The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters

Nucleic Acids Research

Volumn 38, Issue 11, 2010, Pages 3570-3581

  Ferrándiz, María José ^a   Martín Galiano, Antonio J ^b   Schvartzman, Jorge B ^c   de la Campa, Adela G ^a  

^a INSTITUTO DE SALUD CARLOS III   (Spain)

^b Department of Protein Science ^*  (Spain)

^c CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE; DNA TOPOISOMERASE (ATP HYDROLYSING); DNA TOPOISOMERASE IV;

ARTICLE; AT RICH SEQUENCE; BACTERIAL GENETICS; BACTERIAL GENOME; CODON; CONTROLLED STUDY; DNA SUPERCOILING; DOWN REGULATION; GENE CLUSTER; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; STREPTOCOCCUS PNEUMONIAE; UPREGULATION;

CODON; DNA GYRASE; DNA TOPOISOMERASES, TYPE I, BACTERIAL; DNA TOPOISOMERASES, TYPE II, BACTERIAL; DNA, BACTERIAL; DNA, SUPERHELICAL; ENZYME INHIBITORS; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; NOVOBIOCIN; RNA, MESSENGER; STREPTOCOCCUS PNEUMONIAE; TRANSCRIPTION, GENETIC;

STREPTOCOCCUS PNEUMONIAE;

EID: 77954376773     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq106     Document Type: Article

References (32)

