In silico prediction of horizontal gene transfer in Streptococcus thermophilus

Archives of Microbiology

Volumn 193, Issue 4, 2011, Pages 287-297

  Eng, Catherine ^a,b   Thibessard, Annabelle ^a   Danielsen, Morten ^c   Rasmussen, Thomas Bovbjerg ^c   Mari, Jean François ^b   Leblond, Pierre ^a  

^a UNIVERSITÉ DE LORRAINE   (France)

^b LORIA   (France)

^c CHR HANSEN A S   (Denmark)

Author keywords

Gene transfer; Genome mining; Streptococcus thermophilus

Indexed keywords

EXOPOLYSACCHARIDE; RECOMBINASE;

ADAPTATION; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIOPHAGE; COMPUTER MODEL; CONTROLLED STUDY; DATA MINING; FIRMICUTES; GENE LOSS; GENE SEQUENCE; HORIZONTAL GENE TRANSFER; MILK; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; STATISTICAL ANALYSIS; STREPTOCOCCUS THERMOPHILUS;

ALGORITHMS; DATA MINING; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMIC ISLANDS; MARKOV CHAINS; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; STOCHASTIC PROCESSES; STREPTOCOCCUS THERMOPHILUS;

FIRMICUTES; STREPTOCOCCUS THERMOPHILUS;

EID: 79954414407     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-010-0671-8     Document Type: Article

References (32)

