Global dinucleotide signatures and analysis of genomic heterogeneity

Current Opinion in Microbiology

Volumn 1, Issue 5, 1998, Pages 598-610

  Karlin, Samuel ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

OLIGODEOXYRIBONUCLEOTIDE;

BACTERIAL GENOME; BACTERIUM; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENOME; METHODOLOGY; PHYLOGENY; REVIEW;

BACTERIA; BASE COMPOSITION; GENOME, ARCHAEAL; GENOME, BACTERIAL; OLIGODEOXYRIBONUCLEOTIDES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 0032173634     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(98)80095-7     Document Type: Article

References (51)

1. Karlin S, Burge C: Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 1995, 11:283-290.
2. Blaisdell BE, Campbell AM, Karlin S: Similarities and dissimilarities of phage genomes. Proc Natl Acad Sci USA 1996, 93:5854-5859.
3. Karlin S, Mrázek J, Campbell AM: Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 1997, 179:3899-3913. Genome-wide compositional biases and distributions are compared for more than a dozen complete bacterial genomes. The constancy of the genomic signature (dinucleotide relative abundance profiles) over disjoint 50 kb contigs is confirmed. Interpretations center on the role of the genome signature as a chronometer of molecular phylogeny, on implications with respect to domains of life and on the origin and early evolution of eukaryotes.
4. Karlin S, Mrázek J: Compositional differences within and between eukaryotic genomes. Proc Natl Acad Sci USA 1997, 94:10227-10232.
5. Karlin S, Campbell AM, Mrázek J: Comparative DNA analysis across diverse genomes. Annu Rev Genet 1998, 32:185-225.
6. Josse J, Kaiser AD, Kornberg A: Enzymatic synthesis of deoxyribonucleic acid VIII. Frequencies of nearest neighbor base sequences in dexoyribonucleic acid. J Biol Chem 1961, 263:864-875.
7. Russell GJ, Walker PM, Elton RA, Subak-Sharpe JH: Doublet frequency analysis of fractionated vertebrate nuclear DNA. J Mol Biol 1976, 108:1-23.
8. Russell GJ, Subak-Sharpe JH: Similarity of the general designs of protochordates and invertebrates. Nature 1977, 266:533-535.
9. Karlin S, Ladunga I: Comparisons of eukaryotic genomic sequences. Proc Natl Acad Sci USA 1994, 91:12832-12836.
10. Karlin S, Mrázek J: What drives codon choices in human genes? J Mol Biol 1996, 262:459-472.
11. Cardon LR, Burge C, Clayton DA, Karlin S: Pervasive CpG suppression in animal mitochondrial genomes. Proc Natl Acad Sci USA 1994, 91:3799-3803.
12. Karlin S, Campbell AM: Which bacterium is the ancestor of the animal mitochondrial genome? Proc Natl Acad Sci USA 1994, 91: 12842-12846.
13. Karlin S, Doerfler W, Cardon LR: Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? J Virol 1994, 68:2889-2897.
14. Breslauer KJ, Frank E, Blöcker H, Marky LA: Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986, 83:3746-3750.
15. Delcourt SG, Blake RD: Stacking energies in DNA. J Biol Chem 1991, 266:15160-15169.
16. Beutler E, Gelbart T, Han J, Koziol JA, Beutler B: Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc Natl Acad Sci USA 1989, 86:192-196.
17. Travers AA: DNA-Protein Interactions. New York: Chapman and Hall; 1993.
18. Hunter CA: Sequence-dependent DNA structure: the role of base-stacking interactions. J Mol Biol 1993, 230:1025-1054.
19. Calladine CR, Drew HR: Understanding DNA. San Diego: Academic Press; 1992.
20. Kreig AM: Lymphocyte activation by microbiol DNA. Trends Microbiol 1996, 4:73-77.
21. Kreig AM, Ae-Kyung Y, Schon J, Davis HL: The role of CpG dinucleotides in DNA vaccines. Trends Microbiol 1998, 6:23-27.
22. Gupta RS, Singh B: Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr Biol 1994, 4:1104-1114.
23. Brown JR, Doolittle WR: Archaea and the prokaryote-to-eukaryotic transition. Microbiol Rev 1997, 61:456-502.
24. Pace NR: A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740.
