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Volumn 6, Issue 1, 2015, Pages

Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis

Author keywords

BrickBuilt; DNA structure; Miniature inverted repeat transposable element; Porphyromonas; Species specific repeat; Transcriptional regulation

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOINFORMATICS; DNA SEQUENCE; DNA STRUCTURE; GENE EXPRESSION; GENETIC TRANSCRIPTION; INVERTED REPEAT; MICROARRAY ANALYSIS; MINIATURE INVERTED REPEAT TRANSPOSABLE ELEMENT; MINISATELLITE; NONHUMAN; PORPHYROMONAS GINGIVALIS; PRIORITY JOURNAL; PROMOTER REGION; TANDEM REPEAT; TRANSPOSON;

EID: 84943172262     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/s13100-015-0049-1     Document Type: Article
Times cited : (9)

References (88)
  • 1
    • 81755166205 scopus 로고    scopus 로고
    • Low-abundance biofilm species orchestrates inflammatory periodontal disease through the commensal microbiota and complement
    • Hajishengallis G, Liang S, Payne MA, Hashim A, Jotwani R, Eskan MA, et al. Low-abundance biofilm species orchestrates inflammatory periodontal disease through the commensal microbiota and complement. Cell Host Microbe. 2011;10:497-506.
    • (2011) Cell Host Microbe. , vol.10 , pp. 497-506
    • Hajishengallis, G.1    Liang, S.2    Payne, M.A.3    Hashim, A.4    Jotwani, R.5    Eskan, M.A.6
  • 2
    • 80054921127 scopus 로고    scopus 로고
    • The relationship of the oral microbiotia to periodontal health and disease
    • Curtis MA, Zenobia C, Darveau RP. The relationship of the oral microbiotia to periodontal health and disease. Cell Host Microbe. 2011;10:302-6.
    • (2011) Cell Host Microbe. , vol.10 , pp. 302-306
    • Curtis, M.A.1    Zenobia, C.2    Darveau, R.P.3
  • 3
    • 0028027710 scopus 로고
    • Characterisation of IS1126 from Porphyromonas gingivalis W83: A new member of the IS4 family of insertion sequence elements
    • Maley J, Roberts IS. Characterisation of IS1126 from Porphyromonas gingivalis W83: A new member of the IS4 family of insertion sequence elements. FEMS Microbiol Lett. 1994;123:219-24.
    • (1994) FEMS Microbiol Lett. , vol.123 , pp. 219-224
    • Maley, J.1    Roberts, I.S.2
  • 4
    • 0030970448 scopus 로고    scopus 로고
    • Identification of a second endogenous Porphyromonas gingivalis insertion element
    • Wang C, Bond VC, Genco CA. Identification of a second endogenous Porphyromonas gingivalis insertion element. J Bacteriol. 1997;179:3808-12.
    • (1997) J Bacteriol. , vol.179 , pp. 3808-3812
    • Wang, C.1    Bond, V.C.2    Genco, C.A.3
  • 5
    • 0031842401 scopus 로고    scopus 로고
    • IS195, an insertion sequence-like element associated with protease genes in Porphyromonas gingivalis
    • Lewis JP, Macrina FL. IS195, an insertion sequence-like element associated with protease genes in Porphyromonas gingivalis. Infect Immun. 1998;66:3035-42.
    • (1998) Infect Immun. , vol.66 , pp. 3035-3042
    • Lewis, J.P.1    Macrina, F.L.2
  • 6
    • 0032750080 scopus 로고    scopus 로고
    • Identification by subtractive hybridization of a novel insertion sequence specific for virulent strains of Porphyromonas gingivalis
    • Sawada K, Kokeguchi S, Hongyo H, Sawada S, Miyamoto M, Maeda H, et al. Identification by subtractive hybridization of a novel insertion sequence specific for virulent strains of Porphyromonas gingivalis. Infect Immun. 1999;67:5621-5.
