메뉴 건너뛰기




Volumn 194, Issue 1, 2012, Pages 195-196

Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN;

EID: 84855865488     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.06275-11     Document Type: Note
Times cited : (117)

References (52)
  • 1
    • 0031879986 scopus 로고    scopus 로고
    • The normal Lactobacillus flora of healthy human rectal and oral mucosa
    • Ahrné S, et al. 1998. The normal Lactobacillus flora of healthy human rectal and oral mucosa. J. Appl. Microbiol. 85:88-94.
    • (1998) J. Appl. Microbiol. , vol.85 , pp. 88-94
    • Ahrné, S.1
  • 2
    • 35748953471 scopus 로고    scopus 로고
    • The microbial ecology of a typical Italian salami during its natural fermentation
    • Aquilanti L, et al. 2007. The microbial ecology of a typical Italian salami during its natural fermentation. Int. J. Food Microbiol. 120:136-145.
    • (2007) Int. J. Food Microbiol. , vol.120 , pp. 136-145
    • Aquilanti, L.1
  • 3
    • 0025900434 scopus 로고
    • The occurrence and growth of microorganisms during the fermentation of fish sausage
    • Aryanta RW, Fleet GH, Buckle KA. 1991. The occurrence and growth of microorganisms during the fermentation of fish sausage. Int. J. Food Microbiol. 13:143-155.
    • (1991) Int. J. Food Microbiol. , vol.13 , pp. 143-155
    • Aryanta, R.W.1    Fleet, G.H.2    Buckle, K.A.3
  • 4
    • 0043031233 scopus 로고    scopus 로고
    • Microbial quality and direct PCR identification of lactic acid bacteria and nonpathogenic staphylococci from artisanal low-acid sausages
    • Aymerich T, Martin B, Garriga M, Hugas M. 2003. Microbial quality and direct PCR identification of lactic acid bacteria and nonpathogenic staphylococci from artisanal low-acid sausages. Appl. Environ. Microbiol. 69:4583-4594.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 4583-4594
    • Aymerich, T.1    Martin, B.2    Garriga, M.3    Hugas, M.4
  • 5
    • 40549120596 scopus 로고    scopus 로고
    • The RAST server: rapid annotations using subsystems technology
    • Aziz RK, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75.
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.K.1
  • 6
    • 9144222162 scopus 로고    scopus 로고
    • The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content
    • Boekhorst J, et al. 2004. The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology 150:3601-3611.
    • (2004) Microbiology , vol.150 , pp. 3601-3611
    • Boekhorst, J.1
  • 7
    • 33750963625 scopus 로고    scopus 로고
    • The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment
    • Boekhorst J, Wels M, Kleerebezem M, Siezen RJ. 2006. The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology 152:3175-3183.
    • (2006) Microbiology , vol.152 , pp. 3175-3183
    • Boekhorst, J.1    Wels, M.2    Kleerebezem, M.3    Siezen, R.J.4
  • 8
    • 4344567816 scopus 로고    scopus 로고
    • Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice
    • Bron PA, Grangette C, Mercenier A, de Vos WM, Kleerebezem M. 2004. Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice. J. Bacteriol. 186:5721-5729.
    • (2004) J. Bacteriol. , vol.186 , pp. 5721-5729
    • Bron, P.A.1    Grangette, C.2    Mercenier, A.3    de Vos, W.M.4    Kleerebezem, M.5
  • 9
    • 9244249176 scopus 로고    scopus 로고
    • Genetic characterization of the bile salt response in Lactobacillus plantarum and analysis of responsive promoters in vitro and in situ in the gastrointestinal tract
    • Bron PA, et al. 2004. Genetic characterization of the bile salt response in Lactobacillus plantarum and analysis of responsive promoters in vitro and in situ in the gastrointestinal tract. J. Bacteriol. 186:7829-7835.
    • (2004) J. Bacteriol. , vol.186 , pp. 7829-7835
    • Bron, P.A.1
  • 10
    • 35448945678 scopus 로고    scopus 로고
    • Dynamics of competitive population abundance of Lactobacillus plantarum ivi gene mutants in faecal samples after passage through the gastrointestinal tract of mice
    • Bron PA, Meijer M, Bongers RS, de Vos WM, Kleerebezem M. 2007. Dynamics of competitive population abundance of Lactobacillus plantarum ivi gene mutants in faecal samples after passage through the gastrointestinal tract of mice. J. Appl. Microbiol. 103:1424-1434.