1. Jacobs,M.R., Felmingham,D., Appelbaum,P.C. and Grüneberg,R.N., the Alexander Project Group. (2003) The Alexander project 1998-2000: susceptibility of pathogens isolated from community-acquired respiratory tract infection to commomnly used antimicrobial agents. J. Antimicrob. Chemother., 52, 229-246.
2. Mandell,L.A., Wunderink,R.G., Anzueto,A., Bartlett,J.G., Campbell,G.D., Dean,N.C., Dowell,S.F., File,T.M. Jr, Musher,D.M., Niederman,M.S. et al. (2007) Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults. Clin. Infect. Dis., 44(Suppl 2), S27-S72.
3. Drlica,K., Malik,M., Kerns,R.J. and Zhao,X. (2008) Quinolone-mediated bacterial death. Antimicrob. Agents Chemother., 52, 385-392.
4. Muñoz,R. and de la Campa,A.G. (1996) ParC subunit of DNA topoisomerase IV of Streptococcus pneumoniae is a primary target of fluoroquinolones and cooperates with DNA gyrase A subunit in forming resistance phenotype. Antimicrob. Agents Chemother., 40, 2252-2257.
5. Fernández-Moreira,E., Balas,D., González,I. and de la Campa,A.G. (2000) Fluoroquinolones inhibit preferentially Streptococcus pneumoniae DNA topoisomerase IV than DNA gyrase native proteins. Microb. Drug Resist., 6, 259-267.
6. Tse-Dinh,Y.C. (1985) Regulation of the Escherichia coli DNA topoisomerase I gene by DNA supercoiling. Nucleic Acids Res., 13, 4751-4763.
7. Menzel,R. and Gellert,M. (1983) Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell, 34, 105-113.
8. Menzel,R. and Gellert,M. (1987) Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters. Proc. Natl Acad. Sci. USA, 84, 4185-4189.
9. Menzel,R. and Gellert,M. (1987) Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment. J. Bacteriol., 169, 1272-1278.
10. Thiara,A.S. and Cundliffe,E. (1993) Expression and analysis of two gyrB genes from the novobiocin producer, Streptomyces sphaeroides. Mol. Microbiol., 8, 495-506.
11. Unniraman,S., Chatterji,M. and Nagaraja,V. (2002) DNA gyrase genes in Mycobacterium tuberculosis: a single operon driven by multiple promoters. J. Bacteriol., 184, 5449-5456.
12. Dorman,C.J. (1991) DNA supercoiling and environmental regulation of gene expression in pathogenic bacteria. Infect. Immun., 59, 745-749.
13. Rui,S. and Tse-Dhin,Y.C. (2003) Topoisomerase function during bacterial responses to environmental challenge. Front. Biosci., 8, d256-d263.
14. Travers,A. and Muskhelishvili,G. (2005) DNA supercoiling-a global transcriptional regulator for enterobacterial growth? Nat. Rev., 3, 157-169.
15. Peter,B.J., Arsuaga,J., Breier,A.M., Khodursky,A.B., Brown,P.O. and Cozzarelli,N.R. (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol., 5, R87.
16. Jeong,K.S., Xie,Y., Hiasa,H. and Khodursky,A.B. (2006) Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition. PLoS Genet., 2, e152.
17. Gmuender,H., Kuratli,K., Di Padova,K., Gray,C.P., Keck,W. and Evers,S. (2001) Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis. Genome Res., 11, 28-42.
18. Vora,T., Hottes,A.K. and Tavazoie,S. (2009) Protein occupancy landscape of a bacterial genome. Mol. Cell, 35, 247-253.
19. Muñoz,R., Bustamante,M. and de la Campa,A.G. (1995) Ser-127-to-Leu substitution in the DNA gyrase B subunit of Streptococcus pneumoniae is implicated in novobiocin resistance. J. Bacteriol., 177, 4166-4170.
20. Lacks,S.A., López,P., Greenberg,B. and Espinosa,M. (1986) Identification and analysis of genes for tetracycline resistance and replication functions in the broad-host-range plasmid pLS1. J. Mol. Biol., 192, 753-765.
21. Martín-Parras,L., Lucas,I., Martínez-Robles,M.L., Hernández,P., Krimer,D.B., Hyrien,O. and Schvartzman,J.B. (1998) Topological complexity of different populations of pBR322 as visualized by two-dimensional agarose gel electrophoresis. Nucleic Acids Res., 26, 3424-3432.
22. Balsalobre,L. and de la Campa,A.G. (2008) Fitness of Streptococcus pneumoniae fluoroquinolone-resistant strains with topoisomerase IV recombinant genes. Antimicrob. Agents Chemother., 52, 822-830.
23. Irizarry,R.A., Hobbs,B., Collin,F., Beazer-Barclay,Y.D., Antonellis,K.J., Scherf,U. and Speed,T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
24. Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: an updated version includes eukaryotes. BMC bioinformatics, 4, 41.
25. de la Campa,A.G., del Solar,G.H. and Espinosa,M. (1990) Initiation of replication of plasmid pLS1. The initiator protein RepB acts on two distant DNA regions. J. Mol. Biol., 213, 247-262.
26. Olavarrieta,L., Hernández,P., Krimer,D.B. and Schvartzman,J.B. (2002) DNA knotting caused by head-on collision of transcription and replication. J. Mol. Biol, 322, 1-6.
27. Martín-Galiano,A.J., Wells,J.M. and de la Campa,A.G. (2004) Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae. Microbiology, 150, 2313-2325.
28. Deng,S., Stein,R.A. and Higgins,N.P. (2005) Organization of supercoil domains and their reorganization by transcription. Mol. Microbiol., 57, 1511-1521.
29. Drlica,K. (1992) Control of bacterial supercoiling. Mol. Microbiol., 6, 425-433.
30. Balas,D., Fernández-Moreira,E. and de la Campa,A.G. (1998) Molecular characterization of the gene encoding the DNA gyrase A subunit of Streptococcus pneumoniae. J. Bacteriol., 180, 2854-2861.
31. Higgins,N.P., Yang,X., Fu,Q. and Roth,J.R. (1996) Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium. J. Bacteriol., 178, 2825-2835.
32. Sinden,R.R. and Pettijohn,D.E. (1981) Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling. Proc. Natl Acad. Sci. USA, 78, 224-228.