    • (1999) Infect Immun. , vol.67 , pp. 5621-5625
    • Sawada, K.1    Kokeguchi, S.2    Hongyo, H.3    Sawada, S.4    Miyamoto, M.5    Maeda, H.6
  • 8
    • 0141448863 scopus 로고    scopus 로고
    • The genetic relatedness of Porphyromonas gingivalis clinical and laboratory strains assessed by analysis of insertion sequence (IS) element distribution
    • Califano JV, Arimoto T, Kitten T. The genetic relatedness of Porphyromonas gingivalis clinical and laboratory strains assessed by analysis of insertion sequence (IS) element distribution. J Periodontal Res. 2003;38:411-6.
    • (2003) J Periodontal Res. , vol.38 , pp. 411-416
    • Califano, J.V.1    Arimoto, T.2    Kitten, T.3
  • 9
    • 3843110041 scopus 로고    scopus 로고
    • Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis
    • Chen T, Hosogi Y, Nishikawa K, Abbey K, Fleischmann RD, Walling J, et al. Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis. J Bacteriol. 2004;186:5473-9.
    • (2004) J Bacteriol. , vol.186 , pp. 5473-5479
    • Chen, T.1    Hosogi, Y.2    Nishikawa, K.3    Abbey, K.4    Fleischmann, R.D.5    Walling, J.6
  • 10
    • 56149117939 scopus 로고    scopus 로고
    • Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. Gingivalis
    • Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H, et al. Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res. 2008;15:215-25.
    • (2008) DNA Res. , vol.15 , pp. 215-225
    • Naito, M.1    Hirakawa, H.2    Yamashita, A.3    Ohara, N.4    Shoji, M.5    Yukitake, H.6
  • 11
    • 79959962123 scopus 로고    scopus 로고
    • Characterization of the Porphyromonas gingivalis conjugative transposon CTnPg1: Determination of the integration site and the genes essential for conjugal transfer
    • Naito M, Sato K, Shoji M, Yukitake H, Ogura Y, Hayashi T, et al. Characterization of the Porphyromonas gingivalis conjugative transposon CTnPg1: Determination of the integration site and the genes essential for conjugal transfer. Microbiology. 2011;157:2022-32.
    • (2011) Microbiology , vol.157 , pp. 2022-2032
    • Naito, M.1    Sato, K.2    Shoji, M.3    Yukitake, H.4    Ogura, Y.5    Hayashi, T.6
  • 12
    • 84924706161 scopus 로고    scopus 로고
    • Deletion of a 77-base-pair inverted repeat element alters the synthesis of surface polysaccharides in Porphyromonas gingivalis
    • Bainbridge BW, Hirano T, Grieshaber N, Davey ME. Deletion of a 77-base-pair inverted repeat element alters the synthesis of surface polysaccharides in Porphyromonas gingivalis. J Bacteriol. 2015;197:1208-20.
    • (2015) J Bacteriol. , vol.197 , pp. 1208-1220
    • Bainbridge, B.W.1    Hirano, T.2    Grieshaber, N.3    Davey, M.E.4
  • 13
  • 14
    • 79961160009 scopus 로고    scopus 로고
    • Complete genome sequence of the bacterium Porphyromonas gingivalis TDC60, which causes periodontal disease
    • Watanabe T, Maruyama F, Nozawa T, Aoki A, Okano S, Shibata Y, et al. Complete genome sequence of the bacterium Porphyromonas gingivalis TDC60, which causes periodontal disease. J Bacteriol. 2011;193:4259-60.
    • (2011) J Bacteriol. , vol.193 , pp. 4259-4260
    • Watanabe, T.1    Maruyama, F.2    Nozawa, T.3    Aoki, A.4    Okano, S.5    Shibata, Y.6
  • 15
    • 84877126520 scopus 로고    scopus 로고
    • Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
    • McLean JS, Lombardo M, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, et al. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Res. 2013;23:867-77.
    • (2013) Genome Res. , vol.23 , pp. 867-877
    • McLean, J.S.1    Lombardo, M.2    Ziegler, M.G.3    Novotny, M.4    Yee-Greenbaum, J.5    Badger, J.H.6
  • 18
    • 84891633577 scopus 로고    scopus 로고
    • The role of variable DNA tandem repeats in bacterial adaptation
    • Zhou K, Aertsen A, Michiels CW. The role of variable DNA tandem repeats in bacterial adaptation. FEMS Microbiol Rev. 2014;38:119-41.