25. Gupta R: Sequence data mandate prokarya and eukarya as highest taxa: both antebacteria and Gram-positive bacteria are "Monodermata" prokaryotes. Theor Pop Biol 1998, 54:93-106. This is a stimulating paper concerning prokaryote taxonomy on the basis of membrane morphology. Substantial analysis is also presented challenging the three domains (Eubacteria, Archaea, Eukaryota) of life hypothesis.
26. Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci USA 1990, B7:4576-4579.
27. Olsen GJ, Woese CR: Archaea I genomes: an overview. Cell 1997, 89:991-994.
28. Deckert G, Warren PV, Gasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M et al.: The complete genome of the hyperthermophilic bacterium, Aquifex aeolicus. Nature 1998, 392:353-359.
29. Rivera MC, Lake JA: Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 1992, 257:74-76.
30. Karlin S, Cardon LR: Computational DNA sequence analysis. Annu Rev Microbiol 1994, 48:619-654.
31. Viale AM, Arakaki AK: The chaperone connection to the origins of the eukaryotic organelles. FEBS Lett 1994, 341:146-151.
32. Brocchieri L, Karlin S: A symmetric-iterated multiple alignment of protein sequences. J Mol Biol 1998, 276:249-264.
33. Covacci A, Falkow S, Berg DE, Rappuoli R: Did the inheritance of a pathogenicity island modify the virulence of Helicobacter pylori. Trends Microbiol 1997, 5:205-208.
34. Stern DB, Palmer JD: Extensive and widepread homologies between mitochondrial-DNA and chloroplast DNA in plants. Proc Natl Acad Sci USA 1984, 81:1946-1950.
35. Palmer JD, Delwicke CF: The origin and evolution of plastids and their genomes. In Molecular Systematics of Plants II. Edited by Soltis DE, Soltis PS, Doylej JJ, Chapman-Hall; New York: 1998:375-409.
36. Finlay BB, Sansonetti P: Host-microbe interactions: bacteria. The new age of bacterial infectious diseases. Curr Opin Microbiol 1998, 1:9-12. This is an introduction to the first issue of a new timely and exciting journal on microbiology focusing on bacterial pathogenesis.
37. Finley BB, Falkow S: Common themes in microbial pathogenicity II. Mol Biol Microbiol Rev 1997, 61:136-169.
38. Covacci A, Rappuoli R: Helicobacter pylori: molecular evolution of a bacterial quasi-species. Curr Opin Microbiol 1998, 1:96-103.
39. Segal ED, Lange C, Corvacci A, Tompkins LS, Falkow S: Induction of host signal transduction pathways by Helicobacter pylori. Proc Natl Acad Sci USA 1997, 94:7595-7599.
40. Orme IM: The immunopathogenesis of tuberculosis: a new working hypothesis. Trends Microbiol 1998, 6:94-97.
41. Karlin S, Mrázek J, Campbell AM: Codon usage in different gene classes of the E. coli genome, Mol Microbiol 1998, 29:in press.
42. Tomb J-F, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA et al.: The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 1997, 388:539-547.
43. Hess ST, Blake JD, Blake RD: Wide variations in neighbor-dependent substitution rates. J Mol Biol 1994, 236:1022-1033.
44. Hall DB, Homlin RE, Barton JK: Oxidative DNA damage through long-range electron transfer. Nature 1996, 382:731-735.
45. Arkin MR, Stemp EDA, Pulver SC, Barton JK: Long-range oxidation of guanine by RuIII in duplex DNA. Curr Biol 1997, 4:389-400.
46. Kunkel TA: Biological asymmetries and the fidelity of eukaryotic DNA replication. Bioessays 1992, 14:303-308.
47. Echols H, Goodman MF: Fidelity mechanisms in DNA replication. Annu Rev Biochem 1991, 60:477-511.
48. Bolshoy A: Dinucleotides contribute to the bending of DNA in chromatin. Nat Structure 1995, 2:446-448.
49. Heinemann JA, Sprague GF: Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 1989, 340:205-209.
50. Lorenz MG, Wackernagel W: Bacterial gene-transfer by natural genetic-transformation in the environment. Microbiol Rev 1994, 58:563-602.
51. Rainey PB, Moxon ER, Thompson IP: Intraclonal polymorphism in bacteria. Adv Microbiol Ecol 1993, 4:24-33.