메뉴 건너뛰기




Volumn 508, Issue 2, 2012, Pages 221-228

Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression

Author keywords

Hairpin; Horizontal gene transfer; Intrinsic termination; Pathogenicity; RNA polymerase

Indexed keywords

BACTERIAL DNA; RHO FACTOR;

EID: 84865716910     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.07.064     Document Type: Article
Times cited : (9)

References (54)
  • 2
    • 34547726221 scopus 로고    scopus 로고
    • Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli
    • Becq J., et al. Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli. Mol. Biol. Evol. 2007, 24:1861-1871.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1861-1871
    • Becq, J.1
  • 3
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner F.R., et al. The complete genome sequence of Escherichia coli K-12. Science 1997, 277:1453-1462.
    • (1997) Science , vol.277 , pp. 1453-1462
    • Blattner, F.R.1
  • 4
    • 1542395706 scopus 로고    scopus 로고
    • Comparative analysis of the complete cag pathogenicity island sequence in four Helicobacter pylori isolates
    • Blomstergren A., Lundin A., Nilsson C., Engstrand L., Lundeberg J. Comparative analysis of the complete cag pathogenicity island sequence in four Helicobacter pylori isolates. Gene 2004, 328:85-93.
    • (2004) Gene , vol.328 , pp. 85-93
    • Blomstergren, A.1    Lundin, A.2    Nilsson, C.3    Engstrand, L.4    Lundeberg, J.5
  • 5
    • 77950195231 scopus 로고    scopus 로고
    • Horizontal gene transfer in evolution: facts and challenges
    • Boto L. Horizontal gene transfer in evolution: facts and challenges. Proc. R. Soc. Biol. 2010, 277:819-827.
    • (2010) Proc. R. Soc. Biol. , vol.277 , pp. 819-827
    • Boto, L.1
  • 6
    • 60349117754 scopus 로고    scopus 로고
    • Genomic islands are dynamic, ancient integrative elements in bacterial evolution
    • Boyd E.F., Almagro-Moreno S., Parent M.A. Genomic islands are dynamic, ancient integrative elements in bacterial evolution. Trends Microbiol. 2009, 17:47-53.
    • (2009) Trends Microbiol. , vol.17 , pp. 47-53
    • Boyd, E.F.1    Almagro-Moreno, S.2    Parent, M.A.3
  • 8
    • 3142514466 scopus 로고    scopus 로고
    • The impact of prophages on bacterial chromosomes
    • Canchaya C., Fournous G., Brussow H. The impact of prophages on bacterial chromosomes. Mol. Microbiol. 2004, 53:9-18.
    • (2004) Mol. Microbiol. , vol.53 , pp. 9-18
    • Canchaya, C.1    Fournous, G.2    Brussow, H.3
  • 10
    • 0037825641 scopus 로고    scopus 로고
    • Prophages and bacterial genomics: what have we learned so far?
    • Casjens S. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol. 2003, 49:277-300.
    • (2003) Mol. Microbiol. , vol.49 , pp. 277-300
    • Casjens, S.1
  • 11
    • 10744229660 scopus 로고    scopus 로고
    • The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129
    • Cerdeno-Tarraga A.M., et al. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res. 2003, 31:6516-6523.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6516-6523
    • Cerdeno-Tarraga, A.M.1
  • 12
    • 33748767376 scopus 로고    scopus 로고
    • Rho-dependent terminators and transcription termination
    • Ciampi M.S. Rho-dependent terminators and transcription termination. Microbiology 2006, 152:2515-2528.
    • (2006) Microbiology , vol.152 , pp. 2515-2528
    • Ciampi, M.S.1
  • 13
    • 55449129670 scopus 로고    scopus 로고
    • Prediction of transcriptional terminators in Bacillus subtilis and related species
    • de Hoon M.J., Makita Y., Nakai K., Miyano S. Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput. Biol. 2005, 1:e25.
    • (2005) PLoS Comput. Biol. , vol.1
    • de Hoon, M.J.1    Makita, Y.2    Nakai, K.3    Miyano, S.4
  • 14
    • 50649101517 scopus 로고    scopus 로고
    • Transcription termination factor Rho prefers catalytically active elongation complexes for releasing RNA