    • (2014) FEMS Microbiol Rev. , vol.38 , pp. 119-141
    • Zhou, K.1    Aertsen, A.2    Michiels, C.W.3
  • 20
    • 84925228858 scopus 로고    scopus 로고
    • Bacterial insertion sequences: Their genomic impact and diversity
    • Siguier P, Gourbeyre E, Chandler M. Bacterial insertion sequences: Their genomic impact and diversity. FEMS Microbiol Rev. 2014;38:865-91.
    • (2014) FEMS Microbiol Rev. , vol.38 , pp. 865-891
    • Siguier, P.1    Gourbeyre, E.2    Chandler, M.3
  • 21
    • 84925957223 scopus 로고    scopus 로고
    • A survey of transposable element classification systems - A call for a fundamental update to meet the challenge of their diversity and complexity
    • Piégu B, Bire S, Arensburger P, Bigot Y. A survey of transposable element classification systems - A call for a fundamental update to meet the challenge of their diversity and complexity. Mol Phylogenet Evol. 2015;86:90-109.
    • (2015) Mol Phylogenet Evol. , vol.86 , pp. 90-109
    • Piégu, B.1    Bire, S.2    Arensburger, P.3    Bigot, Y.4
  • 22
    • 70249138303 scopus 로고    scopus 로고
    • MITEs - The ultimate parasites
    • Gonzalez J, Petrov D. MITEs - the ultimate parasites. Science. 2009;325:1352-3.
    • (2009) Science , vol.325 , pp. 1352-1353
    • Gonzalez, J.1    Petrov, D.2
  • 23
    • 79952840472 scopus 로고    scopus 로고
    • Miniature repetitive mobile elements of bacteria: Structural organization and properties
    • Ilyina TS. Miniature repetitive mobile elements of bacteria: Structural organization and properties. Mol Genet Microbiol Virol. 2010;25:139-47.
    • (2010) Mol Genet Microbiol Virol. , vol.25 , pp. 139-147
    • Ilyina, T.S.1
  • 24
    • 84887461976 scopus 로고    scopus 로고
    • Miniature inverted-repeat transposable elements: Discovery, distribution, and activity
    • Fattash I, Rooke R, Wong A, Hui C, Luu T, Bhardwaj P, et al. Miniature inverted-repeat transposable elements: Discovery, distribution, and activity. Genome. 2013;56:475-86.
    • (2013) Genome , vol.56 , pp. 475-486
    • Fattash, I.1    Rooke, R.2    Wong, A.3    Hui, C.4    Luu, T.5    Bhardwaj, P.6
  • 26
    • 0036250001 scopus 로고    scopus 로고
    • Plant transposable elements: Where genetics meets genomics
    • Feschotte C, Jiang N, Wessler SR. Plant transposable elements: Where genetics meets genomics. Nat Rev Genet. 2002;3:329-41.
    • (2002) Nat Rev Genet. , vol.3 , pp. 329-341
    • Feschotte, C.1    Jiang, N.2    Wessler, S.R.3
  • 27
    • 70350515004 scopus 로고    scopus 로고
    • Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
    • Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, et al. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature. 2009;461:1130-4.
    • (2009) Nature , vol.461 , pp. 1130-1134
    • Naito, K.1    Zhang, F.2    Tsukiyama, T.3    Saito, H.4    Hancock, C.N.5    Richardson, A.O.6
  • 28
    • 84863116863 scopus 로고    scopus 로고
    • Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in oryza sativa
    • Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H. Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in oryza sativa. Mol Biol Evol. 2012;29:1005-17.
    • (2012) Mol Biol Evol. , vol.29 , pp. 1005-1017
    • Lu, C.1    Chen, J.2    Zhang, Y.3    Hu, Q.4    Su, W.5    Kuang, H.6
  • 29
    • 84883521490 scopus 로고    scopus 로고
    • Detection and characterization of miniature inverted-repeat transposable elements in "candidatus liberibacter asiaticus"
    • Wang X, Tan J, Bai Z, Deng X, Li Z, Zhou C, et al. Detection and characterization of miniature inverted-repeat transposable elements in "candidatus liberibacter asiaticus". J Bacteriol. 2013;195:3979-86.