    • (2007) J. Appl. Microbiol. , vol.103 , pp. 1424-1434
    • Bron, P.A.1    Meijer, M.2    Bongers, R.S.3    de Vos, W.M.4    Kleerebezem, M.5
  • 11
    • 58149200943 scopus 로고    scopus 로고
    • The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics
    • Cantarel BL, et al. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37: D233-D238.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 233-238
    • Cantarel, B.L.1
  • 12
    • 56649123520 scopus 로고    scopus 로고
    • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
    • Carver T, et al. 2008. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24:2672-2676.
    • (2008) Bioinformatics , vol.24 , pp. 2672-2676
    • Carver, T.1
  • 13
    • 24044433279 scopus 로고    scopus 로고
    • ACT: the Artemis comparison tool
    • Carver TJ, et al. 2005. ACT: the Artemis comparison tool. Bioinformatics 21:3422-3423.
    • (2005) Bioinformatics , vol.21 , pp. 3422-3423
    • Carver, T.J.1
  • 14
    • 0037640904 scopus 로고    scopus 로고
    • Bacterial community structure and location in Stilton cheese
    • Ercolini D, Hill PJ, Dodd CE. 2003. Bacterial community structure and location in Stilton cheese. Appl. Environ. Microbiol. 69:3540-3548.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 3540-3548
    • Ercolini, D.1    Hill, P.J.2    Dodd, C.E.3
  • 15
    • 33644876020 scopus 로고    scopus 로고
    • Pfam: clans, web tools and services
    • Finn RD, et al. 2006. Pfam: clans, web tools and services. Nucleic Acids Res. 34:D247-D251.
    • (2006) Nucleic Acids Res. , vol.34
    • Finn, R.D.1
  • 16
    • 75549090603 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Finn RD, et al. 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211-D222.
    • (2010) Nucleic Acids Res. , vol.38
    • Finn, R.D.1
  • 17
    • 42449147860 scopus 로고    scopus 로고
    • A generic approach to identify transcription factor-specific operator motifs; inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1
    • Francke C, Kerkhoven R, Wels M, Siezen RJ. 2008. A generic approach to identify transcription factor-specific operator motifs; inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.BMC Genomics 9:145.
    • (2008) BMC Genomics , vol.9 , pp. 145
    • Francke, C.1    Kerkhoven, R.2    Wels, M.3    Siezen, R.J.4
  • 18
    • 27144533653 scopus 로고    scopus 로고
    • Reconstructing the metabolic network of a bacterium from its genome
    • Francke C, Siezen RJ, Teusink B. 2005. Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 13:550-558.
    • (2005) Trends Microbiol. , vol.13 , pp. 550-558
    • Francke, C.1    Siezen, R.J.2    Teusink, B.3
  • 19
    • 33748917136 scopus 로고    scopus 로고
    • Carbohydrate, peptide and lipid metabolism of lactic acid bacteria in sourdough
    • Gänzle MG, Vermeulen N, Vogel RF. 2007. Carbohydrate, peptide and lipid metabolism of lactic acid bacteria in sourdough. Food Microbiol. 24:128-138.
    • (2007) Food Microbiol. , vol.24 , pp. 128-138
    • Gänzle, M.G.1    Vermeulen, N.2    Vogel, R.F.3
  • 20
    • 0035916981 scopus 로고    scopus 로고
    • Selection and characterization of mixed starter cultures for lactic acid fermentation of carrot, cabbage, beet and onion vegetable mixtures
    • Gardner NJ, Savard T, Obermeier P, Caldwell G, Champagne CP. 2001. Selection and characterization of mixed starter cultures for lactic acid fermentation of carrot, cabbage, beet and onion vegetable mixtures. Int. J. Food Microbiol. 64:261-275.
    • (2001) Int. J. Food Microbiol. , vol.64 , pp. 261-275
    • Gardner, N.J.1    Savard, T.2    Obermeier, P.3    Caldwell, G.4    Champagne, C.P.5
  • 21
    • 75749141176 scopus 로고    scopus 로고
    • Biodiversity of mannose-specific adhesion in Lactobacillus plantarum revisited: strain-specific domain composition of the mannose-adhesin
    • Gross G, Snel J, Boekhorst J, Smits MA, Kleerebezem M. 2010. Biodiversity of mannose-specific adhesion in Lactobacillus plantarum revisited: strain-specific domain composition of the mannose-adhesin. Benef. Microbes 1:61-66.
