Abundant oligonucleotides common to most bacteria

PLoS ONE

Volumn 5, Issue 3, 2010, Pages

  Davenport, Colin F ^a   Tümmler, Burkhard ^a  

^a HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; PURINE DERIVATIVE; PYRIMIDINE DERIVATIVE;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM; GENETIC PROCEDURES; GENETIC VARIABILITY; GENETICS; OPEN READING FRAME; PROBABILITY; STATISTICAL MODEL;

ARCHAEA; BACTERIA; GENES, BACTERIAL; GENETIC TECHNIQUES; GENETIC VARIATION; GENOME, BACTERIAL; MARKOV CHAINS; MODELS, STATISTICAL; OLIGONUCLEOTIDES; OPEN READING FRAMES; PURINES; PYRIMIDINES;

EID: 79951742914     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009841     Document Type: Article

References (52)

1. Dobrindt U, Hochhut B, Hentschel U, Hacker J (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2: 414-424.
2. Karlin S (1998) Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1: 598-610.
3. Davenport CF, Wiehlmann L, Reva ON, Tümmler B (2009) Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides. Environ Microbiol 11: 1092-1104.
4. Karlin S, Mrázek J, Campbell AM (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179: 3899-3913.
5. Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ (2003) Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 13: 145-158.
6. Reva ON, Tümmler B (2004) Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics 5: 90.
7. Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B (1999) Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol 16: 1391-1399.
8. van Passel M, Bart A, Luyf A, van Kampen A, van der Ende A (2006) Compositional discordance between prokaryotic plasmids and host chromosomes. BMC Genomics 7: 26.
9. Bohlin J, Skjerve E, Ussery DW (2008) Investigations of oligonucleotide usage variance within and between prokaryotes. PLoS Comput Biol 4: e1000057.
10. Karlin S, Mrázek J, Campbell AM (1996) Frequent oligonucleotides and peptides of the Haemophilus influenzae genome. Nucleic Acids Res 24: 4263-4272.
11. Mrázek J, Gaynon LH, Karlin S (2002) Frequent oligonucleotide motifs in genomes of three streptococci. Nucleic Acids Res 30: 4216-4221.
12. Mrázek J, Karlin S (2007) Distinctive features of large complex virus genomes and proteomes. Proc Natl Acad Sci USA 104: 5127-5132.
13. Hampson S, Kibler D, Baldi P (2002) Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics 18: 513-528.
14. Wang Y, Hill K, Singh S, Kari L (2005) The spectrum of genomic signatures: from dinucleotides to chaos game representation. Gene 346: 173-185.
15. Chor B, Horn D, Levy Y, Goldman N, Massingham T (2009) Genomic DNA kmer spectra: models and modalities. Genome Biol 10: R108.
16. Rohs R, West SM, Sosinsky A, Liu P, Mann RS, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461: 1248-1253.
17. Greenwood PE, Nikulin MS (1996) A Guide to Chi-Squared Testing. Wiley, New York.
18. Schbath S (2000) An overview of the distribution of word counts in Markov chains. Journal of Computational Biology 7: 193-201.
19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
20. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench.
21. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
22. Hoebeke M, Schbath S;R'MES: Finding Exceptional Motifs, version 3. User guide. http://genome.jouy.inra.fr/ssb/rmes.
23. R Development Core Team (2008) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
24. Baldi P, Baisnée PF (2000) Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics 16: 865-89.
25. Packer MJ, Dauncey MP, Hunter CA (2000) Sequence-dependent DNA structure: tetranucleotide conformational maps. J Mol Biol 295: 85-103.
26. El Hassan MA, Calladine CR (1997) Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil Trans Roy Soc Ser A 355: 43-100.
27. Brukner I, Sánchez 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.
28. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB (1998) DNA sequencedependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci U S A 95: 11163-11168.
29. Ornstein RL, Rein R, Breen DL, MacElroy RD (1978) An optimised potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers 17: 2341-2360.
30. El Hassan MA, Calladine CR (1996a) Structural mechanics of bent DNA. Endeavour 20: 61-7.
31. El Hassan MA, Calladine CR (1996b) Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J Mol Biol 259: 95-103.
32. Haran TE, Mohanty U (2009) The unique structure of A-tracts and intrinsic DNA bending. Q Rev Biophys 42: 41-81.
33. El Hassan MA, Calladine CR (1995) The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. J Mol Biol 251: 648-664.
34. Leroy JL, Charretier E, Kochoyan M, Gueron M (1988) Evidence from basepair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry 27: 8894-8898.
35. Nadeau JG, Crothers DM (1989) Structural basis for DNA bending. Proc Natl Acad Sci U S A 86: 2622-2626.
36. Haran TE, Crothers DM (1989) Cooperativity in A-tract structure and bending properties of composite TnAn blocks. Biochemistry 28: 2763-2767.
37. Nelson HC, Finch JT, Luisi BF, Klug A (1987) The structure of an oligo(dA)? oligo(dT) tract and its biological implications. Nature 330: 221-226.
38. Woods KK, Maehigashi T, Howerton SB, Sines CC, Tannenbaum S, et al. (2004) High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2. J Am Chem Soc 126: 15330-15331.
39. Tolstorukov MY, Virnik KM, Adhya S, Zhurkin VB (2005) A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res 33: 3907-3918.
40. Beutel BA, Gold L (1992) In vitro evolution of intrinsically bent DNA. Journal of Molecular Biology 228: 803-812.
41. Swinger KK, Rice PA (2004) IHF and HU: flexible architects of bent DNA. Curr Opin Struct Biol 14: 28-35.
42. Segal E, Widom J (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71.
43. Swinger KK, Rice PA (2007) Structure-based analysis of HU-DNA binding. J Mol Biol 365: 1005-1016.
44. Coker C, Bakare OO, Mobley HL (2000) H-NS is a repressor of the Proteus mirabilis urease transcriptional activator gene ureR. J Bacteriol 182: 2649-2653.
45. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
46. Cohanim AB, Haran TE (2009) The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes. Nucleic Acids Res 37: 6466-6476.
47. Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB (2008) The triple helix: 50 years later, the outcome. Nucleic Acids Res 36: 5123-5138.
48. Felsenfeld G, Rich A (1957) Studies on the formation of two-and three-stranded polyribonucleotides. Biochim Biophys Acta 26: 457-468.
49. 4. Nature 339: 637-640.
50. Roberts RW, Crothers DM (1996) Prediction of the stability of DNA triplexes. Proc Natl Acad Sci U S A 93: 4320-4325.
51. Sandström K, Wärmländer S, Gräslund A, Leijon M (2002) A-tract DNA disfavours triplex formation. J Mol Biol 315: 737-748.
52. Fofanov Y, Luo Y, Katili C, Wang J, Belosludtsev Y, et al. (2004) How independent are the appearances of n-mers in different genomes? Bioinformatics 20: 2421-2428.