    • (2013) J Bacteriol. , vol.195 , pp. 3979-3986
    • Wang, X.1    Tan, J.2    Bai, Z.3    Deng, X.4    Li, Z.5    Zhou, C.6
  • 30
    • 0026940433 scopus 로고
    • Tourist: A large family of small inverted repeat elements frequently associated with maize genes
    • Bureau TE, Wessler SR. Tourist: A large family of small inverted repeat elements frequently associated with maize genes. Plant Cell. 1992;4:1283-94.
    • (1992) Plant Cell. , vol.4 , pp. 1283-1294
    • Bureau, T.E.1    Wessler, S.R.2
  • 31
    • 0028450046 scopus 로고
    • Stowaway: A new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants
    • Bureau TE, Wessler SR. Stowaway: A new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell. 1994;6:907-16.
    • (1994) Plant Cell. , vol.6 , pp. 907-916
    • Bureau, T.E.1    Wessler, S.R.2
  • 32
    • 0042031249 scopus 로고    scopus 로고
    • Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria
    • Chen SL, Shapiro L. Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria. J Bacteriol. 2003;185:4997-5002.
    • (2003) J Bacteriol. , vol.185 , pp. 4997-5002
    • Chen, S.L.1    Shapiro, L.2
  • 33
    • 34447097348 scopus 로고    scopus 로고
    • Spring: A novel family of miniature inverted-repeat transposable elements is associated with genes in apple
    • Han Y, Korban SS. Spring: A novel family of miniature inverted-repeat transposable elements is associated with genes in apple. Genomics. 2007;90:195-200.
    • (2007) Genomics , vol.90 , pp. 195-200
    • Han, Y.1    Korban, S.S.2
  • 34
    • 84864020007 scopus 로고    scopus 로고
    • Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population
    • Nelson WC, Bhaya D, Heidelberg JF. Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population. J Bacteriol. 2012;194:3636-42.
    • (2012) J Bacteriol. , vol.194 , pp. 3636-3642
    • Nelson, W.C.1    Bhaya, D.2    Heidelberg, J.F.3
  • 35
    • 84885422879 scopus 로고    scopus 로고
    • Scatter: A novel family of miniature inverted-repeat transposable elements in the fungus Botrytis cinerea
    • Deng H, Shu D, Luo D, Gong T, Sun F, Tan H. Scatter: A novel family of miniature inverted-repeat transposable elements in the fungus Botrytis cinerea. J Basic Microbiol. 2013;53:815-22.
    • (2013) J Basic Microbiol. , vol.53 , pp. 815-822
    • Deng, H.1    Shu, D.2    Luo, D.3    Gong, T.4    Sun, F.5    Tan, H.6
  • 36
    • 84899701665 scopus 로고    scopus 로고
    • Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. Oleracea
    • Sampath P, Murukarthick J, Izzah NK, Lee J, Choi HI, Shirasawa K, et al. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea. PLoS ONE. 2014;9.
    • (2014) PLoS One , pp. 9
    • Sampath, P.1    Murukarthick, J.2    Izzah, N.K.3    Lee, J.4    Choi, H.I.5    Shirasawa, K.6
  • 37
    • 78651312094 scopus 로고    scopus 로고
    • A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatellites
    • Coates BS, Kroemer JA, Sumerford DV, Hellmich RL. A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatellites. Insect Mol Biol. 2011;20:15-27.
    • (2011) Insect Mol Biol. , vol.20 , pp. 15-27
    • Coates, B.S.1    Kroemer, J.A.2    Sumerford, D.V.3    Hellmich, R.L.4
  • 38
    • 84892541773 scopus 로고    scopus 로고
    • Tandem repeat-containing MITEs in the clam Donax trunculus
    • Satovic E, Plohl M. Tandem repeat-containing MITEs in the clam Donax trunculus. Genome Biol Evol. 2013;5:2549-59.