    • (2010) Benef. Microbes , vol.1 , pp. 61-66
    • Gross, G.1    Snel, J.2    Boekhorst, J.3    Smits, M.A.4    Kleerebezem, M.5
  • 22
    • 53549117107 scopus 로고    scopus 로고
    • Mannose-specific interaction of Lactobacillus plantarum with porcine jejunal epithelium
    • Gross G, et al. 2008. Mannose-specific interaction of Lactobacillus plantarum with porcine jejunal epithelium. FEMS Immunol. Med. Microbiol. 54:215-223.
    • (2008) FEMS Immunol. Med. Microbiol. , vol.54 , pp. 215-223
    • Gross, G.1
  • 24
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12:656-664.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 25
    • 0037452621 scopus 로고    scopus 로고
    • Complete genome sequence of Lactobacillus plantarum WCFS1
    • Kleerebezem M, et al. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. U. S. A. 100:1990-1995.
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 1990-1995
    • Kleerebezem, M.1
  • 26
    • 75749140534 scopus 로고    scopus 로고
    • The extracellular biology of the lactobacilli
    • Kleerebezem M, et al. 2010. The extracellular biology of the lactobacilli. FEMS Microbiol. Rev. 34:199-230.
    • (2010) FEMS Microbiol. Rev. , vol.34 , pp. 199-230
    • Kleerebezem, M.1
  • 27
    • 33846152023 scopus 로고    scopus 로고
    • Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice
    • Marco ML, Bongers RS, de Vos WM, Kleerebezem M. 2007. Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice. Appl. Environ. Microbiol. 73:124-132.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 124-132
    • Marco, M.L.1    Bongers, R.S.2    de Vos, W.M.3    Kleerebezem, M.4
  • 28
    • 77958455790 scopus 로고    scopus 로고
    • Convergence in probiotic Lactobacillus gutadaptive responses in humans and mice
    • Marco ML, et al. 2010. Convergence in probiotic Lactobacillus gutadaptive responses in humans and mice. ISME J. 4:1481-1484.
    • (2010) ISME J. , vol.4 , pp. 1481-1484
    • Marco, M.L.1
  • 29
    • 70349684488 scopus 로고    scopus 로고
    • Lifestyle of Lactobacillus plantarum in the mouse caecum
    • Marco ML, et al. 2009. Lifestyle of Lactobacillus plantarum in the mouse caecum. Environ. Microbiol. 11:2747-2757.
    • (2009) Environ. Microbiol. , vol.11 , pp. 2747-2757
    • Marco, M.L.1
  • 30
    • 77956288094 scopus 로고    scopus 로고
    • Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization
    • Meijerink M, et al. 2010. Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization. PLoS One 5:e10632.
    • (2010) PLoS One , vol.5
    • Meijerink, M.1
  • 31
    • 24344475251 scopus 로고    scopus 로고
    • Exploring Lactobacillus plantarum genome diversity by using microarrays
    • Molenaar D, et al. 2005. Exploring Lactobacillus plantarum genome diversity by using microarrays. J. Bacteriol. 187:6119-6127.
    • (2005) J. Bacteriol. , vol.187 , pp. 6119-6127
    • Molenaar, D.1
  • 33
    • 0037208159 scopus 로고    scopus 로고
    • The ERGO genome analysis and discovery system
    • Overbeek R, et al. 2003. The ERGO genome analysis and discovery system. Nucleic Acids Res. 31:164-171.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 164-171
    • Overbeek, R.1
  • 34
    • 23944432874 scopus 로고    scopus 로고
    • Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum
    • Pretzer G, et al. 2005. Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum. J. Bacteriol. 187:6128-6136.
    • (2005) J. Bacteriol. , vol.187 , pp. 6128-6136
    • Pretzer, G.1
  • 35
    • 23144458473 scopus 로고    scopus 로고
    • InterProScan: protein domains identifier
    • Quevillon E, et al. 2005. InterProScan: protein domains identifier. Nucleic Acids Res. 33:W116-W120.
    • (2005) Nucleic Acids Res. , vol.33
    • Quevillon, E.1
  • 36
    • 0033635022 scopus 로고    scopus 로고
    • Artemis: sequence visualization and annotation
    • Rutherford K, et al. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945.
