Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides

Environmental Microbiology

Volumn 11, Issue 5, 2009, Pages 1092-1104

  Davenport, Colin F ^a   Wiehlmann, Lutz ^a   Reva, Oleg N ^b   Tümmler, Burkhard ^a  

^a HANNOVER MEDICAL SCHOOL   (Germany)

^b UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; OLIGONUCLEOTIDE;

ARTICLE; BACTERIAL GENOME; GENETICS; NUCLEOTIDE REPEAT; PSEUDOMONAS;

DNA, BACTERIAL; GENOME, BACTERIAL; OLIGONUCLEOTIDES; PSEUDOMONAS; REPETITIVE SEQUENCES, NUCLEIC ACID;

BACTERIA (MICROORGANISMS); PSEUDOMONAS;

EID: 65349096125     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2008.01839.x     Document Type: Article

References (58)

1. Allen, T.E., Price, N.D., Joyce, A.R. Palsson, B.Ø. (2006) Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS Comput Biol 2 : e2.
2. Almagor, H. (1983) A Markov analysis of DNA sequences. J Theor Biol 104 : 633 645.
3. Aranda-Olmedo, I., Tobes, R., Manzanera, M., Ramos, J.L. Marqués, S. (2002) Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. Nucleic Acids Res 30 : 1826 1833. (Pubitemid 34679761)
4. Baldi, P. Baisnee, P.F. (2000) Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics 16 : 865 889.
5. Blow, N. (2008) Metagenomics: benchmarks and standards. Nature 453 : 687.
6. Bohlin, J., Skjerve, E. Ussery, D.W. (2008a) Investigations of oligonucleotide usage variance within and between prokaryotes. PLoS Comput Biol 4 : e1000057. (Pubitemid 350122613)
7. Bohlin, J., Skjerve, E. Ussery, D.W. (2008b) Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. BMC Genomics 9 : 104.
8. Boyle, A.P., Davis, S., Shulha, H.P., Meltzer, P., Margulies, E.H., Wenig, Z., et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132 : 311 322. (Pubitemid 350295366)
9. Brukner, I., Sanchez, R., Suck, D. Pongor, S. (1995) Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J 14 : 1812 1818.
10. Buell, C.R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I.T., Gwinn, M.L., et al. (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 100 : 10181 10186. (Pubitemid 37071853)
11. Burge, C., Campbell, A.M. Karlin, S. (1992) Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci USA 89 : 1358 1362.
12. Chen, S.L., Lee, W., Hottes, A.K., Shapiro, L. McAdams, H.H. (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci USA 101 : 3480 3485. (Pubitemid 38338220)
13. Cloonan, N., Forrest, A.R., Kolle, G., Gardiner, B.B., Faulkner, G.J., Brown, M.K., et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5 : 613 619.
14. Dlakic, M., Ussery, D. Brunak, S. (2004) DNA bendability and nucleosome positioning in transcriptional regulation. In DNA Conformation in Transcription. Ohyama, T. (ed.) Austin, USA : Landes Bioscience, Springer, pp. 189 203.
15. Dos Santos, V.A., Heim, S., Moore, E.R., Strätz, M. Timmis, K.N. (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6 : 1264 1286. (Pubitemid 39606296)
16. Ernst, R.K., D'Argenio, D.A., Ichikawa, J.K., Bangera, M.G., Selgrade, S., Burns, J.L., et al. (2003) Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic fibrosis. Environ Microbiol 5 : 1341 1349. (Pubitemid 38038944)
17. Feil, H., Feil, W.S., Chain, P., Larimer, F., DiBartolo, G., Copeland, A., et al. (2005) Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci USA 102 : 11064 11069. (Pubitemid 41105993)
18. Ganesan, H., Rakitianskaia, A.S., Davenport, C.F., Tümmler, B.T. Reva, O.N. (2008) The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 9 : 333.
19. Gelfand, M.S. Koonin, E.V. (1997) Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res 25 : 2430 2439. (Pubitemid 27303704)
20. Greenwood, P.E. Nikulin, M.S. (1996) A Guide to Chi-Squared Testing. New York, USA : Wiley.
21. He, J., Baldini, R.L., Déziel, E., Saucier, M., Zhang, Q., Liberati, N.T., et al. (2004) The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc Natl Acad Sci USA 101 : 2530 2535. (Pubitemid 38269345)
22. Hillier, L.W., Marth, G.T., Quinlan, A.R., Dooling, D., Fewell, G., Barnett, D., et al. (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5 : 183 188.
23. Ikemura, T. (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2 : 13 34. (Pubitemid 15152046)
24. Joardar, V., Lindeberg, M., Jackson, R.W., Selengut, J., Dodson, R., Brinkac, L.M., et al. (2005) Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 187 : 6488 6498. (Pubitemid 41318408)
25. Karlin, S., Mrazek, J. Campbell, A. (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179 : 3899 3913. (Pubitemid 27259908)
26. Klockgether, J., Würdemann, D., Reva, O., Wiehlmann, L. Tümmler, B. (2007) Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol 189 : 2443 2459. (Pubitemid 46411359)
27. Lee, D.G., Urbach, J.M., Wu, G., Liberati, N.T., Feinbaum, R.L., Miyata, S., et al. (2006) Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol 7 : R90.
28. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 : 376 380. (Pubitemid 41613494)
29. Massana, R., Karniol, B., Pommier, T., Bodaker, I. Béjà, O. (2008) Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate. Environ Microbiol 10 : 1335 1343.
30. Mathee, K., Narasimhan, G., Valdes, C., Qiu, X., Matewish, J.M., Koehrsen, M., et al. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA 105 : 3100 3105. (Pubitemid 350293915)
31. Médigue, C. Moszer, I. (2007) Annotation, comparison and databases for hundreds of bacterial genomes. Res Microbiol 158 : 724 736. (Pubitemid 350245437)
32. Mrázek, J., Gaynon, L.H. Karlin, S. (2002) Frequent oligonucleotide motifs in genomes of three streptococci. Nucleic Acids Res 30 : 4216 4221. (Pubitemid 35175190)
33. Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V.A., et al. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4 : 799 808. (Pubitemid 36064171)
34. Olsen, G.J. Woese, C.R. (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7 : 113 123. (Pubitemid 23034021)
35. Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G.S., Mavrodi, D.V., et al. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 23 : 873 878. (Pubitemid 43093131)
36. Pedersen, A.G., Jensen, L.J., Brunak, S., Staerfeldt, H.H. Ussery, D.W. (2000) A DNA structural atlas for Escherichia coli. J Mol Biol 299 : 907 930.
37. Peterson, J.D., Umayam, L.A., Dickinson, T., Hickey, E.K. White, O. (2001) The comprehensive microbial resource. Nucleic Acids Res 29 : 123 125. (Pubitemid 32054424)
38. Pride, D.T., Meinersmann, R.J., Wassenaar, T.M. Blaser, M.J. (2003) Evolutionary implications of microbial genome tetanucleotide frequency biases. Genome Res 13 : 145 155. (Pubitemid 36575764)
39. Ramos, J.-L., ed. (2004) Pseudomonas, Volumes 1-3. New York, USA : Kluwer Academic/Plenum Publishers.
40. Reva, O. Tümmler, B. (2008) Think big - giant genes in bacteria. Environ Microbiol 10 : 768 777.
41. Reva, O.N. Tümmler, B. (2004) Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics 5 : 90. (Pubitemid 40195413)
42. Reva, O.N. Tümmler, B. (2005) Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics 6 : 251. (Pubitemid 41554944)
43. Reva, O.N., Hallin, P.F., Willenbrock, H., Sicheritz-Ponten, T., Tümmler, B. Ussery, D.W. (2008) Global features of the Alcanivorax borkumensis SK2 genome. Environ Microbiol 10 : 614 625.
44. Schuster, S.C. (2008) Next-generation sequencing transforms today's biology. Nat Methods 5 : 16 18.
45. Sharp, P.M. Li, W.H. (1987) The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol 4 : 222 230. (Pubitemid 17116760)
46. Shpigelman, E.S., Trifonov, E.N. Bolshoy, A. (1993) CURVATURE: software for the analysis of curved DNA. Comput Appl Biosci 9 : 435 440. (Pubitemid 23233970)
47. Skovgaard, M., Jensen, L.J., Friis, C., Stærfeldt, H.H., Worning, P., Brunak, S. Ussery, D.W. (2002) The atlas visualisation of genome-wide information. In Methods in Microbiology. Wren, B. Dorrell, N. (eds). London, UK : Academic Press, pp. 49 63.
48. Sourice, S., Biaudet, V., Karoui, M.E., Ehrlich, S.D. Gruss, A. (1998) Identification of the Chi site of Haemophilus influenzae as several sequences related to the Escherichia coli Chi site. Mol Microbiol 27 : 1021 1029. (Pubitemid 28254951)
49. Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406 : 959 964.
50. Teeling, H., Waldmann, J., Lombardot, T., Bauer, M. Glöckner, F.O. (2004) TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics 5 : 163. (Pubitemid 40195345)
51. Tobes, R. Pareja, E. (2006) Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements. BMC Genomics 7 : 62. (Pubitemid 44173065)
52. Urich, T., Lanzén, A., Qi, J., Huson, D.H., Schleper, C. Schuster, S.C. (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3 : e2527.
53. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 : 66 74. (Pubitemid 38451457)
54. Vodovar, N., Vallenet, D., Cruveiller, S., Rouy, Z., Barbe, V., Acosta, C., et al. (2006) Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila. Nat Biotechnol 24 : 673 679. (Pubitemid 43882118)
55. Weinel, C., Ussery, D.W., Ohlsson, H., Sicheritz-Ponten, T., Kiewitz, C. Tümmler, B. (2002a) Comparative genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: orthologs, codon usage, repetitive extragenic palindromic elements, and oligonucleotide signatures. Genome Lett 1 : 175 187.
56. Weinel, C., Nelson, K.E. Tümmler, B. (2002b) Global features of the Pseudomonas putida KT2440 genome sequence. Environ Microbiol 4 : 809 818. (Pubitemid 36064172)
57. Willenbrock, H., Friis, C., Juncker, A.S. Ussery, D.W. (2006) An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol 7 : R114. (Pubitemid 46995601)
58. Yan, Y., Yang, J., Dou, Y., Chen, M., Ping, S., Peng, J., et al. (2008) Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501. Proc Natl Acad Sci USA 105 : 7564 7569.