    • (2013) Genome Biol Evol. , vol.5 , pp. 2549-2559
    • Satovic, E.1    Plohl, M.2
  • 39
    • 0034732226 scopus 로고    scopus 로고
    • Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491
    • Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, et al. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature. 2000;404:502-6.
    • (2000) Nature , vol.404 , pp. 502-506
    • Parkhill, J.1    Achtman, M.2    James, K.D.3    Bentley, S.D.4    Churcher, C.5    Klee, S.R.6
  • 40
    • 37049009528 scopus 로고    scopus 로고
    • Quantitative proteomics of intracellular Porphyromonas gingivalis
    • Xia Q, Wang T, Taub F, Park Y, Capestany CA, Lamont RJ, et al. Quantitative proteomics of intracellular Porphyromonas gingivalis. Proteomics. 2007;7:4323-37.
    • (2007) Proteomics , vol.7 , pp. 4323-4337
    • Xia, Q.1    Wang, T.2    Taub, F.3    Park, Y.4    Capestany, C.A.5    Lamont, R.J.6
  • 41
    • 67449107568 scopus 로고    scopus 로고
    • Proteomics of Porphyromonas gingivalis within a model oral microbial community
    • 2180-9-98
    • Kuboniwa M, Hendrickson EL, Xia Q, Wang T, Xie H, Hackett M, et al. Proteomics of Porphyromonas gingivalis within a model oral microbial community. BMC Microbiol. 2009;9:98,2180-9-98.
    • (2009) BMC Microbiol. , vol.9 , pp. 98
    • Kuboniwa, M.1    Hendrickson, E.L.2    Xia, Q.3    Wang, T.4    Xie, H.5    Hackett, M.6
  • 42
    • 84920288397 scopus 로고    scopus 로고
    • Proteomic and transcriptional analysis of interaction between oral microbiota Porphyromonas gingivalis and Streptococcus oralis
    • Maeda K, Nagata H, Ojima M, Amano A. Proteomic and transcriptional analysis of interaction between oral microbiota Porphyromonas gingivalis and Streptococcus oralis. J Proteome Res. 2015;14:82-94.
    • (2015) J Proteome Res. , vol.14 , pp. 82-94
    • Maeda, K.1    Nagata, H.2    Ojima, M.3    Amano, A.4
  • 44
  • 45
    • 84994533293 scopus 로고    scopus 로고
    • Draft genome sequences of 26 Porphyromonas strains isolated from the canine oral microbiome
    • Coil DA, Alexiev A, Wallis C, O'Flynn C, Deusch O, Davis I, et al. Draft genome sequences of 26 Porphyromonas strains isolated from the canine oral microbiome. Genome Announc. 2015;3:doi:10.1128/genomeA.00187-15.
    • (2015) Genome Announc. , vol.3
    • Coil, D.A.1    Alexiev, A.2    Wallis, C.3    O'Flynn, C.4    Deusch, O.5    Davis, I.6
  • 46
    • 33646560923 scopus 로고    scopus 로고
    • Characterization of mononucleotide repeats in sequenced prokaryotic genomes
    • Coenye T, Vandamme P. Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA Res. 2005;12:221-33.
    • (2005) DNA Res. , vol.12 , pp. 221-233
    • Coenye, T.1    Vandamme, P.2
  • 47
    • 0038205473 scopus 로고    scopus 로고
    • Genomics of oral bacteria
    • Duncan MJ. Genomics of oral bacteria. Crit Rev Oral Biol Med. 2003;14:175-87.
    • (2003) Crit Rev Oral Biol Med. , vol.14 , pp. 175-187
    • Duncan, M.J.1
  • 48
    • 84877287199 scopus 로고    scopus 로고
    • Genetic diversity in the oral pathogen Porphyromonas gingivalis: Molecular mechanisms and biological consequences
    • Accessed 2 May 2015
    • Tribble GD, Kerr JE, Wang B. Genetic diversity in the oral pathogen Porphyromonas gingivalis: Molecular mechanisms and biological consequences. Future Microbiol. 2013;8:607-20. Accessed 2 May 2015.