    • Dutta D., Chalissery J., Sen R. Transcription termination factor Rho prefers catalytically active elongation complexes for releasing RNA. J. Biol. Chem. 2008, 283:20243-20251.
    • (2008) J. Biol. Chem. , vol.283 , pp. 20243-20251
    • Dutta, D.1    Chalissery, J.2    Sen, R.3
  • 16
    • 74549191169 scopus 로고    scopus 로고
    • An allosteric mechanism of Rho-dependent transcription termination
    • Epshtein V., Dutta D., Wade J., Nudler E. An allosteric mechanism of Rho-dependent transcription termination. Nature 2010, 463:245-249.
    • (2010) Nature , vol.463 , pp. 245-249
    • Epshtein, V.1    Dutta, D.2    Wade, J.3    Nudler, E.4
  • 17
    • 0025303975 scopus 로고
    • Structural and functional properties of the segments of lambda cro mRNA that interact with transcription termination factor Rho
    • Faus I., Richardson J.P. Structural and functional properties of the segments of lambda cro mRNA that interact with transcription termination factor Rho. J. Mol. Biol. 1990, 212:53-66.
    • (1990) J. Mol. Biol. , vol.212 , pp. 53-66
    • Faus, I.1    Richardson, J.P.2
  • 18
    • 77950419841 scopus 로고    scopus 로고
    • Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis
    • Gordon B.R., et al. Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:5154-5159.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 5154-5159
    • Gordon, B.R.1
  • 19
    • 7644223774 scopus 로고    scopus 로고
    • Why is transcription coupled to translation in bacteria?
    • Gowrishankar J., Harinarayanan R. Why is transcription coupled to translation in bacteria?. Mol. Microbiol. 2004, 54:598-603.
    • (2004) Mol. Microbiol. , vol.54 , pp. 598-603
    • Gowrishankar, J.1    Harinarayanan, R.2
  • 20
    • 0031053290 scopus 로고    scopus 로고
    • Analysis of the boundaries of salmonella pathogenicity island 2 and the corresponding chromosomal region of Escherichia coli K-12
    • Hensel Micheal, J.E.S., Baumler Andreas J., Gleeson Colin, Blattner Fredrick, Holden David W. Analysis of the boundaries of salmonella pathogenicity island 2 and the corresponding chromosomal region of Escherichia coli K-12. J. Bacteriol. 1997, 179:1105-1111.
    • (1997) J. Bacteriol. , vol.179 , pp. 1105-1111
    • Hensel, M.J.E.S.1    Baumler, A.J.2    Gleeson, C.3    Blattner, F.4    Holden, D.W.5
  • 21
    • 58149498183 scopus 로고    scopus 로고
    • Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69
    • Iguchi A., et al. Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J. Bacteriol. 2009, 191:347-354.
    • (2009) J. Bacteriol. , vol.191 , pp. 347-354
    • Iguchi, A.1
  • 22
    • 0032904686 scopus 로고    scopus 로고
    • Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis
    • Ingham C.J., Dennis J., Furneaux P.A. Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis. Mol. Microbiol. 1999, 31:651-663.
    • (1999) Mol. Microbiol. , vol.31 , pp. 651-663
    • Ingham, C.J.1    Dennis, J.2    Furneaux, P.A.3
  • 24
    • 73649086853 scopus 로고    scopus 로고
    • A bacterial transcription terminator with inefficient molecular motor action but with a robust transcription termination function
    • Kalarickal N.C., Ranjan A., Kalyani B.S., Wal M., Sen R. A bacterial transcription terminator with inefficient molecular motor action but with a robust transcription termination function. J. Mol. Biol. 2009, 395:966-982.
    • (2009) J. Mol. Biol. , vol.395 , pp. 966-982
    • Kalarickal, N.C.1    Ranjan, A.2    Kalyani, B.S.3    Wal, M.4    Sen, R.5
  • 25
    • 68549135026 scopus 로고    scopus 로고
    • Genomic island excisions in Bordetella petrii
    • Lechner M., et al. Genomic island excisions in Bordetella petrii. BMC Microbiol. 2009, 9:141.
    • (2009) BMC Microbiol. , vol.9 , pp. 141
    • Lechner, M.1
  • 26
    • 34247601641 scopus 로고    scopus 로고
    • Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli
    • Lloyd A.L., Rasko D.A., Mobley H.L. Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli. J. Bacteriol. 2007, 189:3532-3546.
    • (2007) J. Bacteriol. , vol.189 , pp. 3532-3546
    • Lloyd, A.L.1    Rasko, D.A.2    Mobley, H.L.3
  • 27
    • 66149083657 scopus 로고    scopus 로고
    • Genomic islands of uropathogenic Escherichia coli contribute to virulence
    • Lloyd A.L., Henderson T.A., Vigil P.D., Mobley H.L. Genomic islands of uropathogenic Escherichia coli contribute to virulence. J. Bacteriol. 2009, 191:3469-3481.
    • (2009) J. Bacteriol. , vol.191 , pp. 3469-3481
    • Lloyd, A.L.1    Henderson, T.A.2    Vigil, P.D.3    Mobley, H.L.4
  • 28
    • 0035675991 scopus 로고    scopus 로고
    • The salmonella pathogenicity island-1 type III secretion system
    • Lostroh C.P., Lee C.A. The salmonella pathogenicity island-1 type III secretion system. Microbes Infect. 2001, 3:1281-1291.
    • (2001) Microbes Infect. , vol.3 , pp. 1281-1291
    • Lostroh, C.P.1    Lee, C.A.2
  • 30
    • 67649976624 scopus 로고    scopus 로고
    • Occurrence, divergence and evolution of intrinsic terminators across eubacteria
    • Mitra A., Angamuthu K., Jayashree H.V., Nagaraja V. Occurrence, divergence and evolution of intrinsic terminators across eubacteria. Genomics 2009, 94:110-116.
    • (2009) Genomics , vol.94 , pp. 110-116
    • Mitra, A.1    Angamuthu, K.2    Jayashree, H.V.3    Nagaraja, V.4
  • 32
    • 3042849253 scopus 로고    scopus 로고
    • Biased biological functions of horizontally transferred genes in prokaryotic genomes
    • Nakamura Y., Itoh T., Matsuda H., Gojobori T. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 2004, 36:760-766.
    • (2004) Nat. Genet. , vol.36 , pp. 760-766
    • Nakamura, Y.1    Itoh, T.2    Matsuda, H.3    Gojobori, T.4
  • 33
    • 33746008173 scopus 로고    scopus 로고
    • Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella
    • Navarre W.W., et al. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 2006, 313:236-238.
    • (2006) Science , vol.313 , pp. 236-238
    • Navarre, W.W.1
  • 34
    • 34250724903 scopus 로고    scopus 로고
    • Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA
    • Navarre W.W., McClelland M., Libby S.J., Fang F.C. Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev. 2007, 21:1456-1471.
    • (2007) Genes Dev. , vol.21 , pp. 1456-1471
    • Navarre, W.W.1    McClelland, M.2    Libby, S.J.3    Fang, F.C.4
  • 35
    • 0030755556 scopus 로고    scopus 로고
    • Transcription termination factor Rho is essential for Micrococcus luteus
    • Nowatzke W.L., Keller E., Koch G., Richardson J.P. Transcription termination factor Rho is essential for Micrococcus luteus. J. Bacteriol. 1997, 179:5238-5240.
    • (1997) J. Bacteriol. , vol.179 , pp. 5238-5240
    • Nowatzke, W.L.1    Keller, E.2    Koch, G.3    Richardson, J.P.4
  • 36
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman H., Lawrence J.G., Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
    • (2000) Nature , vol.405 , pp. 299-304
    • Ochman, H.1    Lawrence, J.G.2    Groisman, E.A.3
  • 38
    • 79960395328 scopus 로고    scopus 로고
    • Bacterial transcription terminators: the RNA 3'-end chronicles
    • Peters J.M., Vangeloff A.D., Landick R. Bacterial transcription terminators: the RNA 3'-end chronicles. J. Mol. Biol. 2011, 412:793-813.
    • (2011) J. Mol. Biol. , vol.412 , pp. 793-813
    • Peters, J.M.1    Vangeloff, A.D.2    Landick, R.3
  • 39
    • 0037073063 scopus 로고    scopus 로고
    • Rho-dependent termination and ATPases in transcript termination
    • Richardson J.P. Rho-dependent termination and ATPases in transcript termination. Biochim. Biophys. Acta 2002, 1577:251-260.
    • (2002) Biochim. Biophys. Acta , vol.1577 , pp. 251-260
    • Richardson, J.P.1
  • 40
    • 0041696782 scopus 로고    scopus 로고
    • Loading Rho to terminate transcription
    • Richardson J.P. Loading Rho to terminate transcription. Cell 2003, 114:157-159.
    • (2003) Cell , vol.114 , pp. 157-159