    • (2000) Bioinformatics , vol.16 , pp. 944-945
    • Rutherford, K.1
  • 38
    • 78651330012 scopus 로고    scopus 로고
    • BRENDA, the enzyme information system in 2011
    • Scheer M, et al. 2011. BRENDA, the enzyme information system in 2011. Nucleic Acids Res. 39:D670-D676.
    • (2011) Nucleic Acids Res. , vol.39
    • Scheer, M.1
  • 39
    • 33747012649 scopus 로고    scopus 로고
    • Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria
    • Siezen R, et al. 2006. Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics 7:126.
    • (2006) BMC Genomics , vol.7 , pp. 126
    • Siezen, R.1
  • 40
    • 80052255726 scopus 로고    scopus 로고
    • Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer
    • Siezen RJ, van Hylckama Vlieg JET. 2011. Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb. Cell Fact. 10:S3.
    • (2011) Microb. Cell Fact. , vol.10
    • Siezen, R.J.1    van Hylckama Vlieg, J.E.T.2
  • 41
    • 75749155705 scopus 로고    scopus 로고
    • Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches
    • Siezen RJ, et al. 2010. Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ. Microbiol. 12:758-773.
    • (2010) Environ. Microbiol. , vol.12 , pp. 758-773
    • Siezen, R.J.1
  • 43
    • 29244461323 scopus 로고    scopus 로고
    • In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments
    • Teusink B, et al. 2005. In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl. Environ. Microbiol. 71:7253-7262.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 7253-7262
    • Teusink, B.1
  • 44
    • 67650904950 scopus 로고    scopus 로고
    • Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation
    • Teusink B, Wiersma A, Jacobs L, Notebaart RA, Smid EJ. 2009. Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput. Biol. 5:e1000410.
    • (2009) PLoS Comput. Biol , vol.5
    • Teusink, B.1    Wiersma, A.2    Jacobs, L.3    Notebaart, R.A.4    Smid, E.J.5
  • 45
    • 33846015888 scopus 로고    scopus 로고
    • Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
    • Teusink B, et al. 2006. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J. Biol. Chem. 281:40041-40048.
    • (2006) J. Biol. Chem. , vol.281 , pp. 40041-40048
    • Teusink, B.1
  • 46
    • 50249150951 scopus 로고    scopus 로고
    • Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo
    • Troost FJ, et al. 2008. Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo. BMC Genomics 9:374.
    • (2008) BMC Genomics , vol.9 , pp. 374
    • Troost, F.J.1
  • 47
    • 60549089819 scopus 로고    scopus 로고
    • Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance
    • van Baarlen P, et al. 2009. Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc. Natl. Acad. Sci. U. S. A. 106:2371-2376.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 2371-2376
    • van Baarlen, P.1
  • 48
    • 65549169958 scopus 로고    scopus 로고
    • Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome
    • Wels M, et al. 2009. Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome. J. Bacteriol. 191:3420-3423.
    • (2009) J. Bacteriol. , vol.191 , pp. 3420-3423
    • Wels, M.1
  • 49
    • 33645832957 scopus 로고    scopus 로고
    • Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups
    • Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ. 2006. Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res. 34:1947-1958.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 1947-1958
    • Wels, M.1    Francke, C.2    Kerkhoven, R.3    Kleerebezem, M.4    Siezen, R.J.5
  • 50
    • 48649110623 scopus 로고    scopus 로고
    • An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters
    • Wels M, Groot Kormelink T, Kleerebezem M, Siezen RJ, Francke C. 2008. An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters. BMC Genomics 9:330.
    • (2008) BMC Genomics , vol.9 , pp. 330
    • Wels, M.1    Groot Kormelink, T.2    Kleerebezem, M.3    Siezen, R.J.4    Francke, C.5
  • 51
    • 79955439727 scopus 로고    scopus 로고
    • Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs
    • Wels M, Overmars L, Francke C, Kleerebezem M, Siezen RJ. 2011. Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs. Microb. Biotechnol. 4:333-344.
    • (2011) Microb. Biotechnol. , vol.4 , pp. 333-344
    • Wels, M.1    Overmars, L.2    Francke, C.3    Kleerebezem, M.4    Siezen, R.J.5
  • 52
    • 78549296762 scopus 로고    scopus 로고
    • LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of lactic acid bacteria
    • Zhou M, Theunissen D, Wels M, Siezen RJ. 2010. LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of lactic acid bacteria. BMC Genomics 11:651.
    • (2010) BMC Genomics , vol.11 , pp. 651
    • Zhou, M.1    Theunissen, D.2    Wels, M.3    Siezen, R.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.