    • (2013) Future Microbiol. , vol.8 , pp. 607-620
    • Tribble, G.D.1    Kerr, J.E.2    Wang, B.3
  • 49
    • 11944257757 scopus 로고    scopus 로고
    • Lineage-specific tandem repeats riding on a transposable element of MITE in Xenopus evolution: A new mechanism for creating simple sequence repeats
    • Hikosaka A, Kawahara A. Lineage-specific tandem repeats riding on a transposable element of MITE in Xenopus evolution: A new mechanism for creating simple sequence repeats. J Mol Evol. 2004;59:738-46.
    • (2004) J Mol Evol. , vol.59 , pp. 738-746
    • Hikosaka, A.1    Kawahara, A.2
  • 50
    • 43549088103 scopus 로고    scopus 로고
    • Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes
    • 2008-9-2-r39. Epub 2008 Feb 21
    • Yang HP, Barbash DA. Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes. Genome Biol. 2008;9:R39,2008-9-2-r39. Epub 2008 Feb 21.
    • (2008) Genome Biol. , vol.9 , pp. R39
    • Yang, H.P.1    Barbash, D.A.2
  • 51
    • 84863604154 scopus 로고    scopus 로고
    • Characterization of species-specific repeats in 613 prokaryotic species
    • Koressaar T, Remm M. Characterization of species-specific repeats in 613 prokaryotic species. DNA Res. 2012;19:219-30.
    • (2012) DNA Res. , vol.19 , pp. 219-230
    • Koressaar, T.1    Remm, M.2
  • 53
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406-15.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 54
    • 84883563787 scopus 로고    scopus 로고
    • RNAstructure: Web servers for RNA secondary structure prediction and analysis
    • Bellaousov S, Reuter JS, Seetin MG, Mathews DH. RNAstructure: Web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. 2013;41:W471-4.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W471-W474
    • Bellaousov, S.1    Reuter, J.S.2    Seetin, M.G.3    Mathews, D.H.4
  • 55
    • 84884197513 scopus 로고    scopus 로고
    • An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs
    • 2105-14-S2-S4. Epub 2013 Jan 21
    • Chang TH, Huang HY, Hsu JB, Weng SL, Horng JT, Huang HD. An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics. 2013;14 Suppl 2:S4,2105-14-S2-S4. Epub 2013 Jan 21.
    • (2013) BMC Bioinformatics , vol.14 , pp. S4
    • Chang, T.H.1    Huang, H.Y.2    Hsu, J.B.3    Weng, S.L.4    Horng, J.T.5    Huang, H.D.6
  • 57
    • 36849025572 scopus 로고    scopus 로고
    • Nezha, a novel active miniature inverted-repeat transposable element in Cyanobacteria
    • Zhou F, Tran T, Xu Y. Nezha, a novel active miniature inverted-repeat transposable element in Cyanobacteria. Biochem Biophys Res Commun. 2008;365:790-4.
    • (2008) Biochem Biophys Res Commun. , vol.365 , pp. 790-794
    • Zhou, F.1    Tran, T.2    Xu, Y.3
  • 58
    • 84856264333 scopus 로고    scopus 로고
    • Impact of small repeat sequences on bacterial genome evolution
    • Delihas N. Impact of small repeat sequences on bacterial genome evolution. Genome Biol Evol. 2011;3:959-73.
    • (2011) Genome Biol Evol. , vol.3 , pp. 959-973
    • Delihas, N.1
  • 59
    • 84892664537 scopus 로고    scopus 로고
    • The origin and evolution of six miniature inverted-repeat transposable elements in Bombyx mori and Rhodnius prolixus
    • Zhang HH, Xu HE, Shen YH, Han MJ, Zhang Z. The origin and evolution of six miniature inverted-repeat transposable elements in Bombyx mori and Rhodnius prolixus. Genome Biol Evol. 2013;5:2020-31.
