., Hu S., Zhang H. Complete nucleotide sequence of plasmid plca36 isolated from Lactobacillus casei Zhang. Plasmid 2008, 60:131-135.
45. Zucker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.