1. A Ammann H Neve A Geis KJ Heller 2008 Plasmid transfer via transduction from Streptococcus thermophilus to Lactococcus lactis J Bacteriol 190 3083 3087 18263725 10.1128/JB.01448-07 1:CAS:528:DC%2BD1cXkslygtr4%3D (Pubitemid 351508209)
2. Angel CS, Ruzek M, Hostetter MK (1994) Degradation of C3 by Streptococcus pneumoniae. J Infect Dis 170:600-608 (Pubitemid 24262261)
3. LE Baum T Petrie G Soules N Weiss 1970 A maximization technique occurring in the statistical analysis of probabilistic functions of markov chains Ann Math Stat 41 164 171 10.1214/aoms/1177697196
4. T Blomqvist H Steinmoen LS Havarstein 2006 Natural genetic transformation: a novel tool for efficient genetic engineering of the dairy bacterium Streptococcus thermophilus Appl Environ Microbiol 72 6751 6756 17021227 10.1128/AEM.01156-06 1:CAS:528:DC%2BD28XhtFalsLjF (Pubitemid 44582918)
5. F Bourgoin A Pluvinet B Gintz B Decaris G Guedon 1999 Are horizontal transfers involved in the evolution of the Streptococcus thermophilus exopolysaccharide synthesis loci? Gene 233 151 161 10375631 10.1016/S0378- 1119(99)00144-4 1:CAS:528:DyaK1MXksV2rsbw%3D (Pubitemid 29353234)
6. M Brochet E Couve P Glaser G Guedon S Payot 2008 Integrative conjugative elements and related elements are major contributors to the genome diversity of Streptococcus agalactiae J Bacteriol 190 6913 6917 18708498 10.1128/JB.00824-08 1:CAS:528:DC%2BD1cXht1ChtrnO
7. V Burrus G Pavlovic B Decaris G Guedon 2002 The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration Plasmid 48 77 97 12383726 10.1016/S0147-619X(02)00102-6 1:CAS:528:DC%2BD38XnsVerurk%3D (Pubitemid 35300800)
8. C Delorme C Poyart SD Ehrlich P Renault 2007 Extent of horizontal gene transfer in evolution of Streptococci of the salivarius group J Bacteriol 189 1330 1341 17085557 10.1128/JB.01058-06 1:CAS:528:DC%2BD2sXhvVKkurg%3D (Pubitemid 46239754)
9. WF Doolittle 1999 Phylogenetic classification and the universal tree Science 284 2124 2129 10381871 10.1126/science.284.5423.2124 1:CAS:528:DyaK1MXkt1Kgsbs%3D (Pubitemid 29297466)
10. JA Du Preez 1998 Efficient training of high-order hidden Markov model using first-order representations Comput Speech Lang 12 23 39 10.1006/csla.1997.0037 (Pubitemid 128395375)
11. C Eng C Asthana B Aigle S Hergalant JF Mari P Leblond 2009 A new data mining approach for the detection of bacterial promoters combining stochastic and combinatorial methods J Comput Biol 16 1211 1225 19772433 10.1089/cmb.2008.0122 1:CAS:528:DC%2BD1MXhtFGlu73I
12. A Fernandez A Thibessard F Borges B Gintz B Decaris N Leblond-Bourget 2004 Characterization of oxidative stress-resistant mutants of Streptococcus thermophilus CNRZ368 Arch Microbiol 182 364 372 15378231 10.1007/s00203-004- 0712-2 1:CAS:528:DC%2BD2cXosVSlu7o%3D (Pubitemid 39506387)
13. L Fontaine, et al. 2007 Quorum-sensing regulation of the production of Blp bacteriocins in Streptococcus thermophilus J Bacteriol 189 7195 7205 17693498 10.1128/JB.00966-07 1:CAS:528:DC%2BD2sXhtFOnurrO (Pubitemid 47557333)
14. L Fontaine, et al. 2010 A novel pheromone quorum-sensing system controls the development of natural competence in Streptococcus thermophilus and Streptococcus salivarius J Bacteriol 192 1444 1454 20023010 10.1128/JB.01251-09 1:CAS:528:DC%2BC3cXivVSns7g%3D
15. S Garcia-Vallve E Guzman MA Montero A Romeu 2003 HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes Nucleic Acids Res 31 187 189 12519978 10.1093/nar/gkg004 1:CAS:528:DC%2BD3sXhvFSntL0%3D (Pubitemid 36150361)
16. Y He 1988 Extended Viterbi algorithm for second-order hidden Markov process Proc IEEE Int Conf Pattern Recognit 2 718 720
17. Kullback S, Leibler RA (1951) On information and sufficiency. Ann Math Stat 22(1):79-86
18. S Layec B Decaris N Leblond-Bourget 2008 Diversity of firmicutes peptidoglycan hydrolases and specificities of those involved in daughter cell separation Res Microbiol 159 507 515 18656532 10.1016/j.resmic.2008.06.008 1:CAS:528:DC%2BD1cXhtFOltrvJ
19. F Le Ber M Benoît C Schott JF Mari C Mignolet 2006 Studying crop sequences with carrotage, a HMM-based data mining software Ecol Modell 191 170 185 10.1016/j.ecolmodel.2005.08.031 (Pubitemid 41735461)
20. Liu M, Siezen RJ, Nauta A (2009) In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing. Appl Environ Microbiol 75(12):4120-4129
21. Mari J-F, Haton J-P, Kriouile A (1997) Automatic word recognition based on second-order hidden Markov models. IEEE Trans. Speech Audio Process 5:22-25 (Pubitemid 127746031)
22. Y Nakamura T Itoh H Matsuda T Gojobori 2004 Biased biological functions of horizontally transferred genes in prokaryotic genomes Nat Genet 36 760 766 15208628 10.1038/ng1381 1:CAS:528:DC%2BD2cXlt1Cku7s%3D (Pubitemid 38886640)
23. P Nicolas, et al. 2002 Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models Nucleic Acids Res 30 1418 1426 11884641 10.1093/nar/30.6.1418 1:CAS:528:DC%2BD38XisVakt70%3D (Pubitemid 34679721)
24. H Nielsen J Engelbrecht S Brunak G von Heijne 1997 A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Int J Neural Syst 8 581 599 10065837 10.1142/S0129065797000537 1:STN:280:DyaK1M7mtlOhsg%3D%3D
25. G Pavlovic V Burrus A Toulmay F Choulet B Decaris G Guedon 2004 Characterization and evolution of a family of integrative and potentially conjugative or mobilizable elements from Streptococcus thermophilus Lait 84 7 14 10.1051/lait:2003042 1:CAS:528:DC%2BD2cXjtlGhsrw%3D (Pubitemid 38257786)
26. TB Rasmussen M Danielsen O Valina C Garrigues E Johansen MB Pedersen 2008 Streptococcus thermophilus core genome: comparative genome hybridization study of 47 strains Appl Environ Microbiol 74 4703 4710 18539806 10.1128/AEM.00132-08 1:CAS:528:DC%2BD1cXpslKktrs%3D
27. EP Rocha E Danchin 2002 Base composition bias might result from competition for metabolic resources Trends Genet 18 291 294 12044357 10.1016/S0168-9525(02)02690-2 1:CAS:528:DC%2BD38XktVCku7Y%3D (Pubitemid 34607118)
28. K Rutherford, et al. 2000 Artemis: sequence visualization and annotation Bioinformatics 16 944 945 11120685 10.1093/bioinformatics/16.10.944 1:CAS:528:DC%2BD3MXjvVWksw%3D%3D
29. EL Sonnhammer G von Heijne A Krogh 1998 A hidden Markov model for predicting transmembrane helices in protein sequences Proc Int Conf Intell Syst Mol Biol 6 175 182 9783223 1:STN:280:DyaK1cvls1GmsA%3D%3D
30. GS Vernikos J Parkhill 2006 Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands Bioinformatics 22 2196 2203 16837528 10.1093/ bioinformatics/btl369 1:CAS:528:DC%2BD28Xps1ygu7w%3D (Pubitemid 44390872)
31. S Waack, et al. 2006 Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models BMC Bioinformatics 7 142 16542435 10.1186/1471-2105-7-142 (Pubitemid 44026712)
32. SH Yoon CG Hur HY Kang YH Kim TK Oh JF Kim 2005 A computational approach for identifying pathogenicity islands in prokaryotic genomes BMC Bioinformatics 6 184 16033657 10.1186/1471-2105-6-184 (Pubitemid 41372482)