    • (2013) Genome Biol Evol. , vol.5 , pp. 2020-2031
    • Zhang, H.H.1    Xu, H.E.2    Shen, Y.H.3    Han, M.J.4    Zhang, Z.5
  • 60
    • 28044466642 scopus 로고    scopus 로고
    • Enterobacterial repetitive intergenic consensus sequence repeats in Yersiniae: Genomic organization and functional properties
    • De Gregorio E, Silvestro G, Petrillo M, Carlomagno MS, Di Nocera PP. Enterobacterial repetitive intergenic consensus sequence repeats in Yersiniae: Genomic organization and functional properties. J Bacteriol. 2005;187:7945-54.
    • (2005) J Bacteriol. , vol.187 , pp. 7945-7954
    • De Gregorio, E.1    Silvestro, G.2    Petrillo, M.3    Carlomagno, M.S.4    Di Nocera, P.P.5
  • 62
    • 79959843994 scopus 로고    scopus 로고
    • Within-genome evolution of REPINs: A new family of miniature mobile DNA in bacteria
    • Bertels F, Rainey PB. Within-genome evolution of REPINs: A new family of miniature mobile DNA in bacteria. PLoS Genet. 2011;7, e1002132.
    • (2011) PLoS Genet. , vol.7 , pp. e1002132
    • Bertels, F.1    Rainey, P.B.2
  • 63
    • 80052757676 scopus 로고    scopus 로고
    • Por secretion system of Porphyromonas gingivalis
    • Sato K. Por secretion system of Porphyromonas gingivalis. J Oral Biosci. 2011;53:187-96.
    • (2011) J Oral Biosci. , vol.53 , pp. 187-196
    • Sato, K.1
  • 64
    • 33749023323 scopus 로고    scopus 로고
    • The RgpB C-terminal domain has a role in attachment of RgpB to the outer membrane and belongs to a novel C-terminal-domain family found in Porphyromonas gingivalis
    • Seers CA, Slakeski N, Veith PD, Nikolof T, Chen YY, Dashper SG, et al. The RgpB C-terminal domain has a role in attachment of RgpB to the outer membrane and belongs to a novel C-terminal-domain family found in Porphyromonas gingivalis. J Bacteriol. 2006;188:6376-86.
    • (2006) J Bacteriol. , vol.188 , pp. 6376-6386
    • Seers, C.A.1    Slakeski, N.2    Veith, P.D.3    Nikolof, T.4    Chen, Y.Y.5    Dashper, S.G.6
  • 67
    • 33947303168 scopus 로고    scopus 로고
    • Transposable elements and the epigenetic regulation of the genome
    • Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007;8:272-85.
    • (2007) Nat Rev Genet. , vol.8 , pp. 272-285
    • Slotkin, R.K.1    Martienssen, R.2
  • 68
    • 42349096534 scopus 로고    scopus 로고
    • Transposable elements and the evolution of regulatory networks
    • Feschotte C. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 2008;9:397-405.
    • (2008) Nat Rev Genet. , vol.9 , pp. 397-405
    • Feschotte, C.1
  • 69
    • 84871329875 scopus 로고    scopus 로고
    • How important are transposons for plant evolution?
    • Lisch D. How important are transposons for plant evolution? Nat Rev Genet. 2013;14:49-61.
    • (2013) Nat Rev Genet. , vol.14 , pp. 49-61
    • Lisch, D.1
  • 70
    • 84862935255 scopus 로고    scopus 로고
    • Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83
    • Høvik H, Wen-Han Y, Olsen I, Chen T. Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83. J Bacteriol. 2012;194:100-14.
    • (2012) J Bacteriol. , vol.194 , pp. 100-114
    • Høvik, H.1    Wen-Han, Y.2    Olsen, I.3    Chen, T.4
  • 72
    • 6344241451 scopus 로고    scopus 로고
    • A regulation cascade controls expression of Porphyromonas gingivalis fimbriae via the FimR response regulator
    • Nishikawa K, Yoshimura F, Duncan MJ. A regulation cascade controls expression of Porphyromonas gingivalis fimbriae via the FimR response regulator. Mol Microbiol. 2004;54:546-60.