    • Richardson, J.P.1
  • 41
    • 33745224521 scopus 로고    scopus 로고
    • How Rho exerts its muscle on RNA
    • Richardson J.P. How Rho exerts its muscle on RNA. Mol. Cell 2006, 22:711-712.
    • (2006) Mol. Cell , vol.22 , pp. 711-712
    • Richardson, J.P.1
  • 43
    • 0029831394 scopus 로고    scopus 로고
    • Rho-dependent termination of transcription is governed primarily by the upstream Rho utilization (rut) sequences of a terminator
    • Richardson L.V., Richardson J.P. Rho-dependent termination of transcription is governed primarily by the upstream Rho utilization (rut) sequences of a terminator. J. Biol. Chem. 1996, 271:21597-21603.
    • (1996) J. Biol. Chem. , vol.271 , pp. 21597-21603
    • Richardson, L.V.1    Richardson, J.P.2
  • 44
    • 67650141987 scopus 로고    scopus 로고
    • Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus
    • Ripoll F., et al. Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. PLoS One 2009, 4:e5660.
    • (2009) PLoS One , vol.4
    • Ripoll, F.1
  • 46
    • 79954597274 scopus 로고    scopus 로고
    • Termination and antitermination: RNA polymerase runs a stop sign
    • Santangelo T.J., Artsimovitch I. Termination and antitermination: RNA polymerase runs a stop sign. Nat. Rev. Microbiol. 2011, 9:319-329.
    • (2011) Nat. Rev. Microbiol. , vol.9 , pp. 319-329
    • Santangelo, T.J.1    Artsimovitch, I.2
  • 47
    • 0025017969 scopus 로고
    • A short intervening structure can block Rho factor helicase action at a distance
    • Steinmetz E.J., Brennan C.A., Platt T. A short intervening structure can block Rho factor helicase action at a distance. J. Biol. Chem. 1990, 265:18408-18413.
    • (1990) J. Biol. Chem. , vol.265 , pp. 18408-18413
    • Steinmetz, E.J.1    Brennan, C.A.2    Platt, T.3
  • 48
    • 0344413496 scopus 로고    scopus 로고
    • The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination
    • Toulokhonov I., Landick R. The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Mol. Cell 2003, 12:1125-1136.
    • (2003) Mol. Cell , vol.12 , pp. 1125-1136
    • Toulokhonov, I.1    Landick, R.2
  • 49
    • 0035957687 scopus 로고    scopus 로고
    • Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins
    • Toulokhonov I., Artsimovitch I., Landick R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 2001, 292:730-733.
    • (2001) Science , vol.292 , pp. 730-733
    • Toulokhonov, I.1    Artsimovitch, I.2    Landick, R.3
  • 50
    • 34547204502 scopus 로고    scopus 로고
    • A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
    • Toulokhonov Innokenti, J.Z., Palangat Murali, Landick Robert A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol. Cell 2007, 27:406-419.
    • (2007) Mol. Cell , vol.27 , pp. 406-419
    • Toulokhonov, I.J.Z.1    Palangat, M.2    Landick, R.3
  • 51
    • 0036464509 scopus 로고    scopus 로고
    • Conserved economics of transcription termination in eubacteria
    • Unniraman S., Prakash R., Nagaraja V. Conserved economics of transcription termination in eubacteria. Nucleic Acids Res. 2002, 30:675-684.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 675-684
    • Unniraman, S.1    Prakash, R.2    Nagaraja, V.3
  • 52
    • 0032584643 scopus 로고    scopus 로고
    • An integrated model of the transcription complex in elongation, termination, and editing
    • von Hippel P.H. An integrated model of the transcription complex in elongation, termination, and editing. Science 1998, 281:660-665.
    • (1998) Science , vol.281 , pp. 660-665
    • von Hippel, P.H.1
  • 54
    • 0347986769 scopus 로고    scopus 로고
    • Genome engineering reveals large dispensable regions in Bacillus subtilis
    • Westers H., et al. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol. Biol. Evol. 2003, 20:2076-2090.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 2076-2090
    • Westers, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.