    • (2004) Mol Microbiol. , vol.54 , pp. 546-560
    • Nishikawa, K.1    Yoshimura, F.2    Duncan, M.J.3
  • 73
    • 84872401413 scopus 로고    scopus 로고
    • Deep sequencing of Porphyromonas gingivalis and comparative transcriptome analysis of a LuxS mutant
    • Hirano T, Beck DA, Demuth DR, Hackett M, Lamont RJ. Deep sequencing of Porphyromonas gingivalis and comparative transcriptome analysis of a LuxS mutant. Front Cell Infect Microbiol. 2012;2:79.
    • (2012) Front Cell Infect Microbiol. , vol.2 , pp. 79
    • Hirano, T.1    Beck, D.A.2    Demuth, D.R.3    Hackett, M.4    Lamont, R.J.5
  • 74
    • 34247253801 scopus 로고    scopus 로고
    • Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes
    • Chen S, Li X. Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes. BMC Evol Biol. 2007;7:46.
    • (2007) BMC Evol Biol. , vol.7 , pp. 46
    • Chen, S.1    Li, X.2
  • 75
    • 0024297354 scopus 로고
    • Multiple sequence alignment with hierarchical clustering
    • Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 1988;16:10881-90.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 10881-10890
    • Corpet, F.1
  • 77
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega
    • Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol. 2011;7:539.
    • (2011) Mol Syst Biol. , vol.7 , pp. 539
    • Sievers, F.1    Wilm, A.2    Dineen, D.3    Gibson, T.J.4    Karplus, K.5    Li, W.6
  • 78
    • 75849133666 scopus 로고    scopus 로고
    • Pathway tools version 13.0: Integrated software for pathway/genome informatics and systems biology
    • Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, et al. Pathway tools version 13.0: Integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 2010;11:40-79.
    • (2010) Brief Bioinform. , vol.11 , pp. 40-79
    • Karp, P.D.1    Paley, S.M.2    Krummenacker, M.3    Latendresse, M.4    Dale, J.M.5    Lee, T.J.6
  • 80
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-80.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 81
    • 84863507534 scopus 로고    scopus 로고
    • Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
    • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28:1647-9.
    • (2012) Bioinformatics , vol.28 , pp. 1647-1649
    • Kearse, M.1    Moir, R.2    Wilson, A.3    Stones-Havas, S.4    Cheung, M.5    Sturrock, S.6
  • 85
    • 23144460835 scopus 로고    scopus 로고
    • The bioinformatics resource for oral pathogens
    • Chen T, Abbey K, Deng W, Cheng M. The bioinformatics resource for oral pathogens. Nucleic Acids Res. 2005;33:W734-40.
    • (2005) Nucleic Acids Res. , vol.33 , pp. W734-W740
    • Chen, T.1    Abbey, K.2    Deng, W.3    Cheng, M.4
  • 86
    • 84875582766 scopus 로고    scopus 로고
    • Visualizing next-generation sequencing data with JBrowse
    • Westesson O, Skinner M, Holmes I. Visualizing next-generation sequencing data with JBrowse. Brief Bioinform. 2013;14:172-7.
    • (2013) Brief Bioinform. , vol.14 , pp. 172-177
    • Westesson, O.1    Skinner, M.2    Holmes, I.3
  • 87
    • 0022529269 scopus 로고
    • Promoter-probe vectors for the analysis of divergently arranged promoters
    • Schneider K, Beck CF. Promoter-probe vectors for the analysis of divergently arranged promoters. Gene. 1986;42:37-48.
    • (1986) Gene , vol.42 , pp. 37-48
    • Schneider, K.1    Beck, C.F.2
  • 88
    • 0036842061 scopus 로고    scopus 로고
    • Effects of environmental changes on expression of the oligopeptide permease (opp) genes of Borrelia burgdorferi
    • Wang XG, Lin B, Kidder JM, Telford S, Hu LT. Effects of environmental changes on expression of the oligopeptide permease (opp) genes of Borrelia burgdorferi. J Bacteriol. 2002;184:6198-206.
    • (2002) J Bacteriol. , vol.184 , pp. 6198-6206
    • Wang, X.G.1    Lin, B.2    Kidder, J.M.3    Telford, S.4    Hu, L.T.5


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